Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T80423 Target Info
Target Name von Hippel-Lindau disease tumor suppressor (VHL)
Synonyms pVHL; Protein G7
Target Type Patented-recorded Target
Gene Name VHL
UniProt ID
VHL_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: trans-4-hydroxy-proline Ligand Info
Structure Description pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol PDB:6GMR
Method X-ray diffraction Resolution 1.75 Å Mutation No [1]
PDB Sequence
RPVLRSVNSR
69
EPSQVIFCNR
79
SPRVVLPVWL
89
NFDGEPQPYP
99
TLPPGTGRRI
109

HSYRGHLWLF
119
RDAGTHDGLL
129
VNQTELFVPS
139
LNVDGQPIFA
149
NITLPVYTLK
159

ERCLQVVRSL
169
VKPENYRRLD
179
IVRSLYEDLE
189
DHPNVQKDLE
199
RLTQERIAH
Residue
Distance (Å)
TRP88
3.380
TYR98
2.647
ILE109
4.791
HIS110
3.244
Residue
Distance (Å)
SER111
2.819
TYR112
3.910
HIS115
2.607
TRP117
3.450
Ligand Name: Pyrrolidine carboxamide derivative 1 Ligand Info
Structure Description pVHL54-213-EloB-EloC complex (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE bound PDB:3ZRC
Method X-ray diffraction Resolution 2.90 Å Mutation No [2]
PDB Sequence
LRSVNSREPS
72
QVIFCNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
QE
Residue
Distance (Å)
ASN67
4.752
SER68
4.327
ARG69
4.576
PHE76
4.356
PRO86
4.086
TRP88
3.485
PHE91
3.511
TYR98
2.952
Residue
Distance (Å)
PRO99
3.233
ARG107
2.931
ILE109
3.465
HIS110
2.898
SER111
2.691
TYR112
3.636
HIS115
3.212
TRP117
3.792
Ligand Name: S-(Dimethylarsenic)Cysteine Ligand Info
Structure Description pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate PDB:6GMN
Method X-ray diffraction Resolution 1.94 Å Mutation No [1]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
PIFANITLPV
155
YTLKERCLQV
165

VRSLVKPENY
175
RRLDIVRSLY
185
EDLEDHPNVQ
195
KDLERL
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CAS or .CAS2 or .CAS3 or :3CAS;style chemicals stick;color identity;select .C:75 or .C:76 or .C:78 or .C:79 or .C:101 or .C:104 or .C:105 or .C:106 or .C:148 or .C:149 or .C:150 or .C:151; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE75
3.581
PHE76
1.325
ASN78
1.332
ARG79
3.138
LEU101
4.814
GLY104
3.179
Residue
Distance (Å)
THR105
3.753
GLY106
3.494
PHE148
3.508
ALA149
2.900
ASN150
3.728
ILE151
2.756
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Ligand Name: N-[5-[4-[[5-[[(2S)-3,3-dimethyl-1-[(2S,4R)-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-5-oxidanylidene-pentyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1H-pyridine-3-carboxamide Ligand Info
Structure Description Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer PDB:7Q2J
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
PRPVLRSVNS
68
REPSQVIFCN
78
RSPRVVLPVW
88
LNFDGEPQPY
98
PTLPPGTGRR
108

IHSYRGHLWL
118
FRDAGTHDGL
128
LVNQTELFVP
138
SLNVDGQPIF
148
ANITLPVYTL
158

KERCLQVVRS
168
LVKPENYRRL
178
DIVRSLYEDL
188
EDHPNVQKDL
198
ERLTQER
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8KH or .8KH2 or .8KH3 or :38KH;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.588
ARG69
4.035
PHE76
3.774
PRO86
3.905
TRP88
3.405
PHE91
3.326
TYR98
2.788
PRO99
3.002
THR100
4.919
Residue
Distance (Å)
LEU101
3.408
ARG107
3.436
ILE109
3.487
HIS110
2.679
SER111
3.162
TYR112
3.060
HIS115
2.543
TRP117
3.396
Ligand Name: N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carbonyl}amino)undecanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide Ligand Info
Structure Description Ternary complex of VHL/BRD4-BD1/Compound9 (4-(3,5-difluoropyridin-2-yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)amino)-11-oxoundecyl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxamide) PDB:7KHH
Method X-ray diffraction Resolution 2.28 Å Mutation No [4]
PDB Sequence
PVLRSVNSRE
70
PSQVIFCNRS
80
PRVVLPVWLN
90
FDGEPQPYPT
100
LPPGTGRRIH
110

SYRGHLWLFR
120
DAGTHDGLLV
130
NQTELFVPSL
140
NVDGQPIFAN
150
ITLPVYTLKE
160

RCLQVVRSLV
170
KPENYRRLDI
180
VRSLYEDLED
190
HPNVQKDLER
200
LTQERIAH
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WEP or .WEP2 or .WEP3 or :3WEP;style chemicals stick;color identity;select .C:67 or .C:69 or .C:88 or .C:91 or .C:96 or .C:98 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.366
ARG69
4.086
TRP88
2.926
PHE91
3.385
GLN96
4.822
TYR98
2.813
Residue
Distance (Å)
ILE109
4.230
HIS110
2.268
SER111
2.942
TYR112
3.292
HIS115
2.554
TRP117
2.897
Ligand Name: (2s,4r)-1-(3-Amino-2-Methylbenzoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)benzyl)pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound PDB:4B9K
Method X-ray diffraction Resolution 2.00 Å Mutation No [5]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNQ
145
PIFANITLPV
155
YTLKERCLQV
165

VRSLVKPENY
175
RRLDIVRSLY
185
EDLEDHPNVQ
195
KDLERLT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TG0 or .TG02 or .TG03 or :3TG0;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
3.979
PRO86
3.976
TRP88
3.526
PHE91
3.626
GLN96
4.434
TYR98
2.651
PRO99
2.950
THR100
4.788
Residue
Distance (Å)
LEU101
4.072
ARG107
3.679
ILE109
3.562
HIS110
2.746
SER111
2.833
TYR112
3.584
HIS115
2.722
TRP117
3.419
Ligand Name: [4-(1H-Pyrrol-1-yl)phenyl]methanol Ligand Info
Structure Description pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol PDB:6GMR
Method X-ray diffraction Resolution 1.75 Å Mutation No [1]
PDB Sequence
RPVLRSVNSR
69
EPSQVIFCNR
79
SPRVVLPVWL
89
NFDGEPQPYP
99
TLPPGTGRRI
109

HSYRGHLWLF
119
RDAGTHDGLL
129
VNQTELFVPS
139
LNVDGQPIFA
149
NITLPVYTLK
159

ERCLQVVRSL
169
VKPENYRRLD
179
IVRSLYEDLE
189
DHPNVQKDLE
199
RLTQERIAH
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .F4K or .F4K2 or .F4K3 or :3F4K;style chemicals stick;color identity;select .V:118 or .V:119 or .V:120 or .V:127 or .V:128 or .V:129 or .V:134 or .V:154 or .V:156 or .V:160 or .V:197 or .V:200 or .V:201; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU118
3.986
PHE119
4.095
ARG120
3.220
GLY127
3.596
LEU128
3.311
LEU129
4.160
GLU134
3.583
Residue
Distance (Å)
PRO154
3.915
TYR156
3.367
GLU160
2.883
ASP197
3.375
ARG200
4.541
LEU201
3.724
Ligand Name: (4r)-1-Acetyl-4-Hydroxy-N-Methyl-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC complex, in complex with capped Hydroxyproline PDB:4AWJ
Method X-ray diffraction Resolution 2.50 Å Mutation No [6]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
PIFANITLPV
155
YTLKERCLQV
165

VRSLVKPENY
175
RRLDIVRSLY
185
EDLEDHPNVQ
195
KDLER
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .V6F or .V6F2 or .V6F3 or :3V6F;style chemicals stick;color identity;select .C:88 or .C:91 or .C:98 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP88
3.489
PHE91
4.971
TYR98
2.592
ILE109
4.791
HIS110
2.943
Residue
Distance (Å)
SER111
2.737
TYR112
3.490
HIS115
2.498
TRP117
3.542
Ligand Name: (4r)-N-[4-(Dihydroxyamino)benzyl]-4-Hydroxy-1-[(3-Methylisoxazol-5-Yl)acetyl]-L-Prolinamide Ligand Info
Structure Description pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-yl)acetyl)-N-(4-nitrobenzyl)pyrrolidine-2-carboxamide bound PDB:3ZUN
Method X-ray diffraction Resolution 2.50 Å Mutation No [7]
PDB Sequence
VLRSVNSREP
71
SQVIFCNRSP
81
RVVLPVWLNF
91
DGEPQPYPTL
101
PPGTGRRIHS
111

YRGHLWLFRD
121
AGTHDGLLVN
131
QTELFVPSLI
147
FANITLPVYT
157
LKERCLQVVR
167

SLVKPENYRR
177
LDIVRSLYED
187
LEDHPNVQKD
197
LERLTQE
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ZUN or .ZUN2 or .ZUN3 or :3ZUN;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:88 or .C:91 or .C:98 or .C:99 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.276
ARG69
4.049
PHE76
4.758
TRP88
3.432
PHE91
3.635
TYR98
2.664
PRO99
3.185
Residue
Distance (Å)
ARG107
3.180
ILE109
3.033
HIS110
2.821
SER111
2.574
TYR112
3.658
HIS115
2.621
TRP117
3.421
Ligand Name: (4r)-N-(Biphenyl-4-Ylmethyl)-4-Hydroxy-1-[(3-Methylisoxazol-5-Yl)acetyl]-L-Prolinamide Ligand Info
Structure Description pVHL54-213-EloB-EloC complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)- 4-hydroxy-1-(2-(3-methylisoxazol-5-yl)acetyl)pyrrolidine-2- carboxamide PDB:3ZTC
Method X-ray diffraction Resolution 2.65 Å Mutation No [6]
PDB Sequence
LRSVNSREPS
72
QVIFCNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLND
143
GQPIFANITL
153
PVYTLKERCL
163

QVVRSLVKPE
173
NYRRLDIVRS
183
LYEDLEDHPN
193
VQKDLERLTQ
203
E
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TR0 or .TR02 or .TR03 or :3TR0;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.342
ARG69
4.027
PHE76
4.225
PRO86
3.932
TRP88
3.448
PHE91
3.968
TYR98
2.600
PRO99
3.249
Residue
Distance (Å)
LEU101
4.573
ARG107
4.243
ILE109
3.468
HIS110
2.947
SER111
2.637
TYR112
3.288
HIS115
2.788
TRP117
3.699
Ligand Name: (2S,4R)-N-[(1R)-2-[(2R)-1-[4-(4-bromo-7-cyclopentyl-5-oxobenzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propan-2-yl]oxy-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2S)-2-[[1-(dimethylamino)cyclopropanecarbonyl]amino]-3,3-dimethylbutanoyl]-4-hydroxypyrrolidine-2-carboxamide Ligand Info
Structure Description Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB PDB:7Z76
Method X-ray diffraction Resolution 1.32 Å Mutation No [8]
PDB Sequence
RPVLRSVNSR
69
EPSQVIFCNR
79
SPRVVLPVWL
89
NFDGEPQPYP
99
TLPPGTGRRI
109

HSYRGHLWLF
119
RDAGTHDGLL
129
VNQTELFVPS
139
LNVDGQPIFA
149
NITLPVYTLK
159

ERCLQVVRSL
169
VKPENYRRLD
179
IVRSLYEDLE
189
DHPNVQKDLE
199
RLT
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IFJ or .IFJ2 or .IFJ3 or :3IFJ;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.922
ARG69
3.621
PHE76
3.886
PRO86
4.055
TRP88
3.470
PHE91
3.532
TYR98
2.674
PRO99
3.101
THR100
4.849
Residue
Distance (Å)
LEU101
4.050
ARG107
2.922
ILE109
3.710
HIS110
3.044
SER111
2.705
TYR112
3.399
HIS115
2.667
TRP117
3.549
Ligand Name: Protac MS33 Ligand Info
Structure Description Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB PDB:7JTO
Method X-ray diffraction Resolution 1.70 Å Mutation No [9]
PDB Sequence
RPRPVLRSVN
67
SREPSQVIFC
77
NRSPRVVLPV
87
WLNFDGEPQP
97
YPTLPPGTGR
107

RIHSYRGHLW
117
LFRDAGTHDG
127
LLVNQTELFV
137
PSLNVDGQPI
147
FANITLPVYT
157

LKERCLQVVR
167
SLVKPENYRR
177
LDIVRSLYED
187
LEDHPNVQKD
197
LERLTQER
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VKA or .VKA2 or .VKA3 or :3VKA;style chemicals stick;color identity;select .L:67 or .L:69 or .L:76 or .L:86 or .L:88 or .L:91 or .L:98 or .L:99 or .L:100 or .L:101 or .L:107 or .L:109 or .L:110 or .L:111 or .L:112 or .L:115 or .L:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.459
ARG69
3.644
PHE76
3.948
PRO86
3.944
TRP88
3.443
PHE91
3.532
TYR98
2.586
PRO99
3.075
THR100
4.807
Residue
Distance (Å)
LEU101
3.531
ARG107
2.921
ILE109
3.707
HIS110
2.812
SER111
2.484
TYR112
3.343
HIS115
2.609
TRP117
3.371
Ligand Name: N-[5-[4-[2-[2-[2-[2-[3-[[(2S)-1-[(2S,4R)-4-hydroxy-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]pyrrolidin-1-yl]-3,3-dimethyl-1-oxobutan-2-yl]amino]-3-oxopropoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1H-pyridine-3-carboxamide Ligand Info
Structure Description Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1) PDB:8BB3
Method X-ray diffraction Resolution 1.80 Å Mutation No [10]
PDB Sequence
GRPRPVLRSV
66
NSREPSQVIF
76
CNRSPRVVLP
86
VWLNFDGEPQ
96
PYPTLPPGTG
106

RRIHSYRGHL
116
WLFRDAGTHD
126
GLLVNQTELF
136
VPSLNVDGQP
146
IFANITLPVY
156

TLKERCLQVV
166
RSLVKPENYR
176
RLDIVRSLYE
186
DLEDHPNVQK
196
DLERLTQERI
206

AHQ
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q3X or .Q3X2 or .Q3X3 or :3Q3X;style chemicals stick;color identity;select .L:67 or .L:69 or .L:76 or .L:86 or .L:88 or .L:91 or .L:98 or .L:99 or .L:100 or .L:101 or .L:107 or .L:109 or .L:110 or .L:111 or .L:112 or .L:115 or .L:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.304
ARG69
3.869
PHE76
3.706
PRO86
3.961
TRP88
3.466
PHE91
3.538
TYR98
2.612
PRO99
3.020
THR100
4.741
Residue
Distance (Å)
LEU101
4.217
ARG107
2.909
ILE109
3.609
HIS110
2.908
SER111
2.750
TYR112
3.400
HIS115
2.679
TRP117
3.489
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (2S,4R)-N-[(1S)-4-[4-(4-bromo-7-cyclopentyl-5-oxobenzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]butyl]-1-[(2S)-2-[(1-fluorocyclopropanecarbonyl)amino]-3,3-dimethylbutanoyl]-4-hydroxypyrrolidine-2-carboxamide Ligand Info
Structure Description Crystal structure of compound 6 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB PDB:7Z77
Method X-ray diffraction Resolution 1.97 Å Mutation No [8]
PDB Sequence
RPVLRSVNSR
69
EPSQVIFCNR
79
SPRVVLPVWL
89
NFDGEPQPYP
99
TLPPGTGRRI
109

HSYRGHLWLF
119
RDAGTHDGLL
129
VNQTELFVPS
139
LNVDGQPIFA
149
NITLPVYTLK
159

ERCLQVVRSL
169
VKPENYRRLD
179
IVRSLYEDLE
189
DHPNVQKDLE
199
RLTQERIAHQ
209

R
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IFF or .IFF2 or .IFF3 or :3IFF;style chemicals stick;color identity;select .C:67 or .C:68 or .C:69 or .C:71 or .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:108 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.416
SER68
2.628
ARG69
2.401
PRO71
4.894
PHE76
3.179
PRO86
2.633
TRP88
2.433
PHE91
2.407
TYR98
1.957
PRO99
2.272
Residue
Distance (Å)
THR100
3.774
LEU101
2.342
ARG107
2.390
ARG108
4.875
ILE109
2.234
HIS110
2.043
SER111
1.885
TYR112
2.483
HIS115
1.832
TRP117
2.055
Ligand Name: (2~{s},4~{r})-1-[(2~{s})-2-(Cyclobutylcarbonylamino)-3,3-Dimethyl-Butanoyl]-~{n}-[[4-(4-Methyl-1,3-Thiazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclobutanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 18) PDB:5NW1
Method X-ray diffraction Resolution 2.10 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9BH or .9BH2 or .9BH3 or :39BH;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.699
ARG69
3.826
PHE76
3.968
PRO86
4.122
TRP88
3.532
PHE91
3.681
GLN96
4.586
TYR98
2.692
PRO99
3.042
Residue
Distance (Å)
THR100
4.909
LEU101
3.939
ARG107
4.040
ILE109
3.522
HIS110
2.895
SER111
2.662
TYR112
3.383
HIS115
2.711
TRP117
3.541
Ligand Name: (2~{s},4~{r})-1-[(2~{s})-3,3-Dimethyl-2-(2-Oxidanylethanoylamino)butanoyl]-~{n}-[[4-(4-Methyl-1,3-Thiazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-4-hydroxy-1-((S)-2-(2-hydroxyacetamido)-3,3-dimethylbutanoyl)-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) PDB:5NVV
Method X-ray diffraction Resolution 2.10 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9BT or .9BT2 or .9BT3 or :39BT;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.086
ARG69
3.684
PHE76
3.902
PRO86
4.033
TRP88
3.484
PHE91
3.522
GLN96
4.707
TYR98
2.604
PRO99
3.027
Residue
Distance (Å)
THR100
4.771
LEU101
3.988
ARG107
3.928
ILE109
3.385
HIS110
2.813
SER111
2.682
TYR112
3.535
HIS115
2.641
TRP117
3.474
Ligand Name: (4r)-1-(3,3-Dimethylbutanoyl)-4-Hydroxy-N-[4-(4-Methyl-1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 5) PDB:4W9F
Method X-ray diffraction Resolution 2.10 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLND
143
GQPIFANITL
153
PVYTLKERCL
163

QVVRSLVKPE
173
NYRRLDIVRS
183
LYEDLEDHPN
193
VQKDLERLTQ
203
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JU or .3JU2 or .3JU3 or :33JU;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
3.976
PRO86
4.037
TRP88
3.454
PHE91
4.112
GLN96
4.700
TYR98
2.626
PRO99
2.960
THR100
4.947
Residue
Distance (Å)
LEU101
4.134
ARG107
3.983
ILE109
3.406
HIS110
2.867
SER111
2.718
TYR112
3.583
HIS115
2.716
TRP117
3.436
Ligand Name: N-Acetyl-3-Methyl-L-Valyl-(4r)-4-Hydroxy-N-[4-(4-Methyl-1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7) PDB:4W9H
Method X-ray diffraction Resolution 2.10 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JF or .3JF2 or .3JF3 or :33JF;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.125
ARG69
4.462
PHE76
3.966
PRO86
4.108
TRP88
3.496
PHE91
3.413
GLN96
4.993
TYR98
2.595
PRO99
2.986
Residue
Distance (Å)
THR100
4.686
LEU101
4.220
ARG107
3.910
ILE109
3.343
HIS110
2.818
SER111
2.604
TYR112
3.320
HIS115
2.606
TRP117
3.446
Ligand Name: N-Acetyl-L-Phenylalanyl-3-Methyl-L-Valyl-(4r)-4-Hydroxy-N-[4-(4-Methyl-1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14) PDB:4W9K
Method X-ray diffraction Resolution 2.10 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JO or .3JO2 or .3JO3 or :33JO;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.794
ARG69
3.335
PHE76
3.856
PRO86
3.959
TRP88
3.553
PHE91
3.548
GLN96
4.803
TYR98
2.599
PRO99
3.066
Residue
Distance (Å)
THR100
4.866
LEU101
4.143
ARG107
3.957
ILE109
3.486
HIS110
2.869
SER111
2.784
TYR112
3.476
HIS115
2.474
TRP117
3.416
Ligand Name: N-(6-fluoro-3'-{[6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carbonyl]amino}-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-carbonyl)glycyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide Ligand Info
Structure Description Crystal structure of Protac MS67 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB PDB:7JTP
Method X-ray diffraction Resolution 2.12 Å Mutation No [9]
PDB Sequence
VLRSVNSREP
71
SQVIFCNRSP
81
RVVLPVWLNF
91
DGEPQPYPTL
101
PPGTGRRIHS
111

YRGHLWLFRD
121
AGTHDGLLVN
131
QTELFVPSLN
141
VDGQPIFANI
151
TLPVYTLKER
161

CLQVVRSLVK
171
PENYRRLDIV
181
RSLYEDLEDH
191
PNVQKDLERL
201
TQE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .X6M or .X6M2 or .X6M3 or :3X6M;style chemicals stick;color identity;select .L:67 or .L:69 or .L:76 or .L:86 or .L:88 or .L:91 or .L:98 or .L:99 or .L:100 or .L:101 or .L:107 or .L:109 or .L:110 or .L:111 or .L:112 or .L:115 or .L:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.300
ARG69
3.530
PHE76
3.928
PRO86
4.166
TRP88
3.515
PHE91
3.595
TYR98
2.688
PRO99
2.974
THR100
4.793
Residue
Distance (Å)
LEU101
4.472
ARG107
3.573
ILE109
3.580
HIS110
3.030
SER111
2.667
TYR112
2.629
HIS115
2.604
TRP117
3.440
Ligand Name: (2s,4r)-1-Ethanoyl-N-[[4-(1,3-Oxazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide PDB:4BKS
Method X-ray diffraction Resolution 2.20 Å Mutation No [13]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNQ
145
PIFANITLPV
155
YTLKERCLQV
165

VRSLVKPENY
175
RRLDIVRSLY
185
EDLEDHPNVQ
195
KDLERLT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .X6C or .X6C2 or .X6C3 or :3X6C;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
4.032
PRO86
4.122
TRP88
3.511
PHE91
4.990
TYR98
2.702
PRO99
3.205
LEU101
4.453
Residue
Distance (Å)
ARG107
4.463
ILE109
3.540
HIS110
2.765
SER111
2.725
TYR112
3.535
HIS115
2.710
TRP117
3.449
Ligand Name: (2~{s},4~{r})-1-[(2~{s})-2-(Cyclopropylcarbonylamino)-3,3-Dimethyl-Butanoyl]-~{n}-[[4-(4-Methyl-1,3-Thiazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) PDB:5NVW
Method X-ray diffraction Resolution 2.20 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9BW or .9BW2 or .9BW3 or :39BW;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.689
ARG69
3.686
PHE76
3.971
PRO86
3.958
TRP88
3.510
PHE91
3.575
GLN96
4.629
TYR98
2.707
PRO99
3.086
Residue
Distance (Å)
THR100
4.853
LEU101
4.154
ARG107
3.961
ILE109
3.337
HIS110
2.750
SER111
2.647
TYR112
3.386
HIS115
2.601
TRP117
3.447
Ligand Name: (2~{s},4~{r})-1-[(2~{s})-3,3-Dimethyl-2-(Oxetan-3-Ylcarbonylamino)butanoyl]-~{n}-[[4-(4-Methyl-1,3-Thiazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane-3-carboxamido)butanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 19) PDB:5NW2
Method X-ray diffraction Resolution 2.20 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9B8 or .9B82 or .9B83 or :39B8;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.652
ARG69
3.555
PHE76
3.939
PRO86
4.075
TRP88
3.545
PHE91
3.470
GLN96
4.410
TYR98
2.738
PRO99
3.042
Residue
Distance (Å)
THR100
4.949
LEU101
4.027
ARG107
4.068
ILE109
3.517
HIS110
2.866
SER111
2.713
TYR112
3.240
HIS115
2.661
TRP117
3.504
Ligand Name: (4r)-1-(3,3-Dimethylbutanoyl)-4-Hydroxy-N-[4-(1,3-Oxazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(oxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 2) PDB:4W9C
Method X-ray diffraction Resolution 2.20 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JG or .3JG2 or .3JG3 or :33JG;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
4.218
PRO86
4.386
TRP88
3.520
PHE91
4.329
GLN96
4.322
TYR98
2.673
PRO99
3.336
LEU101
4.568
Residue
Distance (Å)
ARG107
3.563
ILE109
3.558
HIS110
2.869
SER111
2.696
TYR112
3.430
HIS115
2.593
TRP117
3.533
Ligand Name: (4r)-1-(3,3-Dimethylbutanoyl)-4-Hydroxy-N-[4-(4-Methyl-1,3-Oxazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methyloxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) PDB:4W9D
Method X-ray diffraction Resolution 2.20 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JK or .3JK2 or .3JK3 or :33JK;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
4.024
PRO86
4.209
TRP88
3.555
PHE91
4.114
GLN96
4.530
TYR98
2.744
PRO99
3.225
LEU101
4.012
Residue
Distance (Å)
ARG107
4.136
ILE109
3.606
HIS110
2.867
SER111
2.608
TYR112
3.465
HIS115
2.637
TRP117
3.491
Ligand Name: N-Acetyl-3-Methyl-L-Valyl-3-Methyl-L-Valyl-(4r)-4-Hydroxy-N-[4-(4-Methyl-1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15) PDB:4W9L
Method X-ray diffraction Resolution 2.20 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JJ or .3JJ2 or .3JJ3 or :33JJ;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
2.672
ARG69
3.723
PHE76
3.850
PRO86
3.972
TRP88
3.600
PHE91
3.511
GLN96
4.069
TYR98
2.600
PRO99
3.081
Residue
Distance (Å)
LEU101
4.611
ARG107
4.058
ILE109
3.570
HIS110
2.876
SER111
2.677
TYR112
2.924
HIS115
2.515
TRP117
3.484
Ligand Name: N-Acetyl-L-Leucyl-3-Methyl-L-Valyl-(4r)-4-Hydroxy-N-[4-(4-Methyl-1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-4-methylpentanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 13) PDB:4W9J
Method X-ray diffraction Resolution 2.20 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JH or .3JH2 or .3JH3 or :33JH;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.108
ARG69
4.070
PHE76
3.881
PRO86
3.993
TRP88
3.603
PHE91
3.411
GLN96
4.280
TYR98
2.581
PRO99
3.107
Residue
Distance (Å)
LEU101
4.102
ARG107
4.040
ILE109
3.517
HIS110
2.801
SER111
2.756
TYR112
3.410
HIS115
2.506
TRP117
3.504
Ligand Name: N-[(1-Fluorocyclopropyl)carbonyl]-3-Methyl-L-Valyl-(4r)-4-Hydroxy-N-[4-(4-Methyl-1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-fluorocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) PDB:5NVX
Method X-ray diffraction Resolution 2.20 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4YY or .4YY2 or .4YY3 or :34YY;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.496
ARG69
3.777
PHE76
3.902
PRO86
4.022
TRP88
3.509
PHE91
3.476
GLN96
4.348
TYR98
2.698
PRO99
3.069
Residue
Distance (Å)
THR100
4.768
LEU101
4.131
ARG107
3.963
ILE109
3.405
HIS110
2.818
SER111
2.825
TYR112
3.304
HIS115
2.634
TRP117
3.496
Ligand Name: N-[5-[4-[[4-[2-[[(2S)-1-[(2S,4R)-4-hydroxy-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]pyrrolidin-1-yl]-3,3-dimethyl-1-oxobutan-2-yl]amino]-2-oxoethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1H-pyridine-3-carboxamide Ligand Info
Structure Description Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker PDB:8BB5
Method X-ray diffraction Resolution 2.20 Å Mutation No [14]
PDB Sequence
GRPRPVLRSV
66
NSREPSQVIF
76
CNRSPRVVLP
86
VWLNFDGEPQ
96
PYPTLPPGTG
106

RRIHSYRGHL
116
WLFRDAGTHD
126
GLLVNQTELF
136
VPSLNVDGQP
146
IFANITLPVY
156

TLKERCLQVV
166
RSLVKPENYR
176
RLDIVRSLYE
186
DLEDHPNVQK
196
DLERLTQERI
206

AHQR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q43 or .Q432 or .Q433 or :3Q43;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.243
ARG69
2.729
PHE76
3.711
PRO86
4.023
TRP88
3.424
PHE91
3.535
TYR98
2.636
PRO99
3.086
THR100
4.861
Residue
Distance (Å)
LEU101
4.104
ARG107
2.821
ILE109
3.519
HIS110
3.005
SER111
2.582
TYR112
3.382
HIS115
2.779
TRP117
3.517
Ligand Name: (2S,4R)-N-[[2-[3-[4-(4-bromo-7-cyclopentyl-5-oxobenzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2S)-2-[(1-fluorocyclopropanecarbonyl)amino]-3,3-dimethylbutanoyl]-4-hydroxypyrrolidine-2-carboxamide Ligand Info
Structure Description Crystal structure of PROTAC 5 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB PDB:7Z6L
Method X-ray diffraction Resolution 2.24 Å Mutation No [8]
PDB Sequence
PVLRSVNSRE
70
PSQVIFCNRS
80
PRVVLPVWLN
90
FDGEPQPYPT
100
LPPGTGRRIH
110

SYRGHLWLFR
120
DAGTHDGLLV
130
NQTELFVPSL
140
NVDGQPIFAN
150
ITLPVYTLKE
160

RCLQVVRSLV
170
KPENYRRLDI
180
VRSLYEDLED
190
HPNVQKDLER
200
LTQERIAHQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IEI or .IEI2 or .IEI3 or :3IEI;style chemicals stick;color identity;select .B:68 or .B:69 or .B:76 or .B:86 or .B:88 or .B:91 or .B:98 or .B:99 or .B:100 or .B:101 or .B:107 or .B:109 or .B:110 or .B:111 or .B:112 or .B:115 or .B:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER68
4.064
ARG69
4.898
PHE76
3.781
PRO86
4.055
TRP88
3.530
PHE91
3.644
TYR98
2.777
PRO99
3.090
THR100
4.871
Residue
Distance (Å)
LEU101
3.921
ARG107
3.436
ILE109
3.505
HIS110
2.926
SER111
2.681
TYR112
2.792
HIS115
2.695
TRP117
3.455
Ligand Name: (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide Ligand Info
Structure Description Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB PDB:6HAY
Method X-ray diffraction Resolution 2.24 Å Mutation No [15]
PDB Sequence
PRPVLRSVNS
68
REPSQVIFCN
78
RSPRVVLPVW
88
LNFDGEPQPY
98
PTLPPGTGRR
108

IHSYRGHLWL
118
FRDAGTHDGL
128
LVNQTELFVP
138
SLNVDGQPIF
148
ANITLPVYTL
158

KERCLQVVRS
168
LVKPENYRRL
178
DIVRSLYEDL
188
EDHPNVQKDL
198
ERLTQERIAH
208

QR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FX8 or .FX82 or .FX83 or :3FX8;style chemicals stick;color identity;select .B:67 or .B:69 or .B:76 or .B:86 or .B:88 or .B:91 or .B:97 or .B:98 or .B:99 or .B:100 or .B:101 or .B:107 or .B:109 or .B:110 or .B:111 or .B:112 or .B:115 or .B:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.192
ARG69
3.512
PHE76
3.949
PRO86
3.848
TRP88
3.436
PHE91
3.558
PRO97
4.924
TYR98
2.716
PRO99
3.021
Residue
Distance (Å)
THR100
4.646
LEU101
3.892
ARG107
2.922
ILE109
3.481
HIS110
3.139
SER111
2.668
TYR112
3.099
HIS115
2.773
TRP117
3.335
Ligand Name: (2~{R},3~{S},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with modified VH032 containing (3S,4S)-3-fluoro-4-hydroxyproline (ligand 14b) PDB:6GFZ
Method X-ray diffraction Resolution 2.30 Å Mutation No [16]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EXE or .EXE2 or .EXE3 or :3EXE;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.400
ARG69
4.742
PHE76
3.877
PRO86
3.851
TRP88
3.543
PHE91
3.502
GLN96
4.822
TYR98
2.782
PRO99
2.956
Residue
Distance (Å)
THR100
4.749
LEU101
4.091
ARG107
3.983
ILE109
3.446
HIS110
2.894
SER111
2.669
TYR112
3.366
HIS115
2.609
TRP117
3.270
Ligand Name: (2~{s},4~{r})-1-[(2~{s})-2-[(1-Acetamidocyclopropyl)carbonylamino]-3,3-Dimethyl-Butanoyl]-~{n}-[[4-(4-Methyl-1,3-Thiazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetamidocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 17) PDB:5NW0
Method X-ray diffraction Resolution 2.30 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9BK or .9BK2 or .9BK3 or :39BK;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.473
ARG69
3.764
PHE76
4.042
PRO86
4.150
TRP88
3.616
PHE91
3.571
GLN96
4.813
TYR98
2.683
PRO99
3.103
Residue
Distance (Å)
THR100
4.911
LEU101
4.198
ARG107
4.206
ILE109
3.416
HIS110
2.941
SER111
2.801
TYR112
3.305
HIS115
2.625
TRP117
3.594
Ligand Name: (2s,4r)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)ethanoyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide PDB:4BKT
Method X-ray diffraction Resolution 2.35 Å Mutation No [13]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
QPIFANITLP
154
VYTLKERCLQ
164

VVRSLVKPEN
174
YRRLDIVRSL
184
YEDLEDHPNV
194
QKDLERL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QD0 or .QD02 or .QD03 or :3QD0;style chemicals stick;color identity;select .C:67 or .C:69 or .C:88 or .C:91 or .C:98 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.671
ARG69
4.137
TRP88
3.472
PHE91
3.391
TYR98
2.653
Residue
Distance (Å)
HIS110
2.765
SER111
2.751
TYR112
3.721
HIS115
2.693
TRP117
3.495
Ligand Name: (2S,4R)-1-((S)-2-(1-cyanocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with VH298 PDB:5LLI
Method X-ray diffraction Resolution 2.40 Å Mutation No [17]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Q
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6Z3 or .6Z32 or .6Z33 or :36Z3;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.516
ARG69
3.846
PHE76
4.096
PRO86
4.146
TRP88
3.605
PHE91
3.451
GLN96
4.868
TYR98
2.560
PRO99
3.183
Residue
Distance (Å)
THR100
4.976
LEU101
4.262
ARG107
4.087
ILE109
3.328
HIS110
3.017
SER111
2.835
TYR112
3.225
HIS115
2.787
TRP117
3.604
Ligand Name: (4r)-1-Acetyl-4-Hydroxy-L-Prolyl-(4r)-4-Hydroxy-N-[4-(4-Methyl-1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-carbonyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) PDB:4W9I
Method X-ray diffraction Resolution 2.40 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JS or .3JS2 or .3JS3 or :33JS;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
3.960
PRO86
4.171
TRP88
3.482
PHE91
4.079
GLN96
4.567
TYR98
2.587
PRO99
3.154
THR100
4.956
Residue
Distance (Å)
LEU101
4.052
ARG107
4.041
ILE109
3.485
HIS110
2.755
SER111
2.591
TYR112
3.388
HIS115
2.763
TRP117
3.478
Ligand Name: (4r)-1-(3,3-Dimethylbutanoyl)-4-Hydroxy-N-[4-(1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 4) PDB:4W9E
Method X-ray diffraction Resolution 2.60 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JT or .3JT2 or .3JT3 or :33JT;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
3.996
PRO86
4.206
TRP88
3.612
PHE91
4.098
GLN96
4.721
TYR98
2.572
PRO99
3.251
THR100
4.891
Residue
Distance (Å)
LEU101
4.118
ARG107
3.357
ILE109
3.497
HIS110
2.987
SER111
2.642
TYR112
3.620
HIS115
2.655
TRP117
3.507
Ligand Name: (2~{R},3~{R},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with modified VH032 containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 14a) PDB:6GFY
Method X-ray diffraction Resolution 2.70 Å Mutation No [16]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EXH or .EXH2 or .EXH3 or :3EXH;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.171
ARG69
4.575
PHE76
4.126
PRO86
4.106
TRP88
3.550
PHE91
3.544
GLN96
4.702
TYR98
2.577
PRO99
3.116
Residue
Distance (Å)
LEU101
4.181
ARG107
4.082
ILE109
3.429
HIS110
3.050
SER111
2.792
TYR112
3.465
HIS115
2.645
TRP117
3.215
Ligand Name: (2~{s},4~{r})-1-[(2~{s})-2-[(1-Ethanoylcyclopropyl)carbonylamino]-3,3-Dimethyl-Butanoyl]-~{n}-[[4-(4-Methyl-1,3-Thiazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetylcyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 16) PDB:5NVZ
Method X-ray diffraction Resolution 2.70 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Q
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9BN or .9BN2 or .9BN3 or :39BN;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:100 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.788
ARG69
3.772
PHE76
4.144
PRO86
4.141
TRP88
3.640
PHE91
3.852
GLN96
4.577
TYR98
2.438
PRO99
3.169
Residue
Distance (Å)
THR100
4.995
LEU101
4.246
ARG107
4.065
ILE109
3.387
HIS110
2.986
SER111
2.829
TYR112
3.439
HIS115
2.585
TRP117
3.584
Ligand Name: (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Ligand Info
Structure Description The PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB PDB:5T35
Method X-ray diffraction Resolution 2.70 Å Mutation No [18]
PDB Sequence
PVLRSVNSRE
70
PSQVIFCNRS
80
PRVVLPVWLN
90
FDGEPQPYPT
100
LPPGTGRRIH
110

SYRGHLWLFR
120
DAGTHDGLLV
130
NQTELFVPSL
140
NVDGQPIFAN
150
ITLPVYTLKE
160

RCLQVVRSLV
170
KPENYRRLDI
180
VRSLYEDLED
190
HPNVQKDLER
200
LTQERIAHQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .759 or .7592 or .7593 or :3759;style chemicals stick;color identity;select .D:67 or .D:69 or .D:76 or .D:86 or .D:88 or .D:91 or .D:98 or .D:99 or .D:100 or .D:101 or .D:107 or .D:109 or .D:110 or .D:111 or .D:112 or .D:115 or .D:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.496
ARG69
4.399
PHE76
4.148
PRO86
3.995
TRP88
3.536
PHE91
3.716
TYR98
2.565
PRO99
3.083
THR100
4.976
Residue
Distance (Å)
LEU101
3.954
ARG107
3.092
ILE109
3.515
HIS110
3.008
SER111
2.696
TYR112
3.208
HIS115
2.875
TRP117
3.633
Ligand Name: (4r)-1-(3,3-Dimethylbutanoyl)-4-Hydroxy-N-[3-Methyl-4-(1,3-Thiazol-5-Yl)benzyl]-L-Prolinamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(3-methyl-4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) PDB:4W9G
Method X-ray diffraction Resolution 2.70 Å Mutation No [12]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3JV or .3JV2 or .3JV3 or :33JV;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
4.107
PRO86
3.996
TRP88
3.616
PHE91
4.015
GLN96
4.423
TYR98
2.580
PRO99
3.237
LEU101
3.981
Residue
Distance (Å)
ARG107
3.455
ILE109
3.676
HIS110
3.134
SER111
2.791
TYR112
3.535
HIS115
2.679
TRP117
3.593
Ligand Name: Methyl 4-[({(4r)-4-Hydroxy-1-[(3-Methylisoxazol-5-Yl)acetyl]-L-Prolyl}amino)methyl]benzoate Ligand Info
Structure Description pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate PDB:3ZTD
Method X-ray diffraction Resolution 2.79 Å Mutation No [6]
PDB Sequence
LRSVNSREPS
72
QVIFCNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSDGQ
145
PIFANITLPV
155
YTLKERCLQV
165

VRSLVKPENY
175
RRLDIVRSLY
185
EDLEDHPNVQ
195
KDLERLTQE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ZTD or .ZTD2 or .ZTD3 or :3ZTD;style chemicals stick;color identity;select .C:67 or .C:69 or .C:88 or .C:91 or .C:98 or .C:99 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.370
ARG69
4.006
TRP88
3.333
PHE91
3.990
TYR98
2.481
PRO99
3.461
ARG107
3.447
Residue
Distance (Å)
ILE109
3.462
HIS110
2.882
SER111
2.573
TYR112
3.038
HIS115
2.792
TRP117
3.440
Ligand Name: (2s,4r)-1-(2-Chlorophenyl)carbonyl-N-[(4-Chlorophenyl)methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide bound PDB:4B95
Method X-ray diffraction Resolution 2.80 Å Mutation No [5]
PDB Sequence
VLRSVNSREP
71
SQVIFCNRSP
81
RVVLPVWLNF
91
DGEPQPYPTL
101
PPGTGRRIHS
111

YRGHLWLFRD
121
AGTHDGLLVN
131
QTELFVPIFA
149
NITLPVYTLK
159
ERCLQVVRSL
169

VKPENYRRLD
179
IVRSLYEDLE
189
DHPNVQKDLE
199
RLTQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UCK or .UCK2 or .UCK3 or :3UCK;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
4.735
PRO86
4.607
TRP88
3.536
PHE91
3.492
GLN96
3.769
TYR98
2.823
PRO99
3.441
Residue
Distance (Å)
ARG107
2.786
ILE109
3.601
HIS110
2.684
SER111
3.068
TYR112
3.234
HIS115
2.600
TRP117
3.479
Ligand Name: N-[5-[4-[[4-[[(2S)-1-[(2S,4R)-4-hydroxy-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]pyrrolidin-1-yl]-3,3-dimethyl-1-oxobutan-2-yl]amino]-4-oxobutyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1H-pyridine-3-carboxamide Ligand Info
Structure Description Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker PDB:8BB4
Method X-ray diffraction Resolution 2.80 Å Mutation No [19]
PDB Sequence
VLRSVNSREP
71
SQVIFCNRSP
81
RVVLPVWLNF
91
DGEPQPYPTL
101
PPGTGRRIHS
111

YRGHLWLFRD
121
AGTHDGLLVN
131
QTELFVPSLN
141
VDGQPIFANI
151
TLPVYTLKER
161

CLQVVRSLVK
171
PENYRRLDIV
181
RSLYEDLEDH
191
PNVQKDLERL
201
TQERIAH
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q3R or .Q3R2 or .Q3R3 or :3Q3R;style chemicals stick;color identity;select .P:67 or .P:69 or .P:76 or .P:86 or .P:88 or .P:91 or .P:98 or .P:99 or .P:100 or .P:101 or .P:107 or .P:109 or .P:110 or .P:111 or .P:112 or .P:115 or .P:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
2.655
ARG69
3.096
PHE76
3.679
PRO86
3.954
TRP88
3.685
PHE91
3.547
TYR98
2.555
PRO99
3.044
THR100
4.928
Residue
Distance (Å)
LEU101
4.623
ARG107
2.804
ILE109
3.414
HIS110
2.827
SER111
2.619
TYR112
3.322
HIS115
2.934
TRP117
3.454
Ligand Name: (2~{s},4~{r})-1-[(2~{s})-2-Acetamidopropanoyl]-~{n}-[[4-(4-Methyl-1,3-Thiazol-5-Yl)phenyl]methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamidopropanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl) pyrrolidine-2-carboxamide (ligand 11) PDB:5NVY
Method X-ray diffraction Resolution 2.90 Å Mutation No [11]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9B5 or .9B52 or .9B53 or :39B5;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
3.897
PRO86
4.102
TRP88
3.488
PHE91
3.832
GLN96
4.680
TYR98
2.456
PRO99
3.168
LEU101
3.927
Residue
Distance (Å)
ARG107
3.652
ILE109
3.440
HIS110
2.840
SER111
2.558
TYR112
3.403
HIS115
2.674
TRP117
3.393
Ligand Name: (2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Ligand Info
Structure Description CRYSTAL STRUCTURE OF AT7 IN COMPLEX WITH THE SECOND BROMODOMAIN OF HUMAN BRD4 AND PVHL:ELONGINC:ELONGINB PDB:7ZNT
Method X-ray diffraction Resolution 3.00 Å Mutation No [20]
PDB Sequence
PVLRSVNSRE
70
PSQVIFCNRS
80
PRVVLPVWLN
90
FDGEPQPYPT
100
LPPGTGRRIH
110

SYRGHLWLFR
120
DAGTHDGLLV
130
NQTELFVPSL
140
NVDGQPIFAN
150
ITLPVYTLKE
160

RCLQVVRSLV
170
KPENYRRLDI
180
VRSLYEDLED
190
HPNVQKDLER
200
LTQERIAHQR
210
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IZR or .IZR2 or .IZR3 or :3IZR;style chemicals stick;color identity;select .C:67 or .C:68 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.628
SER68
4.510
ARG69
3.622
PHE76
4.394
PRO86
4.325
TRP88
3.538
PHE91
3.996
TYR98
2.574
PRO99
3.051
Residue
Distance (Å)
LEU101
4.200
ARG107
3.196
ILE109
3.604
HIS110
2.909
SER111
2.472
TYR112
3.119
HIS115
2.803
TRP117
3.395
Ligand Name: N-[(5S,7R,11S,23S)-11-tert-butyl-7-hydroxy-34-(4-methyl-1,3-thiazol-5-yl)-4,10,13-trioxo-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.05,9]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7S,9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.02,6]trideca-2(6),4,10,12-tetraen-9-yl]acetamide Ligand Info
Structure Description Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human Brd4 and pVHL:ElonginC:ElonginB PDB:6SIS
Method X-ray diffraction Resolution 3.50 Å Mutation No [21]
PDB Sequence
PVLRSVNSRE
70
PSQVIFCNRS
80
PRVVLPVWLN
90
FDGEPQPYPT
100
LPPGTGRRIH
110

SYRGHLWLFR
120
DAGTHDGLLV
130
NQTELFVPSL
140
NVDGQPIFAN
150
ITLPVYTLKE
160

RCLQVVRSLV
170
KPENYRRLDI
180
VRSLYEDLED
190
HPNVQKDLER
200
LTQERIAHQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LFE or .LFE2 or .LFE3 or :3LFE;style chemicals stick;color identity;select .D:67 or .D:69 or .D:76 or .D:86 or .D:88 or .D:91 or .D:98 or .D:99 or .D:100 or .D:101 or .D:107 or .D:109 or .D:110 or .D:111 or .D:112 or .D:115 or .D:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.721
ARG69
4.096
PHE76
4.972
PRO86
4.562
TRP88
3.583
PHE91
3.771
TYR98
2.615
PRO99
3.109
THR100
4.456
Residue
Distance (Å)
LEU101
3.900
ARG107
3.310
ILE109
3.729
HIS110
3.100
SER111
2.909
TYR112
3.147
HIS115
2.818
TRP117
3.801
Ligand Name: (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Ligand Info
Structure Description pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-Acetamidopropanethioyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl) benzyl)pyrrolidine-2-carboxamide (ligand 3) PDB:6FMJ
Method X-ray diffraction Resolution 2.45 Å Mutation No [22]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DV5 or .DV52 or .DV53 or :3DV5;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:96 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
3.982
PRO86
4.098
TRP88
3.420
PHE91
3.811
GLN96
4.567
TYR98
2.537
PRO99
3.178
LEU101
3.882
Residue
Distance (Å)
ARG107
3.936
ILE109
3.367
HIS110
2.899
SER111
2.693
TYR112
3.434
HIS115
2.712
TRP117
3.479
Ligand Name: Ac-thionoAla-thionoHyp-Unk Ligand Info
Structure Description pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-thioxopropan-2-yl)acetamide (ligand 4) PDB:6FMK
Method X-ray diffraction Resolution 2.75 Å Mutation No [22]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DV8 or .DV82 or .DV83 or :3DV8;style chemicals stick;color identity;select .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE76
4.080
PRO86
4.068
TRP88
3.584
PHE91
3.885
TYR98
2.845
PRO99
3.166
LEU101
3.638
Residue
Distance (Å)
ARG107
3.570
ILE109
3.449
HIS110
2.852
SER111
2.907
TYR112
3.569
HIS115
2.743
TRP117
3.657
Ligand Name: Ac-Ala-thionoHyp-Unk Ligand Info
Structure Description pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-oxopropan-2-yl)acetamide (ligand 2) PDB:6FMI
Method X-ray diffraction Resolution 2.80 Å Mutation No [22]
PDB Sequence
VLRSVNSREP
71
SQVIFNRSPR
82
VVLPVWLNFD
92
GEPQPYPTLP
102
PGTGRRIHSY
112

RGHLWLFRDA
122
GTHDGLLVNQ
132
TELFVPSLNV
142
DGQPIFANIT
152
LPVYTLKERC
162

LQVVRSLVKP
172
ENYRRLDIVR
182
SLYEDLEDHP
192
NVQKDLERLT
202
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DV2 or .DV22 or .DV23 or :3DV2;style chemicals stick;color identity;select .C:67 or .C:69 or .C:76 or .C:86 or .C:88 or .C:91 or .C:98 or .C:99 or .C:101 or .C:107 or .C:109 or .C:110 or .C:111 or .C:112 or .C:115 or .C:117; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
4.569
ARG69
4.711
PHE76
3.846
PRO86
4.031
TRP88
3.618
PHE91
3.982
TYR98
2.907
PRO99
3.162
Residue
Distance (Å)
LEU101
4.068
ARG107
4.020
ILE109
3.515
HIS110
2.917
SER111
2.718
TYR112
3.351
HIS115
2.600
TRP117
3.571
Ligand Name: (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide Ligand Info
Structure Description Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB PDB:6HR2
Method X-ray diffraction Resolution 1.76 Å Mutation No [15]
PDB Sequence
PVLRSVNSRE
70
PSQVIFCNRS
80
PRVVLPVWLN
90
FDGEPQPYPT
100
LPPGTGRRIH
110

SYRGHLWLFR
120
DAGTHDGLLV
130
NQTELFVPSL
140
NVDGQPIFAN
150
ITLPVYTLKE
160

RCLQVVRSLV
170
KPENYRRLDI
180
VRSLYEDLED
190
HPNVQKDLER
200
LTQERIAHQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FWZ or .FWZ2 or .FWZ3 or :3FWZ;style chemicals stick;color identity;select .B:67 or .B:69 or .B:70 or .B:76 or .B:86 or .B:88 or .B:91 or .B:98 or .B:99 or .B:100 or .B:101 or .B:107 or .B:109 or .B:110 or .B:111 or .B:112 or .B:115 or .B:117; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN67
3.040
ARG69
2.314
GLU70
4.495
PHE76
3.034
PRO86
2.518
TRP88
2.421
PHE91
2.495
TYR98
1.876
PRO99
2.364
Residue
Distance (Å)
THR100
4.205
LEU101
2.358
ARG107
2.250
ILE109
2.370
HIS110
2.100
SER111
1.874
TYR112
2.400
HIS115
1.782
TRP117
2.044
Click to View More Binding Site Information of This Target and Ligand Pair
References  Top
REF 1 Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. J Med Chem. 2018 Aug 23;61(16):7387-7393.
REF 2 Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1Alpha interaction. J Am Chem Soc. 2012 Mar 14;134(10):4465-8.
REF 3 Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer
REF 4 Antibody-Mediated Delivery of Chimeric BRD4 Degraders. Part 2: Improvement of In Vitro Antiproliferation Activity and In Vivo Antitumor Efficacy. J Med Chem. 2021 Mar 11;64(5):2576-2607.
REF 5 Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1Alpha. Angew Chem Int Ed Engl. 2012 Nov 12;51(46):11463-7.
REF 6 Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1Alpha protein-protein interface. Chem Biol. 2012 Oct 26;19(10):1300-12.
REF 7 Elongin-B, Elongin-C, Von Hippel-Lindau Disease Tumor Suppressor Complex
REF 8 A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo. Nat Commun. 2022 Oct 10;13(1):5969.
REF 9 A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models. Sci Transl Med. 2021 Sep 29;13(613):eabj1578.
REF 10 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1)
REF 11 Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298). J Med Chem. 2018 Jan 25;61(2):599-618.
REF 12 Structure-guided design and optimization of small molecules targeting the protein-protein interaction between the von Hippel-Lindau (VHL) E3 ubiquitin ligase and the hypoxia inducible factor (HIF) alpha subunit with in vitro nanomolar affinities. J Med Chem. 2014 Oct 23;57(20):8657-63.
REF 13 Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions?. ACS Med Chem Lett. 2014 Jan 9;5(1):23-28.
REF 14 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker
REF 15 BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat Chem Biol. 2019 Jul;15(7):672-680.
REF 16 3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation. J Am Chem Soc. 2018 Jul 25;140(29):9299-9313.
REF 17 Potent and selective chemical probe of hypoxic signalling downstream of HIF-Alpha hydroxylation via VHL inhibition. Nat Commun. 2016 Nov 4;7:13312.
REF 18 Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat Chem Biol. 2017 May;13(5):514-521.
REF 19 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker
REF 20 Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders. Nat Chem Biol. 2023 Mar;19(3):323-333.
REF 21 Structure-Based Design of a Macrocyclic PROTAC. Angew Chem Int Ed Engl. 2020 Jan 20;59(4):1727-1734.
REF 22 Thioamide substitution to probe the hydroxyproline recognition of VHL ligands. Bioorg Med Chem. 2018 Jul 15;26(11):2992-2995.

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