Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T14030 Target Info
Target Name Ras-related protein Rab-7a (RAB7A)
Synonyms RAB7
Target Type Literature-reported Target
Gene Name RAB7A
Biochemical Class Small GTPase
UniProt ID
RAB7A_HUMAN
Ligand General Information  Top
Ligand Name Guanosine-5'-Triphosphate Ligand Info
Canonical SMILES C1=NC2=C(N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
InChI 1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKey XKMLYUALXHKNFT-UUOKFMHZSA-N
PubChem Compound ID 135398633
Drug Binding Sites of Target  Top
PDB ID: 1T91      crystal structure of human small GTPase Rab7(GTP)
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [1]
PDB Sequence
VLLKVIILGD
16
SGVGKTSLMN
26
QYVNKKFSNQ
36
YKATIGADFL
46
TKEVMVDDRL
56

VTMQIWDTAG
66
LERFQSLGVA
76
FYRGADCCVL
86
VFDVTAPNTF
96
KTLDSWRDEF
106

LIQASPRDPE
116
NFPFVVLGNK
126
IDLENRQVAT
136
KRAQAWCYSK
146
NNIPYFETSA
156

KEAINVEQAF
166
QTIARNALKQ
176
ETEVEL
Residue
Distance (Å)
GLY15
4.708
ASP16
3.717
SER17
2.777
GLY18
2.883
VAL19
3.450
GLY20
3.103
LYS21
2.748
THR22
2.952
SER23
2.945
PHE33
3.543
SER34
3.737
ASN35
3.484
GLN36
4.936
TYR37
2.593
LYS38
4.214
Residue
Distance (Å)
ALA39
3.917
THR40
2.877
ASP63
4.833
THR64
4.153
ALA65
3.947
GLY66
2.774
LEU67
4.233
ASN125
3.398
LYS126
2.529
ASP128
2.754
LEU129
2.971
SER155
3.299
ALA156
2.549
LYS157
2.853
GLU158
4.898
PDB ID: 1YHN      Structure basis of RILP recruitment by Rab7
Method X-ray diffraction Resolution 3.00 Å Mutation Yes [1]
PDB Sequence
SRKKVLLKVI
12
ILGDSGVGKT
22
SLMNQYVNKK
32
FSNQYKATIG
42
ADFLTKEVMV
52

DDRLVTMQIW
62
DTAGLERFQS
72
LGVAFYRGAD
82
CCVLVFDVTA
92
PNTFKTLDSW
102

RDEFLIQASP
112
RDPENFPFVV
122
LGNKIDLENR
132
QVATKRAQAW
142
CYSKNNIPYF
152

ETSAKEAINV
162
EQAFQTIARN
172
ALKQETEVEL
182
YNE
Residue
Distance (Å)
ASP16
4.547
SER17
2.899
GLY18
2.227
VAL19
3.623
GLY20
2.440
LYS21
2.730
THR22
2.914
SER23
2.547
LEU24
4.850
PHE33
3.545
SER34
3.016
ASN35
3.330
GLN36
4.588
TYR37
2.797
LYS38
4.400
Residue
Distance (Å)
ALA39
3.815
THR40
2.525
THR64
3.667
ALA65
3.579
GLY66
2.616
LEU67
4.103
ASN125
2.765
LYS126
3.168
ILE127
4.913
ASP128
2.515
LEU129
3.206
THR154
4.532
SER155
3.094
ALA156
2.745
LYS157
3.144
PDB ID: 7F6J      Crystal structure of the PDZD8 coiled-coil domain - Rab7 complex
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [2]
PDB Sequence
VLLKVIILGD
16
SGVGKTSLMN
26
QYVNKKFSNQ
36
YKATIGADFL
46
TKEVMVDDRL
56

VTMQIWDTAG
66
LERFQSLGVA
76
FYRGADCCVL
86
VFDVTAPNTF
96
KTLDSWRDEF
106

LIQASPRDPE
116
NFPFVVLGNK
126
IDLENRQVAT
136
KRAQAWCYSK
146
NNIPYFETSA
156

KEAINVEQAF
166
QTIARNALKQ
176
E
Residue
Distance (Å)
GLY15
4.797
ASP16
3.875
SER17
2.570
GLY18
2.895
VAL19
3.439
GLY20
2.927
LYS21
2.659
THR22
2.944
SER23
2.707
PHE33
3.524
SER34
2.830
ASN35
2.767
GLN36
3.946
TYR37
2.636
LYS38
4.310
Residue
Distance (Å)
ALA39
3.945
THR40
2.938
ASP63
4.635
THR64
4.073
ALA65
3.980
GLY66
2.810
LEU67
4.417
ASN125
3.064
LYS126
3.119
ASP128
2.806
LEU129
3.578
THR154
4.635
SER155
3.495
ALA156
2.897
LYS157
3.372
PDB ID: 6IYB      Structure of human ORP1 ANK - Rab7 complex
Method X-ray diffraction Resolution 2.09 Å Mutation Yes [3]
PDB Sequence
VLLKVIILGD
16
SGVGKTSLMN
26
QYVNKKFSNQ
36
YKATIGADFL
46
TKEVMVDDRL
56

VTMQIWDTAG
66
LERFQSGVAF
77
YRGADCCVLV
87
FDVTAPNTFK
97
TLDSWRDEFL
107

IQASPRDPEN
117
FPFVVLGNKI
127
DLENRQVATK
137
RAQAWCYSKN
147
NIPYFETSAK
157

EAINVEQAFQ
167
TIARNALKQE
177
T
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GTP or .GTP2 or .GTP3 or :3GTP;style chemicals stick;color identity;select .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:21 or .A:22 or .A:23 or .A:33 or .A:34 or .A:35 or .A:36 or .A:37 or .A:38 or .A:39 or .A:40 or .A:63 or .A:64 or .A:65 or .A:66 or .A:67 or .A:125 or .A:126 or .A:128 or .A:129 or .A:154 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY15
4.818
ASP16
3.856
SER17
2.850
GLY18
2.883
VAL19
3.393
GLY20
3.145
LYS21
2.822
THR22
3.002
SER23
2.717
PHE33
3.175
SER34
2.644
ASN35
2.993
GLN36
3.893
TYR37
2.554
LYS38
4.151
Residue
Distance (Å)
ALA39
3.754
THR40
2.858
ASP63
4.720
THR64
3.881
ALA65
3.896
GLY66
2.753
LEU67
4.308
ASN125
3.110
LYS126
3.309
ASP128
2.791
LEU129
3.352
THR154
4.736
SER155
3.488
ALA156
2.928
LYS157
3.388
PDB ID: 6WCW      Structure of human Rubicon RH domain in complex with GTP-bound Rab7
Method X-ray diffraction Resolution 2.80 Å Mutation Yes [4]
PDB Sequence
VLLKVIILGD
16
SGVGKTSLMN
26
QYVNKKFSNQ
36
YKATIGADFL
46
TKEVMVDDRL
56

VTMQIWDTAG
66
LERFQSLGVA
76
FYRGADCCVL
86
VFDVTAPNTF
96
KTLDSWRDEF
106

LIQASPRDPE
116
NFPFVVLGNK
126
IDLENRQVAT
136
KRAQAWCYSK
146
NNIPYFETSA
156

KEAINVEQAF
166
QTIARNALKQ
176
ETEVEL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GTP or .GTP2 or .GTP3 or :3GTP;style chemicals stick;color identity;select .B:16 or .B:17 or .B:18 or .B:19 or .B:20 or .B:21 or .B:22 or .B:23 or .B:33 or .B:34 or .B:35 or .B:36 or .B:37 or .B:38 or .B:39 or .B:40 or .B:63 or .B:64 or .B:65 or .B:66 or .B:67 or .B:125 or .B:126 or .B:128 or .B:129 or .B:154 or .B:155 or .B:156 or .B:157; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP16
4.282
SER17
3.498
GLY18
2.865
VAL19
3.309
GLY20
2.732
LYS21
2.322
THR22
2.420
SER23
2.846
PHE33
3.240
SER34
3.246
ASN35
2.936
GLN36
4.094
TYR37
2.928
LYS38
4.023
ALA39
3.815
Residue
Distance (Å)
THR40
2.665
ASP63
4.808
THR64
3.229
ALA65
3.920
GLY66
3.039
LEU67
4.436
ASN125
2.821
LYS126
3.270
ASP128
2.629
LEU129
3.226
THR154
4.450
SER155
3.248
ALA156
2.735
LYS157
3.379
References  Top
REF 1 Structural basis for recruitment of RILP by small GTPase Rab7. EMBO J. 2005 Apr 20;24(8):1491-501.
REF 2 Structural basis of human PDZD8-Rab7 interaction for the ER-late endosome tethering. Sci Rep. 2021 Sep 22;11(1):18859.
REF 3 Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting. PLoS One. 2019 Feb 5;14(2):e0211724.
REF 4 Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex. Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):17003-17010.

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