Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T76059 Target Info
Target Name FK506-binding protein 1A (FKBP1A)
Synonyms Rotamase; Peptidyl-prolyl cis-trans isomerase FKBP1A; PPIase FKBP1A; Immunophillin FKBP; Immunophilin FKBP12; FKBP12; FKBP1; FKBP-1A; FKBP-12; FK-binding protein 12; Calstabin-1; 12 kDa FKBP; 12 kDa FK506-binding protein
Target Type Successful Target
Gene Name FKBP1A
Biochemical Class Cis-trans-isomerase
UniProt ID
FKB1A_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Tacrolimus Ligand Info
Structure Description FK506 BINDING PROTEIN FKBP MUTANT R42K/H87V COMPLEX WITH IMMUNOSUPPRESSANT FK506 PDB:1BKF
Method X-ray diffraction Resolution 1.60 Å Mutation Yes [1]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DKNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGVPGI
90
IPPHATLVFD
100

VELLKLE
Residue
Distance (Å)
TYR26
3.636
PHE36
3.401
ASP37
2.608
LYS42
3.770
PHE46
3.622
GLN53
4.661
GLU54
2.703
VAL55
2.972
Residue
Distance (Å)
ILE56
2.964
TRP59
3.580
ALA81
4.048
TYR82
2.566
VAL87
4.461
ILE90
4.605
ILE91
4.143
PHE99
3.603
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Sirolimus Ligand Info
Structure Description ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-12 COMPLEX PDB:1FKB
Method X-ray diffraction Resolution 1.70 Å Mutation No [2]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Residue
Distance (Å)
TYR26
3.446
PHE36
3.262
ASP37
2.498
PHE46
3.276
GLN53
1.864
GLU54
1.963
VAL55
3.194
Residue
Distance (Å)
ILE56
2.107
TRP59
3.609
TYR82
1.876
HIS87
3.480
ILE90
3.931
ILE91
4.258
PHE99
3.688
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Gpi-1046 Ligand Info
Structure Description SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROPHIC LIGAND PDB:1F40
Method Solution NMR Resolution N.A. Mutation No [3]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GPI or .GPI2 or .GPI3 or :3GPI;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:48 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
2.638
PHE36
3.913
ASP37
3.992
ARG42
4.533
PHE46
2.231
PHE48
4.700
GLN53
4.571
GLU54
2.914
Residue
Distance (Å)
VAL55
2.187
ILE56
2.097
TRP59
3.661
TYR82
2.113
HIS87
2.311
ILE90
2.028
ILE91
4.087
PHE99
3.311
Ligand Name: L-685,818 Ligand Info
Structure Description FKBP12 in complex with the BMP potentiator compound 9 at 1.55 A resolution PDB:6YF0
Method X-ray diffraction Resolution 1.55 Å Mutation No [4]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .818 or .8182 or .8183 or :3818;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.351
PHE36
3.368
ASP37
2.775
ARG42
3.516
PHE46
3.462
GLU54
2.492
VAL55
3.214
ILE56
2.922
Residue
Distance (Å)
TRP59
3.444
ALA81
3.320
TYR82
2.712
HIS87
3.659
ILE90
4.040
ILE91
3.936
PHE99
3.528
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: FKB-001 Ligand Info
Structure Description FK506 BINDING PROTEIN COMPLEXED WITH FKB-001 PDB:1J4R
Method X-ray diffraction Resolution 1.80 Å Mutation No [5]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .001 or .0012 or .0013 or :3001;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.177
PHE36
3.021
ASP37
3.090
ARG42
3.566
PHE46
3.407
GLN53
2.664
GLU54
3.786
VAL55
3.136
Residue
Distance (Å)
ILE56
2.988
TRP59
3.347
TYR82
2.752
HIS87
3.763
ILE90
3.301
ILE91
3.659
LEU97
4.681
PHE99
3.685
Ligand Name: 4-Hydroxy-2-butanone Ligand Info
Structure Description FKBP COMPLEXED WITH 4-HYDROXY-2-BUTANONE PDB:1D7J
Method X-ray diffraction Resolution 1.85 Å Mutation No [6]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BUQ or .BUQ2 or .BUQ3 or :3BUQ;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.823
PHE36
4.989
ASP37
3.923
PHE46
4.278
GLU54
4.823
Residue
Distance (Å)
VAL55
3.272
ILE56
2.945
TRP59
3.442
TYR82
4.020
PHE99
3.526
Ligand Name: Methyl Methylsulfinylmethyl Sulfide Ligand Info
Structure Description FKBP COMPLEXED WITH METHYL METHYLSULFINYLMETHYL SULFIDE (DSS) PDB:1D7I
Method X-ray diffraction Resolution 1.90 Å Mutation No [6]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DSS or .DSS2 or .DSS3 or :3DSS;style chemicals stick;color identity;select .A:26 or .A:37 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
2.997
ASP37
4.266
PHE46
3.504
GLU54
4.750
VAL55
3.150
Residue
Distance (Å)
ILE56
2.856
TRP59
4.045
TYR82
3.113
PHE99
3.723
Ligand Name: Heptyl-Beta-D-Glucopyranoside Ligand Info
Structure Description FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858 PDB:1QPF
Method X-ray diffraction Resolution 2.50 Å Mutation No [7]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B7G or .B7G2 or .B7G3 or :3B7G;style chemicals stick;color identity;select .A:82 or .A:85 or .A:87 or .A:90 or .A:91; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR82
3.043
THR85
3.418
HIS87
2.806
Residue
Distance (Å)
ILE90
3.752
ILE91
4.060
Ligand Name: L-709,587 Ligand Info
Structure Description FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-707,587 PDB:1QPL
Method X-ray diffraction Resolution 2.90 Å Mutation No [7]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .587 or .5872 or .5873 or :3587;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.355
PHE36
3.525
ASP37
2.707
ARG42
3.623
PHE46
3.579
GLU54
3.033
VAL55
3.391
ILE56
3.106
Residue
Distance (Å)
TRP59
3.455
ALA81
3.668
TYR82
2.688
HIS87
4.058
ILE90
4.583
ILE91
3.238
PHE99
3.393
Ligand Name: (3R,4E,7E,10R,11S,12R,13S,16R,17R,24aS)-11,17-dihydroxy-10,12,16-trimethyl-3-[(2R)-1-phenylbutan-2-yl]-6,9,10,11,12,13,14,15,16,17,22,23,24,24a-tetradecahydro-3H-13,17-epoxypyrido[2,1-c][1,4]oxazacyclohenicosine-1,18,19(21H)-trione Ligand Info
Structure Description Crystal structure of CEP250 bound to FKBP12 in the presence of FK506-like novel natural product PDB:6OQA
Method X-ray diffraction Resolution 2.20 Å Mutation No [8]
PDB Sequence
MGVQVETISP
10
GDGRTFPKRG
20
QTCVVHYTGM
30
LEDGKKFDSS
40
RDRNKPFKFM
50

LGKQEVIRGW
60
EEGVAQMSVG
70
QRAKLTISPD
80
YAYGATGHPG
90
IIPPHATLVF
100

DVELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .60Z or .60Z2 or .60Z3 or :360Z;style chemicals stick;color identity;select .A:27 or .A:37 or .A:38 or .A:43 or .A:47 or .A:54 or .A:55 or .A:56 or .A:57 or .A:60 or .A:83 or .A:88 or .A:91 or .A:92 or .A:98 or .A:100; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR27
3.481
PHE37
3.599
ASP38
2.805
ARG43
3.785
PHE47
3.816
GLN54
3.453
GLU55
3.208
VAL56
3.333
Residue
Distance (Å)
ILE57
2.805
TRP60
3.255
TYR83
2.675
HIS88
3.482
ILE91
4.282
ILE92
3.705
LEU98
4.976
PHE100
3.476
Ligand Name: 15-O-Desmethylascomycin Ligand Info
Structure Description FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution PDB:6YF3
Method X-ray diffraction Resolution 1.00 Å Mutation No [4]
PDB Sequence
PGVQVETISP
9
GDGRTFPKRG
19
QTCVVHYTGM
29
LEDGKKFDSS
39
RDRNKPFKFM
49

LGKQEVIRGW
59
EEGVAQMSVG
69
QRAKLTISPD
79
YAYGATGHPG
89
IIPPHATLVF
99

DVELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OOZ or .OOZ2 or .OOZ3 or :3OOZ;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.513
PHE36
3.528
ASP37
2.636
ARG42
3.699
PHE46
3.428
GLN53
4.735
GLU54
2.517
VAL55
3.144
Residue
Distance (Å)
ILE56
2.869
TRP59
3.439
ALA81
3.396
TYR82
2.691
HIS87
3.605
ILE90
3.744
ILE91
4.071
PHE99
3.494
Ligand Name: (1R,9S,12S,13R,14S,17R,18E,21S,23S,24R,25S,27R)-1,14-dihydroxy-12-[(E)-1-[(1R,3R,4R)-4-hydroxy-3-methoxycyclohexyl]prop-1-en-2-yl]-23,25-dimethoxy-13,19,21,27-tetramethyl-17-(2-oxopropyl)-11,28-dioxa-4-azatricyclo[22.3.1.04,9]octacos-18-ene-2,3,10,16-tetrone Ligand Info
Structure Description FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution PDB:6YF2
Method X-ray diffraction Resolution 1.03 Å Mutation No [4]
PDB Sequence
PGVQVETISP
9
GDGRTFPKRG
19
QTCVVHYTGM
29
LEDGKKFDSS
39
RDRNKPFKFM
49

LGKQEVIRGW
59
EEGVAQMSVG
69
QRAKLTISPD
79
YAYGATGHPG
89
IIPPHATLVF
99

DVELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OP5 or .OP52 or .OP53 or :3OP5;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.488
PHE36
3.435
ASP37
2.695
ARG42
3.512
PHE46
3.460
GLN53
4.678
GLU54
2.540
VAL55
3.111
ILE56
2.849
Residue
Distance (Å)
TRP59
3.421
ALA81
3.416
TYR82
2.720
HIS87
3.729
ILE90
4.561
ILE91
3.687
LEU97
4.921
PHE99
3.393
Ligand Name: (1aR,3R,5S,6R,7S,9R,10R,17aS,20S,21R,22S,25R,25aR)-25-Ethyl-10,22-dihydroxy-20-{(1E)-1-[(1R,3R,4R)-4-hydroxy-3-methoxycyclohexyl]prop-1-en-2-yl}-5,7-dimethoxy-1a,3,9,21-tetramethyloctadecahydro-2H-6,10-epoxyoxireno[p]pyrido[2,1-c][1,4]oxazacyclotricosine-11,12,18,24(1aH,14H)-tetrone Ligand Info
Structure Description FKBP12 in complex with the BMP potentiator compound 8 at 1.12A resolution PDB:6YF1
Method X-ray diffraction Resolution 1.12 Å Mutation No [4]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OP8 or .OP82 or .OP83 or :3OP8;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.353
PHE36
3.451
ASP37
2.734
ARG42
3.502
PHE46
3.564
GLU54
3.213
VAL55
3.181
ILE56
2.882
Residue
Distance (Å)
TRP59
3.478
ALA81
2.961
TYR82
2.670
HIS87
4.453
ILE90
4.117
ILE91
3.880
PHE99
3.477
Ligand Name: (1R,9S,12S,14Z,15R,16E,18R,19R,21R,23S,24E,26E,28E,30S,32S,35R)-14-ethoxyimino-1,18-dihydroxy-12-[(2R)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl]-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[30.3.1.04,9]hexatriaconta-16,24,26,28-tetraene-2,3,10,20-tetrone Ligand Info
Structure Description FKBP12 mutant V55G bound to Rapa*-3Z PDB:7U8D
Method X-ray diffraction Resolution 1.39 Å Mutation Yes [9]
PDB Sequence
PGVQVETISP
9
GDGRTFPKRG
19
QTCVVHYTGM
29
LEDGKKFDSS
39
RDRNKPFKFM
49

LGKQEGIRGW
59
EEGVAQMSVG
69
QRAKLTISPD
79
YAYGATGHPG
89
IIPPHATLVF
99

DVELLKLE
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LWR or .LWR2 or .LWR3 or :3LWR;style chemicals stick;color identity;select .A:26 or .A:28 or .A:36 or .A:37 or .A:46 or .A:48 or .A:49 or .A:52 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:60 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
2.773
GLY28
4.493
PHE36
2.341
ASP37
2.262
PHE46
2.370
PHE48
2.818
MET49
4.899
LYS52
4.540
GLN53
2.493
GLU54
2.193
GLY55
2.622
Residue
Distance (Å)
ILE56
2.084
TRP59
2.596
GLU60
4.047
ALA81
3.015
TYR82
1.869
HIS87
3.149
ILE90
2.463
ILE91
2.743
LEU97
4.356
PHE99
2.820
Ligand Name: 3-Phenyl-2-{[4-(toluene-4-sulfonyl)-thiomorpholine-3-carbonyl]-amino}-propionic acid ethyl ester Ligand Info
Structure Description crystal structure analysis of the FKBP12 complexed with 000107 small molecule PDB:1J4H
Method X-ray diffraction Resolution 1.80 Å Mutation No [10]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SUB or .SUB2 or .SUB3 or :3SUB;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.543
PHE36
3.869
ASP37
3.740
PHE46
3.606
GLN53
3.483
GLU54
3.335
VAL55
3.075
ILE56
2.894
Residue
Distance (Å)
TRP59
3.446
TYR82
2.669
HIS87
3.676
ILE90
3.898
ILE91
3.929
LEU97
4.477
PHE99
3.222
Ligand Name: 4-Methyl-2-{[4-(toluene-4-sulfonyl)-thiomorpholine-3-carbonyl]-amino}-pentanoic acid Ligand Info
Structure Description crystal structure analysis of the FKBP12 complexed with 000308 small molecule PDB:1J4I
Method X-ray diffraction Resolution 1.80 Å Mutation No [10]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TST or .TST2 or .TST3 or :3TST;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.390
PHE36
3.538
ASP37
3.886
PHE46
3.676
GLU54
3.334
VAL55
3.049
ILE56
2.766
Residue
Distance (Å)
TRP59
3.251
TYR82
2.660
HIS87
3.540
ILE90
3.704
ILE91
3.877
LEU97
4.548
PHE99
3.396
Ligand Name: C15-(R)-Methylthienyl rapamycin Ligand Info
Structure Description ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP PDB:3FAP
Method X-ray diffraction Resolution 1.85 Å Mutation No [11]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ARD or .ARD2 or .ARD3 or :3ARD;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.607
PHE36
3.612
ASP37
2.773
ARG42
3.367
PHE46
3.515
GLN53
2.567
GLU54
2.803
VAL55
3.214
Residue
Distance (Å)
ILE56
2.918
TRP59
3.411
TYR82
2.477
HIS87
4.042
ILE90
3.884
ILE91
3.816
PHE99
3.825
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: {3-[3-(3,4-Dimethoxy-phenyl)-1-(1-{1-[2-(3,4,5-trimethoxy-phenyl)-butyryl]-piperidin-2yl}-vinyloxy)-propyl]-phenoxy}-acetic acid Ligand Info
Structure Description FKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND PDB:1BL4
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [12]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKVDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AP1 or .AP12 or .AP13 or :3AP1;style chemicals stick;color identity;select .A:26 or .A:28 or .A:36 or .A:37 or .A:42 or .A:46 or .A:47 or .A:48 or .A:53 or .A:54 or .A:55 or .A:56 or .A:57 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.642
GLY28
3.993
VAL36
3.117
ASP37
3.661
ARG42
3.647
PHE46
3.467
LYS47
4.710
PHE48
4.775
GLN53
3.101
GLU54
3.308
VAL55
3.316
Residue
Distance (Å)
ILE56
2.898
ARG57
4.079
TRP59
3.425
ALA81
3.632
TYR82
2.593
HIS87
3.554
ILE90
3.984
ILE91
4.507
LEU97
4.815
PHE99
3.523
Ligand Name: 1-Cyclohexyl-3-phenyl-1-propyl-1-(3,3-dimethyl-1,2-dioxypentyl)-2-piperidine carboxylate Ligand Info
Structure Description DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12 PDB:1FKH
Method X-ray diffraction Resolution 1.95 Å Mutation No [13]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SBX or .SBX2 or .SBX3 or :3SBX;style chemicals stick;color identity;select .A:26 or .A:28 or .A:36 or .A:37 or .A:46 or .A:54 or .A:55 or .A:56 or .A:57 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.519
GLY28
4.961
PHE36
2.984
ASP37
3.518
PHE46
3.862
GLU54
3.607
VAL55
2.981
ILE56
1.990
Residue
Distance (Å)
ARG57
4.580
TRP59
3.341
ALA81
4.669
TYR82
1.841
HIS87
3.631
ILE90
3.829
ILE91
4.746
PHE99
3.601
Ligand Name: 1,3-Diphenyl-1-propyl-1-(3,3-dimethyl-1,2-dioxypentyl)-2-piperidine carboxylate Ligand Info
Structure Description DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12 PDB:1FKG
Method X-ray diffraction Resolution 2.00 Å Mutation No [14]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SB3 or .SB32 or .SB33 or :3SB3;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:46 or .A:54 or .A:55 or .A:56 or .A:57 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.586
PHE36
3.461
ASP37
3.670
PHE46
3.552
GLU54
4.146
VAL55
3.053
ILE56
2.081
ARG57
4.760
Residue
Distance (Å)
TRP59
3.390
ALA81
4.691
TYR82
1.823
HIS87
3.740
ILE90
4.534
ILE91
4.640
PHE99
3.615
Ligand Name: (3S,6R,7E,9R,10R,12R,14S,15E,17E,19E,21S,23S,26R,27R,34aS)-27-hydroxy-3-{(2R)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-9,10,21-trimethoxy-6,8,12,14,20,26-hexamethyl-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-3H-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontine-1,5,11,28,29(4H,6H,31H)-pentone 28-O-Methylrapamycin Ligand Info
Structure Description X-ray Crystal Structure of 28-O-Methylrapamycin complexed with FKBP12: Is the Cyclohexyl Moiety Part of the Effector Domain of Rapamycin? PDB:4DH0
Method X-ray diffraction Resolution 2.10 Å Mutation No [15]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MR8 or .MR82 or .MR83 or :3MR8;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.478
PHE36
3.350
ASP37
2.620
PHE46
3.454
GLN53
3.816
GLU54
3.296
VAL55
3.262
ILE56
2.916
Residue
Distance (Å)
TRP59
3.595
ALA81
3.294
TYR82
2.744
HIS87
3.801
ILE90
4.315
ILE91
4.148
PHE99
3.753
Ligand Name: (21S)-1Aza-4,4-dimethyl-6,19-dioxa-2,3,7,20-tetraoxobicyclo[19.4.0] pentacosane Ligand Info
Structure Description DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12 PDB:1FKI
Method X-ray diffraction Resolution 2.20 Å Mutation No [16]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SB1 or .SB12 or .SB13 or :3SB1;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:87 or .A:90 or .A:91 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
2.716
PHE36
3.739
ASP37
3.428
ARG42
3.316
PHE46
3.539
GLU54
3.473
VAL55
3.221
Residue
Distance (Å)
ILE56
2.056
TRP59
3.496
TYR82
1.824
HIS87
3.950
ILE90
4.100
ILE91
3.872
PHE99
3.582
Ligand Name: C49-Methyl rapamycin Ligand Info
Structure Description THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP PDB:1NSG
Method X-ray diffraction Resolution 2.20 Å Mutation No [11]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RAD or .RAD2 or .RAD3 or :3RAD;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.656
PHE36
3.226
ASP37
2.519
PHE46
3.693
GLN53
1.828
GLU54
1.918
VAL55
3.276
ILE56
2.047
Residue
Distance (Å)
TRP59
3.347
TYR82
1.850
HIS87
4.208
ILE90
3.825
ILE91
3.889
LEU97
4.965
PHE99
3.670
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: C32-O-(1-Ethyl-indol-5-YL)ascomycin Ligand Info
Structure Description FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858 PDB:1QPF
Method X-ray diffraction Resolution 2.50 Å Mutation No [7]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .858 or .8582 or .8583 or :3858;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:90 or .A:91 or .A:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.336
PHE36
3.403
ASP37
2.758
ARG42
3.543
PHE46
3.441
GLU54
3.093
VAL55
3.099
Residue
Distance (Å)
ILE56
2.982
TRP59
3.510
ALA81
3.429
TYR82
2.794
ILE90
4.671
ILE91
3.777
PHE99
3.488
Ligand Name: N'-[(3S,4R,5S,8R,9E,12S,14S,15R,16S,18R,19R,26aS)-5,19-dihydroxy-3-{(1E)-1-[(1R,3R,4R)-4-hydroxy-3-methoxycyclohexyl]prop-1-en-2-yl}-14,16-dimethoxy-4,10,12,18-tetramethyl-1,20,21-trioxo-8-(prop-2-en-1-yl)-1,3,4,5,6,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,26a-docosahydro-7H-15,19-epoxypyrido[2,1-c][1,4]oxazacyclotricosin-7-ylidene]acetohydrazide Ligand Info
Structure Description Homo sapiens FKBP12 protein bound with APX879 in P32 space group PDB:6VCU
Method X-ray diffraction Resolution 1.69 Å Mutation No [17]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGWE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .R27 or .R272 or .R273 or :3R27;style chemicals stick;color identity;select .A:26 or .A:36 or .A:37 or .A:42 or .A:46 or .A:53 or .A:54 or .A:55 or .A:56 or .A:59 or .A:81 or .A:82 or .A:87 or .A:90 or .A:91 or .A:97 or .A:99; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
2.927
PHE36
3.403
ASP37
2.847
ARG42
3.147
PHE46
2.850
GLN53
4.643
GLU54
2.382
VAL55
3.215
ILE56
2.780
Residue
Distance (Å)
TRP59
2.711
ALA81
2.898
TYR82
2.714
HIS87
3.067
ILE90
3.437
ILE91
3.074
LEU97
4.913
PHE99
3.359
References  Top
REF 1 Conformation of Fk506 in X-Ray Structures of its Complexes with Human Recombinant Fkbp12 Mutants
REF 2 Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex
REF 3 Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics. Eur J Biochem. 2000 Sep;267(17):5342-55.
REF 4 Phenotypic screen identifies calcineurin-sparing FK506 analogs as BMP potentiators for treatment of acute kidney injury. Cell Chem Biol. 2021 Sep 16;28(9):1271-1282.e12.
REF 5 2-Aryl-2,2-difluoroacetamide FKBP12 ligands: synthesis and X-ray structural studies. Org Lett. 2001 Dec 13;3(25):3987-90.
REF 6 X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies. J Mol Biol. 2000 Jan 28;295(4):953-62.
REF 7 32-Indolyl ether derivatives of ascomycin: three-dimensional structures of complexes with FK506-binding protein. J Med Chem. 1999 Jul 29;42(15):2798-804.
REF 8 Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface. Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):17195-17203.
REF 9 Tissue-restricted inhibition of mTOR using chemical genetics. Proc Natl Acad Sci U S A. 2022 Sep 20;119(38):e2204083119.
REF 10 Design and structure-based study of new potential FKBP12 inhibitors. Biophys J. 2003 Nov;85(5):3194-201.
REF 11 Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution. Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):736-44.
REF 12 Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity. Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10437-42.
REF 13 DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS AND THE X-RAY CRYSTAL-STRUCTURES OF THEIR COMPLEXES WITH FKBP12.
REF 14 DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS AND THE X-RAY CRYSTAL-STRUCTURES OF THEIR COMPLEXES WITH FKBP12.
REF 15 X-ray Crystal Structure of 28-O-Methylrapamycin complexed with FKBP12: Is the Cyclohexyl Moiety Part of the Effector Domain of Rapamycin?. doi:10.1021/ja954328h.
REF 16 DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS AND THE X-RAY CRYSTAL-STRUCTURES OF THEIR COMPLEXES WITH FKBP12.
REF 17 Designing Selective and Non-Immunosuppressive Antifungal FK506 Analogs: Structures, Biophysics and Dynamics of Fungal and Human Calcineurin-Inhibitor Complexes. doi:10.1101/2020.04.14.039800.

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