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 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
Ligand General Information  Top
Ligand Name Sirolimus Ligand Info
Canonical SMILES CC1CCC2CC(C(=CC=CC=CC(CC(C(=O)C(C(C(=CC(C(=O)CC(OC(=O)C3CCCCN3C(=O)C(=O)C1(O2)O)C(C)CC4CCC(C(C4)OC)O)C)C)O)OC)C)C)C)OC
InChI 1S/C51H79NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-40,42-44,46-47,53,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11+,16-12+,31-17+,35-25+/t30-,32-,33-,34-,36-,37+,38+,39+,40-,42+,43+,44-,46-,47+,51-/m1/s1
InChIKey QFJCIRLUMZQUOT-HPLJOQBZSA-N
PubChem Compound ID 5284616
Drug Binding Sites of Target  Top
PDB ID: 1FKB      ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-12 COMPLEX
Method X-ray diffraction Resolution 1.70 Å Mutation No [1]
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
PDB ID: 2DG3      Wildtype FK506-binding protein complexed with Rapamycin
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
3.475
PHE36
3.384
ASP37
2.613
PHE46
3.401
GLN53
2.636
GLU54
2.672
VAL55
3.250
ILE56
2.933
Residue
Distance (Å)
TRP59
3.453
TYR82
2.664
HIS87
3.643
ILE90
3.996
ILE91
4.024
LEU97
4.779
PHE99
3.582
PDB ID: 2DG4      FK506-binding protein mutant WF59 complexed with Rapamycin
Method X-ray diffraction Resolution 1.70 Å Mutation Yes [2]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGFE
60
EGVAQMSVGQ
70
RAKLTISPDY
80
AYGATGHPGI
90
IPPHATLVFD
100

VELLKLE
Residue
Distance (Å)
TYR26
3.372
PHE36
3.281
ASP37
2.624
PHE46
3.365
GLN53
2.678
GLU54
2.770
VAL55
3.227
ILE56
2.896
Residue
Distance (Å)
PHE59
3.561
TYR82
2.628
HIS87
3.560
ILE90
3.942
ILE91
4.313
LEU97
4.983
PHE99
3.701
PDB ID: 2DG9      FK506-binding protein mutant WL59 complexed with Rapamycin
Method X-ray diffraction Resolution 1.70 Å Mutation Yes [2]
PDB Sequence
GVQVETISPG
10
DGRTFPKRGQ
20
TCVVHYTGML
30
EDGKKFDSSR
40
DRNKPFKFML
50

GKQEVIRGLE
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 .RAP or .RAP2 or .RAP3 or :3RAP;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:99; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.343
PHE36
3.338
ASP37
2.686
PHE46
3.395
GLN53
2.821
GLU54
2.704
VAL55
3.235
Residue
Distance (Å)
ILE56
2.888
LEU59
3.557
TYR82
2.672
HIS87
3.668
ILE90
3.944
ILE91
4.193
PHE99
3.636
PDB ID: 1FAP      THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP
Method X-ray diffraction Resolution 2.70 Å 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 .RAP or .RAP2 or .RAP3 or :3RAP;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
3.735
PHE36
2.986
ASP37
2.764
ARG42
4.653
PHE46
3.424
GLN53
2.622
GLU54
2.180
VAL55
3.071
Residue
Distance (Å)
ILE56
1.896
TRP59
3.408
TYR82
1.767
HIS87
4.092
ILE90
3.577
ILE91
3.718
PHE99
3.618
PDB ID: 6M4U      Crystal structure of FKBP-FRB T2098L mutant in complex with rapamycin
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [4]
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 .RAP or .RAP2 or .RAP3 or :3RAP;style chemicals stick;color identity;select .A:27 or .A:37 or .A:38 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:100; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR27
3.379
PHE37
3.542
ASP38
2.732
PHE47
3.529
GLN54
2.781
GLU55
2.649
VAL56
3.179
Residue
Distance (Å)
ILE57
2.863
TRP60
3.385
TYR83
2.504
HIS88
4.589
ILE91
3.720
ILE92
3.797
PHE100
3.590
PDB ID: 6M4W      Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin
Method X-ray diffraction Resolution 3.11 Å Mutation Yes [4]
PDB Sequence
GKKFDSSRDR
43
NKPFKFMLGK
53
QEVIRGWEEG
63
VAQMSVGQRA
73
KLTISPDYAY
83

GATGHPGIIP
93
PHATLVFDVE
103
LLKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RAP or .RAP2 or .RAP3 or :3RAP;style chemicals stick;color identity;select .D:37 or .D:38 or .D:43 or .D:47 or .D:54 or .D:55 or .D:56 or .D:57 or .D:60 or .D:83 or .D:88 or .D:91 or .D:92 or .D:100; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE37
3.763
ASP38
2.696
ARG43
4.016
PHE47
3.667
GLN54
2.749
GLU55
2.760
VAL56
3.278
Residue
Distance (Å)
ILE57
3.085
TRP60
3.471
TYR83
2.330
HIS88
4.775
ILE91
3.783
ILE92
3.802
PHE100
3.825
References  Top
REF 1 Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex
REF 2 Energetic and structural analysis of the role of tryptophan 59 in FKBP12. Biochemistry. 2003 Mar 4;42(8):2364-72.
REF 3 Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP. Science. 1996 Jul 12;273(5272):239-42.
REF 4 Rational design and implementation of a chemically inducible heterotrimerization system. Nat Methods. 2020 Sep;17(9):928-936.

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