Structure of PDB 4gtt Chain B Binding Site BS03

Receptor Information
>4gtt Chain B (length=324) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKDVTIKSDAPDTLLLEKHADYIASYGSDYEYCMSEYLRMSGVYWGLTVM
DLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTL
YDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLG
KLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQL
HQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHW
IDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIK
PVSPVFCMPEEVLQRVNVQPELVS
Ligand information
Ligand ID7TQ
InChIInChI=1S/C37H36N6O5S/c1-41-26-39-22-32(41)25-42-24-31(19-27-8-11-34(12-9-27)48-37(44)40-21-28-6-4-3-5-7-28)43(23-30-18-29(20-38)10-17-36(30)42)49(45,46)35-15-13-33(47-2)14-16-35/h3-18,22,26,31H,19,21,23-25H2,1-2H3,(H,40,44)/t31-/m1/s1
InChIKeyISPKWTLKQCPKQN-WJOKGBTCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Oc1ccc(cc1)CC2N(Cc4cc(C#N)ccc4N(C2)Cc3cncn3C)S(=O)(=O)c5ccc(OC)cc5)NCc6ccccc6
OpenEye OEToolkits 1.7.6Cn1cncc1CN2C[C@H](N(Cc3c2ccc(c3)C#N)S(=O)(=O)c4ccc(cc4)OC)Cc5ccc(cc5)OC(=O)NCc6ccccc6
OpenEye OEToolkits 1.7.6Cn1cncc1CN2CC(N(Cc3c2ccc(c3)C#N)S(=O)(=O)c4ccc(cc4)OC)Cc5ccc(cc5)OC(=O)NCc6ccccc6
CACTVS 3.370COc1ccc(cc1)[S](=O)(=O)N2Cc3cc(ccc3N(C[C@H]2Cc4ccc(OC(=O)NCc5ccccc5)cc4)Cc6cncn6C)C#N
CACTVS 3.370COc1ccc(cc1)[S](=O)(=O)N2Cc3cc(ccc3N(C[CH]2Cc4ccc(OC(=O)NCc5ccccc5)cc4)Cc6cncn6C)C#N
FormulaC37 H36 N6 O5 S
Name4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl benzylcarbamate
ChEMBLCHEMBL2171687
DrugBank
ZINCZINC000095555128
PDB chain4gtt Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4gtt Development of Selective, Potent RabGGTase Inhibitors
Resolution2.05 Å
Binding residue
(original residue number in PDB)		Y44 L96 Q103 F147 Y195 D287 F289
Binding residue
(residue number reindexed from 1)		Y37 L89 Q96 F140 Y188 D280 F282
Annotation score1
Binding affinityMOAD: ic50=6nM
PDBbind-CN: -logKd/Ki=8.22,IC50=6nM
Enzymatic activity
Catalytic site (original residue number in PDB) H190 R232 K235 D238 C240 Y241 D280 D287 H290
Catalytic site (residue number reindexed from 1) H183 R225 K228 D231 C233 Y234 D273 D280 H283
Enzyme Commision number 2.5.1.60: protein geranylgeranyltransferase type II.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004659 prenyltransferase activity
GO:0004661 protein geranylgeranyltransferase activity
GO:0004663 Rab geranylgeranyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008318 protein prenyltransferase activity
GO:0019840 isoprenoid binding
GO:0031267 small GTPase binding
GO:0046872 metal ion binding
Biological Process
GO:0018344 protein geranylgeranylation
Cellular Component
GO:0005968 Rab-protein geranylgeranyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4gtt, PDBe:4gtt, PDBj:4gtt
PDBsum4gtt
PubMed22963166
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

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