Structure of PDB 4gtv Chain B Binding Site BS03

Receptor Information
>4gtv 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 ID7TR
InChIInChI=1S/C34H38N6O5S/c1-5-38(6-2)34(41)45-31-10-7-25(8-11-31)18-28-22-39(23-29-20-36-24-37(29)3)33-16-9-26(19-35)17-27(33)21-40(28)46(42,43)32-14-12-30(44-4)13-15-32/h7-17,20,24,28H,5-6,18,21-23H2,1-4H3/t28-/m1/s1
InChIKeyIQZAPWUUBMPSLO-MUUNZHRXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCN(CC)C(=O)Oc1ccc(cc1)C[C@@H]2CN(c3ccc(cc3CN2S(=O)(=O)c4ccc(cc4)OC)C#N)Cc5cncn5C
CACTVS 3.370CCN(CC)C(=O)Oc1ccc(C[CH]2CN(Cc3cncn3C)c4ccc(cc4CN2[S](=O)(=O)c5ccc(OC)cc5)C#N)cc1
ACDLabs 12.01O=C(Oc1ccc(cc1)CC2N(Cc4cc(C#N)ccc4N(C2)Cc3cncn3C)S(=O)(=O)c5ccc(OC)cc5)N(CC)CC
OpenEye OEToolkits 1.7.6CCN(CC)C(=O)Oc1ccc(cc1)CC2CN(c3ccc(cc3CN2S(=O)(=O)c4ccc(cc4)OC)C#N)Cc5cncn5C
CACTVS 3.370CCN(CC)C(=O)Oc1ccc(C[C@@H]2CN(Cc3cncn3C)c4ccc(cc4CN2[S](=O)(=O)c5ccc(OC)cc5)C#N)cc1
FormulaC34 H38 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 diethylcarbamate
ChEMBLCHEMBL2171688
DrugBank
ZINCZINC000095555667
PDB chain4gtv 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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PDB4gtv Development of Selective, Potent RabGGTase Inhibitors
Resolution1.95 Å
Binding residue
(original residue number in PDB)		Y44 L45 C196 D238 W244 F289 H290
Binding residue
(residue number reindexed from 1)		Y37 L38 C189 D231 W237 F282 H283
Annotation score1
Binding affinityMOAD: ic50=38nM
PDBbind-CN: -logKd/Ki=7.42,IC50=38nM
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:4gtv, PDBe:4gtv, PDBj:4gtv
PDBsum4gtv
PubMed22963166
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

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