Structure of PDB 3hxb Chain B Binding Site BS01

Receptor Information
>3hxb 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 IDBD5
InChIInChI=1S/C35H35N3O8/c39-27-15-11-24(12-16-27)20-30(38-35(45)46-22-26-9-5-2-6-10-26)33(42)36-29(19-23-7-3-1-4-8-23)32(41)37-31(34(43)44)21-25-13-17-28(40)18-14-25/h1-18,29-31,39-40H,19-22H2,(H,36,42)(H,37,41)(H,38,45)(H,43,44)/t29-,30+,31-/m0/s1
InChIKeyNYJFXELTSYMIOY-YPKYBTACSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)C[C@@H](C(=O)N[C@@H](Cc2ccc(cc2)O)C(=O)O)NC(=O)[C@@H](Cc3ccc(cc3)O)NC(=O)OCc4ccccc4
CACTVS 3.341OC(=O)[CH](Cc1ccc(O)cc1)NC(=O)[CH](Cc2ccccc2)NC(=O)[CH](Cc3ccc(O)cc3)NC(=O)OCc4ccccc4
ACDLabs 10.04O=C(OCc1ccccc1)NC(C(=O)NC(C(=O)NC(C(=O)O)Cc2ccc(O)cc2)Cc3ccccc3)Cc4ccc(O)cc4
CACTVS 3.341OC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](Cc3ccc(O)cc3)NC(=O)OCc4ccccc4
OpenEye OEToolkits 1.5.0c1ccc(cc1)CC(C(=O)NC(Cc2ccc(cc2)O)C(=O)O)NC(=O)C(Cc3ccc(cc3)O)NC(=O)OCc4ccccc4
FormulaC35 H35 N3 O8
NameN-[(benzyloxy)carbonyl]-D-tyrosyl-L-phenylalanyl-L-tyrosine
ChEMBL
DrugBank
ZINCZINC000058631348
PDB chain3hxb Chain B Residue 332 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3hxb Design, synthesis, and characterization of Peptide-based rab geranylgeranyl transferase inhibitors
Resolution2.25 Å
Binding residue
(original residue number in PDB)		S48 L96 R144 F147 G192 Q193 Y195 W244
Binding residue
(residue number reindexed from 1)		S41 L89 R137 F140 G185 Q186 Y188 W237
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.39,IC50=4.1uM
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:3hxb, PDBe:3hxb, PDBj:3hxb
PDBsum3hxb
PubMed19894725
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

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