Structure of PDB 3hxd Chain B Binding Site BS03

Receptor Information
>3hxd 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 IDBD7
InChIInChI=1S/C33H36N6O7/c1-39(32(43)28(18-25-19-34-21-35-25)37-33(44)46-20-24-10-6-3-7-11-24)29(17-22-8-4-2-5-9-22)31(42)36-27(30(41)38-45)16-23-12-14-26(40)15-13-23/h2-15,19,21,27-29,40,45H,16-18,20H2,1H3,(H,34,35)(H,36,42)(H,37,44)(H,38,41)/t27-,28-,29-/m0/s1
InChIKeySEPJJYNYJOZSET-AWCRTANDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN([C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(cc2)O)C(=O)NO)C(=O)[C@H](Cc3cnc[nH]3)NC(=O)OCc4ccccc4
CACTVS 3.341CN([CH](Cc1ccccc1)C(=O)N[CH](Cc2ccc(O)cc2)C(=O)NO)C(=O)[CH](Cc3[nH]cnc3)NC(=O)OCc4ccccc4
ACDLabs 10.04O=C(NO)C(NC(=O)C(N(C(=O)C(NC(=O)OCc1ccccc1)Cc2cncn2)C)Cc3ccccc3)Cc4ccc(O)cc4
CACTVS 3.341CN([C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(O)cc2)C(=O)NO)C(=O)[C@H](Cc3[nH]cnc3)NC(=O)OCc4ccccc4
OpenEye OEToolkits 1.5.0CN(C(Cc1ccccc1)C(=O)NC(Cc2ccc(cc2)O)C(=O)NO)C(=O)C(Cc3cnc[nH]3)NC(=O)OCc4ccccc4
FormulaC33 H36 N6 O7
NameN-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-N-hydroxy-L-tyrosinamide
ChEMBLCHEMBL1075800
DrugBank
ZINCZINC000049863840
PDB chain3hxd Chain B Residue 334 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3hxd Design, synthesis, and characterization of Peptide-based rab geranylgeranyl transferase inhibitors
Resolution1.95 Å
Binding residue
(original residue number in PDB)		W52 L96 R144 C148 G192 Q193 C196 D238 C240 W244 F289
Binding residue
(residue number reindexed from 1)		W45 L89 R137 C141 G185 Q186 C189 D231 C233 W237 F282
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.05,IC50=9uM
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:3hxd, PDBe:3hxd, PDBj:3hxd
PDBsum3hxd
PubMed19894725
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

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