Structure of PDB 3hxf Chain B Binding Site BS03

Receptor Information
>3hxf Chain B (length=322) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKDVTIKSDAPDTLLLEKHADYIASYGSYEYCMSEYLRMSGVYWGLTVMD
LMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLY
DSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGK
LDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLH
QVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWI
DREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKP
VSPVFCMPEEVLQRVNVQPELV
Ligand information
Ligand IDBD9
InChIInChI=1S/C40H55N9O5/c1-3-4-5-6-7-8-9-10-14-37(51)46-34(23-31-25-41-27-44-31)38(52)47-35(24-32-26-42-28-45-32)39(53)48-36(22-29-15-17-33(50)18-16-29)40(54)49(2)21-19-30-13-11-12-20-43-30/h11-13,15-18,20,25-28,34-36,50H,3-10,14,19,21-24H2,1-2H3,(H,41,44)(H,42,45)(H,46,51)(H,47,52)(H,48,53)/t34-,35-,36-/m0/s1
InChIKeyXTWPUBVVNIJMOQ-KVBYWJEESA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCC(=O)N[CH](Cc1[nH]cnc1)C(=O)N[CH](Cc2c[nH]cn2)C(=O)N[CH](Cc3ccc(O)cc3)C(=O)N(C)CCc4ccccn4
OpenEye OEToolkits 1.5.0CCCCCCCCCCC(=O)NC(Cc1cnc[nH]1)C(=O)NC(Cc2c[nH]cn2)C(=O)NC(Cc3ccc(cc3)O)C(=O)N(C)CCc4ccccn4
CACTVS 3.341CCCCCCCCCCC(=O)N[C@@H](Cc1[nH]cnc1)C(=O)N[C@@H](Cc2c[nH]cn2)C(=O)N[C@@H](Cc3ccc(O)cc3)C(=O)N(C)CCc4ccccn4
OpenEye OEToolkits 1.5.0CCCCCCCCCCC(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H](Cc2c[nH]cn2)C(=O)N[C@@H](Cc3ccc(cc3)O)C(=O)N(C)CCc4ccccn4
ACDLabs 10.04O=C(N(CCc1ncccc1)C)C(NC(=O)C(NC(=O)C(NC(=O)CCCCCCCCCC)Cc2cncn2)Cc3ncnc3)Cc4ccc(O)cc4
FormulaC40 H55 N9 O5
NameN-undecanoyl-L-histidyl-L-histidyl-N-methyl-N-(2-pyridin-2-ylethyl)-L-tyrosinamide
ChEMBLCHEMBL1075863
DrugBank
ZINCZINC000049778098
PDB chain3hxf Chain B Residue 334 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3hxf Design, synthesis, and characterization of Peptide-based rab geranylgeranyl transferase inhibitors
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y44 L45 S48 Y51 W52 Y97 F147 G192 C240 Y241 W244 F289 H290 F293
Binding residue
(residue number reindexed from 1)		Y36 L37 S40 Y43 W44 Y89 F139 G184 C232 Y233 W236 F281 H282 F285
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.96,IC50=11uM
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) H182 R224 K227 D230 C232 Y233 D272 D279 H282
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:3hxf, PDBe:3hxf, PDBj:3hxf
PDBsum3hxf
PubMed19894725
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

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