Structure of PDB 4ehm Chain B Binding Site BS01

Receptor Information
>4ehm Chain B (length=325) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKDVTIKSDAPDTLLLEKHADYIASYGSDDYEYCMSEYLRMSGVYWGLTV
MDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILT
LYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALL
GKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQ
LHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLH
WIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQI
KPVSPVFCMPEEVLQRVNVQPELVS
Ligand information
Ligand IDPJA
InChIInChI=1S/C18H14O8/c1-7-4-11(20)10(6-19)15-13(7)18(23)26-14-8(2)12(24-3)5-9(17(21)22)16(14)25-15/h4-6,20H,1-3H3,(H,21,22)
InChIKeyFUCWJKJZOHOLEO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c1c2Oc3c(C(=O)Oc2c(c(OC)c1)C)c(cc(O)c3C=O)C
CACTVS 3.370COc1cc(C(O)=O)c2Oc3c(C=O)c(O)cc(C)c3C(=O)Oc2c1C
OpenEye OEToolkits 1.7.6Cc1cc(c(c2c1C(=O)Oc3c(c(cc(c3O2)C(=O)O)OC)C)C=O)O
FormulaC18 H14 O8
Name4-formyl-3-hydroxy-8-methoxy-1,9-dimethyl-11-oxo-11H-dibenzo[b,e][1,4]dioxepine-6-carboxylic acid;
Psoromic acid
ChEMBLCHEMBL176570
DrugBank
ZINCZINC000001598047
PDB chain4ehm Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ehm Psoromic Acid is a Selective and Covalent Rab-Prenylation Inhibitor Targeting Autoinhibited RabGGTase
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R144 G192 Q193 W244 F289
Binding residue
(residue number reindexed from 1)		R138 G186 Q187 W238 F283
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.85,IC50=1.4uM
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) H184 R226 K229 D232 C234 Y235 D274 D281 H284
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:4ehm, PDBe:4ehm, PDBj:4ehm
PDBsum4ehm
PubMed22480322
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

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