Structure of PDB 3c72 Chain B Binding Site BS03

Receptor Information
>3c72 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]
DVTIKSDAPDTLLLEKHADYIASYGSKDDYEYCMSEYLRMSGVYWGLTVM
DLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTL
YDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLG
KLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQL
HQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHW
IDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIK
PVSPVFCMPEEVLQRVNVQPELVS
Ligand information
Ligand IDCX1
InChIInChI=1S/C33H35N5O7/c1-38(31(41)27(18-25-19-34-21-35-25)37-33(44)45-20-24-10-6-3-7-11-24)29(17-22-8-4-2-5-9-22)30(40)36-28(32(42)43)16-23-12-14-26(39)15-13-23/h2-15,19,21,27-29,39H,16-18,20H2,1H3,(H,34,35)(H,36,40)(H,37,44)(H,42,43)/t27-,28-,29-/m0/s1
InChIKeyCPZRYRVSOCXUSE-AWCRTANDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN(C(Cc1ccccc1)C(=O)NC(Cc2ccc(cc2)O)C(=O)O)C(=O)C(Cc3c[nH]cn3)NC(=O)OCc4ccccc4
OpenEye OEToolkits 1.5.0CN([C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(cc2)O)C(=O)O)C(=O)[C@H](Cc3c[nH]cn3)NC(=O)OCc4ccccc4
CACTVS 3.341CN([CH](Cc1ccccc1)C(=O)N[CH](Cc2ccc(O)cc2)C(O)=O)C(=O)[CH](Cc3c[nH]cn3)NC(=O)OCc4ccccc4
CACTVS 3.341CN([C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(O)cc2)C(O)=O)C(=O)[C@H](Cc3c[nH]cn3)NC(=O)OCc4ccccc4
ACDLabs 10.04O=C(O)C(NC(=O)C(N(C(=O)C(NC(=O)OCc1ccccc1)Cc2ncnc2)C)Cc3ccccc3)Cc4ccc(O)cc4
FormulaC33 H35 N5 O7
NameN-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-L-tyrosine
ChEMBL
DrugBank
ZINCZINC000058632219
PDB chain3c72 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3c72 Development of selective RabGGTase inhibitors and crystal structure of a RabGGTase-inhibitor complex.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R144 H190 G192 Q193 Y195 C196 Y241 W244
Binding residue
(residue number reindexed from 1)		R137 H183 G185 Q186 Y188 C189 Y234 W237
Annotation score1
Binding affinityMOAD: ic50=22.7uM
PDBbind-CN: -logKd/Ki=4.64,IC50=22.7uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3c72, PDBe:3c72, PDBj:3c72
PDBsum3c72
PubMed18399557
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

[Back to BioLiP]