Structure of PDB 3cd0 Chain D Binding Site BS01

Receptor Information
>3cd0 Chain D (length=396) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAKFLSDAEIIQLVNAKHLIETHERGVSIRRQLLSKKLSEPSSLQYLPYR
DYNYSLVMGACCENVIGYMPIPVGVAGPLCLDEKEFQVPMATTEGCLVAS
TNRGCRAIGLGGGASSRVLADGMTRGPVVRLPRACDSAEVKAWLETSEGF
AVIKEAFDSTSRFARLQKLHTSIAGRNLYIRFQSRSGDAMGMNMISKGTE
KALSKLHEYFPEMQILAVSGNYCTDKKPAAINWIEGRGKSVVCEAVIPAK
VVREVLKTTTEAMIEVNINKNLVGSAMAGSIGGYNAHAANIVTAIYIACG
QDAAQNVGSSNCITLMEASGPTNEDLYISCTMPSIEIGTVGGGTNLLPQQ
ACLQMLGVQGACKDNPGENARQLARIVCGTVMAGELSLMAALAAGH
Ligand information
Ligand ID6HI
InChIInChI=1S/C27H31F2N3O5/c1-16(2)32-23(12-11-21(33)13-22(34)14-24(35)36)25(18-5-9-20(29)10-6-18)31-26(32)27(37)30-15-17-3-7-19(28)8-4-17/h3-10,16,21-22,33-34H,11-15H2,1-2H3,(H,30,37)(H,35,36)/t21-,22-/m1/s1
InChIKeyKNKKPGAQSAHIHV-FGZHOGPDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)n1c(c(nc1C(=O)NCc2ccc(cc2)F)c3ccc(cc3)F)CCC(CC(CC(=O)O)O)O
CACTVS 3.341CC(C)n1c(CC[C@@H](O)C[C@@H](O)CC(O)=O)c(nc1C(=O)NCc2ccc(F)cc2)c3ccc(F)cc3
OpenEye OEToolkits 1.5.0CC(C)n1c(c(nc1C(=O)NCc2ccc(cc2)F)c3ccc(cc3)F)CC[C@H](C[C@H](CC(=O)O)O)O
CACTVS 3.341CC(C)n1c(CC[CH](O)C[CH](O)CC(O)=O)c(nc1C(=O)NCc2ccc(F)cc2)c3ccc(F)cc3
ACDLabs 10.04O=C(NCc1ccc(F)cc1)c2nc(c(n2C(C)C)CCC(O)CC(O)CC(=O)O)c3ccc(F)cc3
FormulaC27 H31 F2 N3 O5
Name(3R,5R)-7-{2-[(4-fluorobenzyl)carbamoyl]-4-(4-fluorophenyl)-1-(1-methylethyl)-1H-imidazol-5-yl}-3,5-dihydroxyheptanoic acid
ChEMBL
DrugBank
ZINCZINC000011687461
PDB chain3cd0 Chain C Residue 4 [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]
PDB3cd0 Thermodynamic and structure guided design of statin based inhibitors of 3-hydroxy-3-methylglutaryl coenzyme a reductase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		E559 C561 L562 S565 R568 K735 A751 L853
Binding residue
(residue number reindexed from 1)		E94 C96 L97 S100 R103 K270 A286 L388
Annotation score1
Binding affinityMOAD: Kd=26.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) E559 K691 D767
Catalytic site (residue number reindexed from 1) E94 K226 D302
Enzyme Commision number 1.1.1.34: hydroxymethylglutaryl-CoA reductase (NADPH).
Gene Ontology
Molecular Function
GO:0004420 hydroxymethylglutaryl-CoA reductase (NADPH) activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0050661 NADP binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0015936 coenzyme A metabolic process
Cellular Component
GO:0005789 endoplasmic reticulum membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3cd0, PDBe:3cd0, PDBj:3cd0
PDBsum3cd0
PubMed18540668
UniProtP04035|HMDH_HUMAN 3-hydroxy-3-methylglutaryl-coenzyme A reductase (Gene Name=HMGCR)

[Back to BioLiP]