Structure of PDB 2wya Chain A Binding Site BS01

Receptor Information
>2wya Chain A (length=460) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMPKDVGILALEVYFPAQYVDQTDLEKYNNVEAGKYTVGLGQTRMGFCSV
QEDINSLCLTVVQRLMERIQLPWDSVGRLEVGTETIIDKSKAVKTVLMEL
FQDSGNTDIEGIDTTNACYGGTASLFNAANWMESSSWDGRYAMVVCGDIA
VYPSGNARPTGGAGAVAMLIGPKAPLALERGLRGTHMENVYDFYKPNLAS
EYPIVDGKLSIQCYLRALDRCYTSYRKKIQNQWKQAGSDRPFTLDDLQYM
IFHTPFCKMVQKSLARLMFNDFLSASSDTQTSLYKGLEAFGGLKLEDTYT
NKDLDKALLKASQDMFDKKTKASLYLSTHNGNMYTSSLYGCLASLLSHHS
AQELAGSRIGAFSYGSGLAASFFSFRVSQDAAPGSPLDKLVSSTSDLPKR
LASRKCVSPEEFTEIMNQREQFYHKVNFSPPGDTNSLFPGTWYLERVDEQ
HRRKYARRPV
Ligand information
Ligand IDHMG
InChIInChI=1S/C27H44N7O20P3S/c1-26(2,21(40)24(41)30-5-4-15(35)29-6-7-58-17(38)9-27(3,42)8-16(36)37)11-51-57(48,49)54-56(46,47)50-10-14-20(53-55(43,44)45)19(39)25(52-14)34-13-33-18-22(28)31-12-32-23(18)34/h12-14,19-21,25,39-40,42H,4-11H2,1-3H3,(H,29,35)(H,30,41)(H,36,37)(H,46,47)(H,48,49)(H2,28,31,32)(H2,43,44,45)/p-5/t14-,19-,20-,21+,25-,27+/m1/s1
InChIKeyCABVTRNMFUVUDM-VRHQGPGLSA-I
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5C[C@](CC(=O)[O-])(CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])O)O
CACTVS 3.385C[C@](O)(CC([O-])=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P]([O-])([O-])=O)n2cnc3c(N)ncnc23
CACTVS 3.385C[C](O)(CC([O-])=O)CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P]([O-])(=O)O[P]([O-])(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P]([O-])([O-])=O)n2cnc3c(N)ncnc23
ACDLabs 12.01[O-]C(=O)CC(O)(C)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP([O-])(=O)OP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP([O-])([O-])=O
OpenEye OEToolkits 1.7.5CC(C)(COP(=O)([O-])OP(=O)([O-])OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])C(C(=O)NCCC(=O)NCCSC(=O)CC(C)(CC(=O)[O-])O)O
FormulaC27 H39 N7 O20 P3 S
Name3-HYDROXY-3-METHYLGLUTARYL-COENZYME A;
(S)-HMG-COA
ChEMBL
DrugBankDB03169
ZINC
PDB chain2wya Chain A Residue 1509 [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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PDB2wya Crystal Structures of Human Hmg-Coa Synthase Isoforms Provide Insights Into Inherited Ketogenesis Disorders and Inhibitor Design.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		E80 G82 K83 V86 G87 E132 A165 C166 Y200 N204 A205 T208 F241 G255 S258 H301 P303 F304 K310 Y412 G413 S414
Binding residue
(residue number reindexed from 1)		E32 G34 K35 V38 G39 E84 A117 C118 Y152 N156 A157 T160 F193 G207 S210 H253 P255 F256 K262 Y364 G365 S366
Annotation score5
Enzymatic activity
Enzyme Commision number 2.3.3.10: hydroxymethylglutaryl-CoA synthase.
Gene Ontology
Molecular Function
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0042802 identical protein binding
Biological Process
GO:0001822 kidney development
GO:0001889 liver development
GO:0006084 acetyl-CoA metabolic process
GO:0006695 cholesterol biosynthetic process
GO:0007494 midgut development
GO:0007584 response to nutrient
GO:0008299 isoprenoid biosynthetic process
GO:0009266 response to temperature stimulus
GO:0009410 response to xenobiotic stimulus
GO:0009617 response to bacterium
GO:0010038 response to metal ion
GO:0010142 farnesyl diphosphate biosynthetic process, mevalonate pathway
GO:0014070 response to organic cyclic compound
GO:0030324 lung development
GO:0032868 response to insulin
GO:0032869 cellular response to insulin stimulus
GO:0032870 cellular response to hormone stimulus
GO:0033555 multicellular organismal response to stress
GO:0033574 response to testosterone
GO:0033762 response to glucagon
GO:0034014 response to triglyceride
GO:0034284 response to monosaccharide
GO:0034696 response to prostaglandin F
GO:0042594 response to starvation
GO:0043434 response to peptide hormone
GO:0045471 response to ethanol
GO:0046951 ketone body biosynthetic process
GO:0051384 response to glucocorticoid
GO:0051591 response to cAMP
GO:0060416 response to growth hormone
GO:0060612 adipose tissue development
GO:0070542 response to fatty acid
GO:0070543 response to linoleic acid
GO:0071222 cellular response to lipopolysaccharide
GO:0071230 cellular response to amino acid stimulus
GO:0071385 cellular response to glucocorticoid stimulus
GO:0071398 cellular response to fatty acid
GO:0071407 cellular response to organic cyclic compound
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2wya, PDBe:2wya, PDBj:2wya
PDBsum2wya
PubMed20346956
UniProtP54868|HMCS2_HUMAN Hydroxymethylglutaryl-CoA synthase, mitochondrial (Gene Name=HMGCS2)

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