Structure of PDB 1xpm Chain D Binding Site BS01

Receptor Information

>1xpm Chain D (length=389)

AIGIDKINFYVPKYYVDMAKLAEARQVDPNKFLIGIGQTEMAVSPVNQDI
VSMGANAAKDIITDEDKKKIGMVIVATESAVDAAKAAAVQIHNLLGIQPF
ARCFEMKEACYAATPAIQLAKDYLATRPNEKVLVIATDTARYGLNSGGEP
TQGAGAVAMVIAHNPSILALNEDAVAYTEDVYDFWRPTGHKYPLVDGALS
KDAYIRSFQQSWNEYAKRQGKSLADFASLCFHVPFTKMGKKALESIIDNA
DETTQERLRSGYEDAVDYNRYVGNIYTGSLYLSLISLLENRDLQAGETIG
LFSYGSGSVGEFYSATLVEGYKDHLDQAAHKALLNNRTEVSVDAYETFFK
RFDDVEFDEEQDAVHEDRHIFYLSNIENNVREYHRPELE

Ligand information

• Ligand ID: HMG
• InChI: InChI=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
• InChIKey: CABVTRNMFUVUDM-VRHQGPGLSA-I
• SMILES:
  OpenEye OEToolkits 1.7.5: C[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 3.385: C[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 3.385: C[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 1.7.5: CC(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
• Formula: C27 H39 N7 O20 P3 S
• Name: 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A;
  (S)-HMG-COA
• DrugBank: DB03169
• PDB chain: 1xpm Chain D Residue 4401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1xpm 3-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time"
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): D29 N31 K32 G36 E79 A110 C111 G148 F185 S201 H233 P235 F236 S307
• Binding residue (residue number reindexed from 1): D28 N30 K31 G35 E78 A109 C110 G147 F184 S200 H232 P234 F235 S306
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.3.3.10: hydroxymethylglutaryl-CoA synthase.

Gene Ontology

Molecular Function

• GO:0004421 hydroxymethylglutaryl-CoA synthase activity
• GO:0016746 acyltransferase activity

Biological Process

• GO:0006084 acetyl-CoA metabolic process
• GO:0010142 farnesyl diphosphate biosynthetic process, mevalonate pathway

External links

• PDB: RCSB:1xpm, PDBe:1xpm, PDBj:1xpm
• PDBsum: 1xpm
• PubMed: 15498869
• UniProt: A0A0H3K1U2