Structure of PDB 3day Chain A Binding Site BS02

Receptor Information
>3day Chain A (length=535) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQWGHQEVPAKFNFASDVLDHWADMEKAGKRPPSPALWWVNGKGKELMWN
FRELSENSQQAANVLSGACGLQRGDRVAVVLPRVPEWWLVILGCIRAGLI
FMPGTIQMKSTDILYRLQMSKAKAIVAGDEVIQEVDTVASECPSLRIKLL
VSEKSCDGWLNFKKLLNEASTTHHCVETGSQEASAIYFTSGTSGLPKMAE
HSYSSLGLKAKMDAGWTGLQASDIMWTISDTGWILNILCSLMEPWALGAC
TFVHLLPKFDPLVILKTLSSYPIKSMMGAPIVYRMLLQQDLSSYKFPHLQ
NCVTVGESLLPETLENWRAQTGLDIRESYGQTETGLTCMVSKTMKIKPGY
MGTAASCYDVQIIDDKGNVLPPGTEGDIGIRVKPIRPIGIFSGYVDNPDK
TAANIRGDFWLLGDRGIKDEDGYFQFMGRADDIINSSGYRIGPSEVENAL
MEHPAVVETAVISSPDRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSV
TAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWK
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain3day Chain A Residue 606 [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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PDB3day Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		T221 S222 G223 T224 S225 K229 G338 E339 S340 Y361 G362 Q363 T364 D446 F458 R461 K557
Binding residue
(residue number reindexed from 1)		T189 S190 G191 T192 S193 K197 G306 E307 S308 Y329 G330 Q331 T332 D414 F426 R429 K523
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T221 T364 E365 N467 R472 K557
Catalytic site (residue number reindexed from 1) T189 T332 E333 N435 R440 K523
Enzyme Commision number 6.2.1.2: medium-chain acyl-CoA ligase.
6.2.1.25: benzoate--CoA ligase.
Gene Ontology
Molecular Function
GO:0004321 fatty-acyl-CoA synthase activity
GO:0005524 ATP binding
GO:0015645 fatty acid ligase activity
GO:0016874 ligase activity
GO:0018858 benzoate-CoA ligase activity
GO:0031956 medium-chain fatty acid-CoA ligase activity
GO:0046872 metal ion binding
GO:0102391 decanoate-CoA ligase activity
Biological Process
GO:0006631 fatty acid metabolic process
GO:0006633 fatty acid biosynthetic process
GO:0006637 acyl-CoA metabolic process
GO:0036112 medium-chain fatty-acyl-CoA metabolic process
GO:0042593 glucose homeostasis
GO:0070328 triglyceride homeostasis
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3day, PDBe:3day, PDBj:3day
PDBsum3day
PubMed19345228
UniProtQ08AH3|ACS2A_HUMAN Acyl-coenzyme A synthetase ACSM2A, mitochondrial (Gene Name=ACSM2A)

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