Structure of PDB 5y9d Chain B Binding Site BS02

Receptor Information
>5y9d Chain B (length=682) Species: 284591 (Yarrowia lipolytica CLIB122) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTNTFTDPPVEMAKERGKTQFTVRDVTNFLNGGEEETQIVEKIMSSIERD
PVLSVTADYDCNLQQARKQTMERVAALSPYLVTDTEKLSLWRAQLHGMVD
MSTRTRLSIHNNLFIGSIRGSGTPEQFKYWVKKGAVAVKQFYGCFAMTEL
GHGSNLKGLETTATYDQDSDQFIINTPHIGATKWWIGGAAHTSTHCVCFA
KLIVHGKDYGTRNFVVPLRNVHDHSLKVGVSIGDIGKKMGRDGVDNGWIQ
FTNVRIPRQNMLMRYAKVSDTGVVTKPYGALIRGRVSMIADSFHVSKRFL
TIALRYACVRRQFGTSGDTKETKIIDYPYHQRRLLPLLAYCYAMKMGADE
AQKTWIETTDRILALNPNDPAQKNDLEKAVTDTKELFAASAGMKAFTTWG
CAKIIDECRQACGGHGYSGYNGFGQGYADWVVQCTWEGDNNVLCLSMGRG
LVQSALQILAGKHVGASIQYVGDKSKISQNGQGTPREQLLSPEFLVEAFR
TASRNNILRTTDKYQELVKTLNPDQAFEELSQQRFQCARIHTRQHLISSF
YARIATAKDDIKPHLLKLANLFALWSIEEDTGIFLRENILTPGDIDLINS
LVDELCVAVRDQVIGLTDAFGLSDFFINAPIGSYDGNVYEKYFAKVNQQN
PATNPRPPYYESTLKPFLFREEEDDEICDLDE
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain5y9d Chain B Residue 701 [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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PDB5y9d Structural insight into the substrate specificity of acyl-CoA oxidase1 from Yarrowia lipolytica for short-chain dicarboxylyl-CoAs.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		M148 T149 G154 S155 W186 I187 V439 W443 D446 V449
Binding residue
(residue number reindexed from 1)		M147 T148 G153 S154 W185 I186 V432 W436 D439 V442
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.3.6: acyl-CoA oxidase.
Gene Ontology
Molecular Function
GO:0003997 acyl-CoA oxidase activity
GO:0005504 fatty acid binding
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0006631 fatty acid metabolic process
GO:0006635 fatty acid beta-oxidation
GO:0033540 fatty acid beta-oxidation using acyl-CoA oxidase
GO:0055088 lipid homeostasis
Cellular Component
GO:0005777 peroxisome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5y9d, PDBe:5y9d, PDBj:5y9d
PDBsum5y9d
PubMed29198706
UniProtO74934|ACOX1_YARLI Acyl-coenzyme A oxidase 1 (Gene Name=POX1)

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