Structure of PDB 5ys9 Chain A Binding Site BS02

Receptor Information
>5ys9 Chain A (length=692) Species: 284591 (Yarrowia lipolytica CLIB122) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANVEIDGKQYNTFTEPPKALAGERAKVKFPIKDMTEFLHGGEENVTMIER
LMTELERDPVLNVSGDYDMPKEQLRETAVARIAALSGHWKKDTEKEALLR
SQLHGIVDMGTRIRLGVHTGLFMGAIRGSGTKEQYDYWVRKGAADVKGFY
GCFAMTELGHGSNVAGLETTATYIQDTDEFIINTPNTGATKWWIGGAAHS
ATHTACFARLLVDGKDYGVKIFVVQLRDVSSHSLMPGIALGDIGKKMGRD
AIDNGWIQFTNVRIPRQNMLMKYAKVSSTGKVSQPPLAQLTYGALIGGRV
TMIADSFFVSQRFITIALRYACVRRQFGTTPGQPETKIIDYPYHQRRLLP
LLAFTYAMKMAADQSQIQYDQTTDLLQTIDPKDKGALGKAIVDLKELFAS
SAGLKAFTTWTCANIIDQCRQACGGHGYSGYNGFGQAYADWVVQCTWEGD
NNVLCLSMGRGLIQSCLGHRKGKPLGSSVGYLANKGLEQATLSGRDLKDP
KVLIEAWEKVANGAIQRATDKFVELTKGGLSPDQAFEELSQQRFQCAKIH
TRKHLVTAFYERINASAKADVKPYLINLANLFTLWSIEEDSGLFLREGFL
QPKDIDQVTELVNHYCKEVRDQVAGYTDAFGLSDWFINAPIGNYDGDVYK
HYFAKVNQQNPAQNPRPPYYESTLRPFLFREDEDDDICELDE
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 chain5ys9 Chain B Residue 801 [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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PDB5ys9 Crystal Structure of Acyl-CoA Oxidase 3 fromYarrowia lipolyticawith Specificity for Short-Chain Acyl-CoA.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		R331 Q333 F334 Y348 R354 Q428 A429 G432 Y435
Binding residue
(residue number reindexed from 1)		R324 Q326 F327 Y341 R347 Q421 A422 G425 Y428
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ys9, PDBe:5ys9, PDBj:5ys9
PDBsum5ys9
PubMed29429324
UniProtO74936|ACOX3_YARLI Acyl-coenzyme A oxidase 3 (Gene Name=POX3)

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