Structure of PDB 5k3j Chain B Binding Site BS01

Receptor Information
>5k3j Chain B (length=659) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANRSIRDGDNPELLEERRMATFDTDKMAAVIYGSEEFARRRREITDAVSK
IPELADIKPYPFLTREEKVTEGTRKISILTKYLNQLIDRDNEEESLHLHR
EVIGYEGHPFALHDALFIPTLQSQASDEQQEKWLERARRREIIGCYAQTE
LGHGSNLRNLETTAVYDIASQEFVLHTPTTTALKWWPGALGKSCNYALVV
AELNYGPHFFMVQLRDEKTHIPLKGVTVGDIGPKMNFNAADNGYLGLNNL
RVPRTNLLMRHCKVEADGTYVKPPHAKIGYSGMVKIRSQMAMEQGLFLAH
ALTIAARYSAVRRQGHLDDKQVEVKVLDYQTQQHRLFPSLARAYAFIFTG
FETIHLYSQLLKDVDMGNTSGMADLHALTSGLKSVVAHETGEGIEQARMA
CGGHGYSMASYISVVYGIAIGGCTYAGENMVMLLQLARYLVKSVELIKAG
KAKKLGPVASYLADKSDETDLTSLNGYVKMFENMARRQAWKATEKFLKLM
ESGESREVAWNKSAVELTRASRLHTRLFIIEAFMRRVSRIEDIPVKEVLT
DLLHLHVNYELLDVATYALEFMSFTQLDYVRDQLYLYLEKIRPNAVSLVD
SFQISDMQLRSVLGRRDGHVYENLFKWAKSSPLNNADVLPSVEKYLKPMM
EKAKLAAAH
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 chain5k3j Chain A 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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PDB5k3j Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans.
Resolution2.68 Å
Binding residue
(original residue number in PDB)		R318 V332 Y335 Q338 A406 G408 G409 Y412
Binding residue
(residue number reindexed from 1)		R312 V326 Y329 Q332 A400 G402 G403 Y406
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.3.-
Gene Ontology
Molecular Function
GO:0003997 acyl-CoA oxidase activity
GO:0005504 fatty acid binding
GO:0005515 protein binding
GO:0005524 ATP 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:0009058 biosynthetic process
GO:0033540 fatty acid beta-oxidation using acyl-CoA oxidase
GO:0055088 lipid homeostasis
GO:1904070 ascaroside biosynthetic process
Cellular Component
GO:0005777 peroxisome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5k3j, PDBe:5k3j, PDBj:5k3j
PDBsum5k3j
PubMed27551084
UniProtO62137|ACX12_CAEEL Acyl-coenzyme A oxidase acox-1.2 (Gene Name=acox-1.2)

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