Structure of PDB 5k3j Chain A Binding Site BS03

Receptor Information
>5k3j Chain A (length=662) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRSIRDGDNPELLEERRMATFDTDKMAAVIYGSEEFARRRREITDAVSKI
PELADIKPYPFLTREEKVTEGTRKISILTKYLNQLIDRDNEEESLHLHRE
VIGYEGHPFALHDALFIPTLQSQASDEQQEKWLERARRREIIGCYAQTEL
GHGSNLRNLETTAVYDIASQEFVLHTPTTTALKWWPGALGKSCNYALVVA
ELIIKRNNYGPHFFMVQLRDEKTHIPLKGVTVGDIGPKMNFNAADNGYLG
LNNLRVPRTNLLMRHCKVEADGTYVKPPHAKIGYSGMVKIRSQMAMEQGL
FLAHALTIAARYSAVRRQGHLDDKQVEVKVLDYQTQQHRLFPSLARAYAF
IFTGFETIHLYSQLLKDVDMGNTSGMADLHALTSGLKSVVAHETGEGIEQ
ARMACGGHGYSMASYISVVYGIAIGGCTYAGENMVMLLQLARYLVKSVEL
IKAGKAKKLGPVASYLADKSDETDLTSLNGYVKMFENMARRQAWKATEKF
LKLMESGESREVAWNKSAVELTRASRLHTRLFIIEAFMRRVSRIEDIPVK
EVLTDLLHLHVNYELLDVATYALEFMSFTQLDYVRDQLYLYLEKIRPNAV
SLVDSFQISDMQLRSVLGRRDGHVYENLFKWAKSSPLNNADVLPSVEKYL
KPMMEKAKLAAA
Ligand information
Ligand ID6QA
InChIInChI=1S/C32H54N7O21P3S/c1-17-18(40)12-19(41)31(57-17)54-10-5-4-6-22(43)64-11-9-34-21(42)7-8-35-29(46)26(45)32(2,3)14-56-63(52,53)60-62(50,51)55-13-20-25(59-61(47,48)49)24(44)30(58-20)39-16-38-23-27(33)36-15-37-28(23)39/h15-20,24-26,30-31,40-41,44-45H,4-14H2,1-3H3,(H,34,42)(H,35,46)(H,50,51)(H,52,53)(H2,33,36,37)(H2,47,48,49)/t17-,18+,19+,20+,24+,25+,26-,30+,31+/m0/s1
InChIKeyOJJVYBQJWBBERR-XKGQWQQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H]1O[C@@H](OCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O[P](O)(O)=O)n3cnc4c(N)ncnc34)[C@H](O)C[C@H]1O
OpenEye OEToolkits 2.0.5CC1C(CC(C(O1)OCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)OP(=O)(O)O)O)O)O
OpenEye OEToolkits 2.0.5C[C@H]1[C@@H](C[C@H]([C@@H](O1)OCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)OP(=O)(O)O)O)O)O
CACTVS 3.385C[CH]1O[CH](OCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O[P](O)(O)=O)n3cnc4c(N)ncnc34)[CH](O)C[CH]1O
FormulaC32 H54 N7 O21 P3 S
Name~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 5-[(2~{R},3~{R},5~{R},6~{S})-6-methyl-3,5-bis(oxidanyl)oxan-2-yl]oxypentanethioate
ChEMBL
DrugBank
ZINCZINC000584904757
PDB chain5k3j Chain A Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)
L117 Y147 S156 L158 R159 K283 Y286 M289 R293 E299 H382 Y431 A432 G433 Q441 R444
Binding residue
(residue number reindexed from 1)
L115 Y145 S154 L156 R157 K281 Y284 M287 R291 E297 H380 Y429 A430 G431 Q439 R442
Annotation score4
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

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Molecular Function

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Biological Process

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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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