Structure of PDB 2ddh Chain A Binding Site BS01

Receptor Information

>2ddh Chain A (length=622) Species: 10116 (Rattus norvegicus)

MNPDLRKERASATFNPELITHILDGSPENTRRRREIENLILNDPDFQHED
YNFLTRSQRYEVAVKKSATMVKKMREYGISDPEEIMWFKNSVHRGHPEPL
DLHLGMFLPTLLQATAEQQERFFMPAWNLEITGTYAQTEMGHGTHLRGLE
TTATYDPKTQEFILNSPTVTSIKWWPGGLGKTSNHAIVLAQLITQGECYG
LHAFVVPIREIGTHKPLPGITVGDIGPKFGYEEMDNGYLKMDNYRIPREN
MLMKYAQVKPDGTYVKPLMVFVRSFLVGNAAQSLSKACTIAIRYSAVRRQ
SEIKQSEPEPQILDFQTQQYKLFPLLATAYAFHFVGRYMKETYLRSELPE
LHALTAGLKAFTTWTANAGIEECRMACGGHGYSHSSGIPNIYVTFTPACT
FEGENTVMMLQTARFLMKIYDQVRSGKLVGGMVSYLNDLPSVDINSLEGL
TEAYKLRAARLVEIAAKNLQTHVSHRKSKEVAWNLTSVDLVRASEAHCHY
VVVKVFSDKLPKIQDKAVQAVLRNLCLLYSLYGISQKGGDFLEGSIITGA
QLSQVNARILELLTLIRPNAVALVDAFDFKDMTLGSVLGRYDGNVYENLF
EWAKKSPLNKTEVHESYHKHLK

Ligand information

• Ligand ID: FAD
• InChI: InChI=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
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=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 1.5.0: Cc1cc2c(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 1.5.0: Cc1cc2c(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 3.341: Cc1cc2N=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 10.04: O=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
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 2ddh Chain A Residue 699

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ddh Three-Dimensional Structure of Rat-Liver Acyl-CoA Oxidase in Complex with a Fatty Acid: Insights into Substrate-Recognition and Reactivity toward Molecular Oxygen.
• Resolution: 2.07 Å
• Binding residue (original residue number in PDB): T139 G144 T145 W176 P177 E423
• Binding residue (residue number reindexed from 1): T138 G143 T144 W175 P176 E404
• Annotation score: 1

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:0016401 palmitoyl-CoA oxidase activity
• GO:0016491 oxidoreductase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
• GO:0030165 PDZ domain binding
• GO:0042803 protein homodimerization activity
• GO:0050660 flavin adenine dinucleotide binding
• GO:0071949 FAD binding

Biological Process

• GO:0000038 very long-chain fatty acid metabolic process
• GO:0006091 generation of precursor metabolites and energy
• GO:0006629 lipid metabolic process
• GO:0006631 fatty acid metabolic process
• GO:0006635 fatty acid beta-oxidation
• GO:0006693 prostaglandin metabolic process
• GO:0007283 spermatogenesis
• GO:0009062 fatty acid catabolic process
• GO:0019395 fatty acid oxidation
• GO:0033540 fatty acid beta-oxidation using acyl-CoA oxidase
• GO:0050665 hydrogen peroxide biosynthetic process
• GO:0055088 lipid homeostasis
• GO:0140493 very long-chain fatty acid beta-oxidation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005777 peroxisome
• GO:0005778 peroxisomal membrane
• GO:0005782 peroxisomal matrix

External links

• PDB: RCSB:2ddh, PDBe:2ddh, PDBj:2ddh
• PDBsum: 2ddh
• PubMed: 16672280
• UniProt: P07872|ACOX1_RAT Peroxisomal acyl-coenzyme A oxidase 1 (Gene Name=Acox1)