Structure of PDB 7yxl Chain B Binding Site BS03

Receptor Information

>7yxl Chain B (length=305) Species: 7227 (Drosophila melanogaster)

MSEVERALDVLLQEAEELCIGSSVVELDRIPTALEFCREFYSKNQPVVIR
KALNWPAIGKWTPKYLIEALGDRSVDVAITPNGYADGLATQNGQEYFVLP
LETKMKLSEVVRRLDDPTGAVHYIQKQNPELAADLRVSDLDFAQQSFNKP
PDAVNFWLGDERAVTSMHKDPYENVYCVISGHKDFVLIPPHQLSCVPRGI
YPTGVYKTSDSGQFYIEPLRDEEGSDQFTEWVSVDPLSPDLAKYPEYARA
KPLKVRVHAGDILYLPNYWFHHVSQSHKCIAVNFWYDLDYDSRYCYYRML
EQMTS

Ligand information

• Ligand ID: NDF
• InChI: InChI=1S/C11H11NO5/c13-9(11(16)17)12-8(10(14)15)6-7-4-2-1-3-5-7/h1-5,8H,6H2,(H,12,13)(H,14,15)(H,16,17)/t8-/m1/s1
• InChIKey: ULQWGBCNOHBNDB-MRVPVSSYSA-N
• SMILES:
  CACTVS 3.341: OC(=O)[C@@H](Cc1ccccc1)NC(=O)C(O)=O
  ACDLabs 10.04: O=C(O)C(=O)NC(C(=O)O)Cc1ccccc1
  CACTVS 3.341: OC(=O)[CH](Cc1ccccc1)NC(=O)C(O)=O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CC(C(=O)O)NC(=O)C(=O)O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)C[C@H](C(=O)O)NC(=O)C(=O)O
• Formula: C11 H11 N O5
• Name: N-(CARBOXYCARBONYL)-D-PHENYLALANINE
• ChEMBL: CHEMBL486146
• DrugBank: DB08263
• ZINC: ZINC000026637924
• PDB chain: 7yxl Chain B Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yxl Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): T172 H175 N181 Y183 K190 H278 V280 N290 W292
• Binding residue (residue number reindexed from 1): T165 H168 N174 Y176 K183 H271 V273 N283 W285
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.14.11.-
  3.1.1.4: phospholipase A2.

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0016706 2-oxoglutarate-dependent dioxygenase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding
• GO:0106155 peptidyl-lysine 3-dioxygenase activity

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:7yxl, PDBe:7yxl, PDBj:7yxl
• PDBsum: 7yxl
• PubMed: 35410347
• UniProt: Q9VU77