Structure of PDB 6gdy Chain B Binding Site BS02

Receptor Information
>6gdy Chain B (length=334) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVADNVERAD
ALQLSVEEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFK
CGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDY
KVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALV
QGHKRWCLFPTSTPRELIKVTRDEGGNQQDEAITWFNVIYPRTQLPTWPP
EFKPLEILQKPGETVFVPGGWWHVVLNLDTTIAITQNFASSTNFPVVWHK
TVRGRPKLSRKWYRILKQEHPELAVLADSVDLQE
Ligand information
Ligand IDAKG
InChIInChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKeyKPGXRSRHYNQIFN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385OC(=O)CCC(=O)C(O)=O
FormulaC5 H6 O5
Name2-OXOGLUTARIC ACID
ChEMBLCHEMBL1686
DrugBankDB08845
ZINCZINC000001532519
PDB chain6gdy Chain B Residue 402 [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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PDB6gdy Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6.
Resolution2.04 Å
Binding residue
(original residue number in PDB)		Y131 F133 T184 H187 N197 K204 V275
Binding residue
(residue number reindexed from 1)		Y131 F133 T184 H187 N197 K204 V275
Annotation score5
Binding affinityMOAD: Kd=3.5uM
Enzymatic activity
Enzyme Commision number 1.14.11.-
External links
PDB RCSB:6gdy, PDBe:6gdy, PDBj:6gdy
PDBsum6gdy
PubMed31147442
UniProtQ6NYC1|JMJD6_HUMAN Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (Gene Name=JMJD6)

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