Brand  (β version)

PDB ID: 5V9P

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
90S [(3s)-3-(4-bromo-1h-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1h-pyrazol-5-yl]methanone PoSSuM
NI Nickel (II) ion PoSSuM
SO4 Sulfate ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5V9P   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Title : Crystal structure of pyrrolidine amide inhibitor [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone (compound 35) in complex with KDM5A
Release Data : 2017-05-10
Compound :
mol_id molecule chains synonym
1 Lysine-specific demethylase 5A A Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, Retinoblastoma-binding protein 2, RBBP-2, KDM5A
ec: 1.14.11.-
mol_id molecule chains synonym
2 Lysine-specific demethylase 5A B Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, Retinoblastoma-binding protein 2, RBBP-2, KDM5A
fragment: Internal region with unknown reference frame
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Spodoptera frugiperda  (taxid:7108)
gene: KDM5A, JARID1A, RBBP2, RBP2
expression_system_common: Fall armyworm
expression_system_strain: SF9
expression_system_vector_type: baculovirus
expression_system_plasmid: pACGP67
mol_id organism_scientific organism_common expression_system
2 Homo sapiens  (taxid:9606) Human Spodoptera frugiperda  (taxid:7108)
gene: KDM5A, JARID1A, RBBP2, RBP2
expression_system_common: Fall armyworm
expression_system_strain: SF9
expression_system_vector_type: baculovirus
expression_system_plasmid: pACGP67
Authors : Kiefer, J.R., Liang, J., Vinogradova, M.
Keywords : epigenetics, histone demethylase, cancer, inhibitor, selective, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 3.0 Å )
Citation :

From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors.

Liang, J.,Labadie, S.,Zhang, B.  et al.
(2017)  Bioorg. Med. Chem. Lett.  27 : 2974 - 2981

PubMed: 28512031
DOI: 10.1016/j.bmcl.2017.05.016

Reaction

Chain : A
UniProt : P29375 (KDM5A_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
3 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)- [histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl(4)-[histone H3] + 3 succinate 1.14.11.67 PubMed:17320160, PubMed:17320161, PubMed:17320163
-