Brand  (β version)

PDB ID: 5V9T

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
NI Nickel (II) ion PoSSuM
ZN Zinc ion PoSSuM
90V N-{(3r)-1-[3-(propan-2-yl)-1h-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5V9T   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Title : Crystal structure of selective pyrrolidine amide KDM5a inhibitor N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide (compound 48)
Release Data : 2017-05-10
Compound :
mol_id molecule chains synonym
1 Lysine-specific demethylase 5A A,B 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 G 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 : histone demethylase, KDM5, KDM5a, epigenetics, cancer, selective, inhibitor, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 3.050 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, B
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
-