5CEH

Structure of histone lysine demethylase KDM5A in complex with selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells.

Vinogradova, M.Gehling, V.S.Gustafson, A.Arora, S.Tindell, C.A.Wilson, C.Williamson, K.E.Guler, G.D.Gangurde, P.Manieri, W.Busby, J.Flynn, E.M.Lan, F.Kim, H.J.Odate, S.Cochran, A.G.Liu, Y.Wongchenko, M.Yang, Y.Cheung, T.K.Maile, T.M.Lau, T.Costa, M.Hegde, G.V.Jackson, E.Pitti, R.Arnott, D.Bailey, C.Bellon, S.Cummings, R.T.Albrecht, B.K.Harmange, J.C.Kiefer, J.R.Trojer, P.Classon, M.

(2016) Nat.Chem.Biol. 12: 531-538

  • DOI: 10.1038/nchembio.2085

  • PubMed Abstract: 
  • The KDM5 family of histone demethylases catalyzes the demethylation of histone H3 on lysine 4 (H3K4) and is required for the survival of drug-tolerant persister cancer cells (DTPs). Here we report the discovery and characterization of the specific KD ...

    The KDM5 family of histone demethylases catalyzes the demethylation of histone H3 on lysine 4 (H3K4) and is required for the survival of drug-tolerant persister cancer cells (DTPs). Here we report the discovery and characterization of the specific KDM5 inhibitor CPI-455. The crystal structure of KDM5A revealed the mechanism of inhibition of CPI-455 as well as the topological arrangements of protein domains that influence substrate binding. CPI-455 mediated KDM5 inhibition, elevated global levels of H3K4 trimethylation (H3K4me3) and decreased the number of DTPs in multiple cancer cell line models treated with standard chemotherapy or targeted agents. These findings show that pretreatment of cancer cells with a KDM5-specific inhibitor results in the ablation of a subpopulation of cancer cells that can serve as the founders for therapeutic relapse.


    Organizational Affiliation

    Genentech Inc., South San Francisco, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5A
A
790Homo sapiensMutation(s): 0 
Gene Names: KDM5A (JARID1A, RBBP2, RBP2)
EC: 1.14.11.-
Find proteins for P29375 (Homo sapiens)
Go to Gene View: KDM5A
Go to UniProtKB:  P29375
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Unknown Peptide
B
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
50P
Query on 50P

Download SDF File 
Download CCD File 
A
7-oxo-5-phenyl-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile
C16 H14 N4 O
DHXKRMSKXLDZGY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B
L-PEPTIDE LINKINGC4 H9 N O2

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
50PIC50: 10 - 20 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 159.306α = 90.00
b = 159.306β = 90.00
c = 92.462γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2016-07-06
    Type: Database references
  • Version 1.3: 2016-07-20
    Type: Data collection
  • Version 1.4: 2017-11-22
    Type: Derived calculations, Refinement description