5KR7

KDM4C bound to pyrazolo-pyrimidine scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of potent, selective KDM5 inhibitors.

Gehling, V.S.Bellon, S.F.Harmange, J.C.LeBlanc, Y.Poy, F.Odate, S.Buker, S.Lan, F.Arora, S.Williamson, K.E.Sandy, P.Cummings, R.T.Bailey, C.M.Bergeron, L.Mao, W.Gustafson, A.Liu, Y.VanderPorten, E.Audia, J.E.Trojer, P.Albrecht, B.K.

(2016) Bioorg Med Chem Lett 26: 4350-4354

  • DOI: 10.1016/j.bmcl.2016.07.026
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • This communication describes the identification and optimization of a series of pan-KDM5 inhibitors derived from compound 1, a hit initially identified against KDM4C. Compound 1 was optimized to afford compound 20, a 10nM inhibitor of KDM5A. Compound ...

    This communication describes the identification and optimization of a series of pan-KDM5 inhibitors derived from compound 1, a hit initially identified against KDM4C. Compound 1 was optimized to afford compound 20, a 10nM inhibitor of KDM5A. Compound 20 is highly selective for the KDM5 enzymes versus other histone lysine demethylases and demonstrates activity in a cellular assay measuring the increase in global histone 3 lysine 4 tri-methylation (H3K4me3). In addition compound 20 has good ADME properties, excellent mouse PK, and is a suitable starting point for further optimization.


    Organizational Affiliation

    Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4C
A, B
367Homo sapiensMutation(s): 0 
Gene Names: KDM4CGASC1JHDM3CJMJD2CKIAA0780
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
Find proteins for Q9H3R0 (Homo sapiens)
Go to UniProtKB:  Q9H3R0
NIH Common Fund Data Resources
PHAROS  Q9H3R0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6X9
Query on 6X9

Download CCD File 
A, B
6-ethyl-2,5-dimethyl-7-oxidanylidene-4~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile
C11 H12 N4 O
ZCAHZFVKTFERAJ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6X9IC50:  2880   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.817α = 90
b = 89.876β = 90
c = 100.011γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references