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


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2016.07.026
  • Primary Citation of Related Structures:  
    5KR7

  • 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 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. Electronic address: victor.gehling@constellationpharma.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 4C
A, B
367Homo sapiensMutation(s): 0 
Gene Names: KDM4CGASC1JHDM3CJMJD2CKIAA0780
EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R0 (Homo sapiens)
Explore Q9H3R0 
Go to UniProtKB:  Q9H3R0
PHAROS:  Q9H3R0
GTEx:  ENSG00000107077 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3R0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6X9
Query on 6X9

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

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
6X9 Binding MOAD:  5KR7 IC50: 2880 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description