6HGT

Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

wwPDB Validation 3D Report Full Report



Literature

Structure-based design of selective, histone substrate-based inhibitors of histone lysine demethylases 4 (KDM4) subfamily

Maw, J.Le Bihan, Y.V.Bavetsias, V.Blagg, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4A
A, B, C, D
360Homo sapiensMutation(s): 0 
Gene Names: KDM4AJHDM3AJMJD2JMJD2AKIAA0677
EC: 1.14.11
Find proteins for O75164 (Homo sapiens)
Go to UniProtKB:  O75164
NIH Common Fund Data Resources
PHAROS  O75164
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
E, F, G, H
15Homo sapiensMutation(s): 1 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3BH3-3AH3-3B
Find proteins for P84243 (Homo sapiens)
Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS  P84243
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA

Download CCD File 
A, B, C, D
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.44α = 90
b = 103.41β = 99.63
c = 144.52γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC347/A18364

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release