5FPV

Crystal structure of human JMJD2A in complex with compound KDOAM20A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.

Johansson, C.Velupillai, S.Tumber, A.Szykowska, A.Hookway, E.S.Nowak, R.P.Strain-Damerell, C.Gileadi, C.Philpott, M.Burgess-Brown, N.Wu, N.Kopec, J.Nuzzi, A.Steuber, H.Egner, U.Badock, V.Munro, S.Lathangue, N.B.Westaway, S.Brown, J.Athanasou, N.Prinjha, R.Brennan, P.E.Oppermann, U.

(2016) Nat Chem Biol 12: 539

  • DOI: https://doi.org/10.1038/nchembio.2087
  • Primary Citation of Related Structures:  
    4UF0, 5A1F, 5A3P, 5A3T, 5A3W, 5FPU, 5FPV, 5FUN, 5FUP, 5FV3, 5FWJ

  • PubMed Abstract: 

    Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe(2+)-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal structures of the catalytic core of the human KDM5B enzyme in complex with three inhibitor chemotypes. These scaffolds exploit several aspects of the KDM5 active site, and their selectivity profiles reflect their hybrid features with respect to the KDM4 and KDM6 families. Whereas GSK-J1, a previously identified KDM6 inhibitor, showed about sevenfold less inhibitory activity toward KDM5B than toward KDM6 proteins, KDM5-C49 displayed 25-100-fold selectivity between KDM5B and KDM6B. The cell-permeable derivative KDM5-C70 had an antiproliferative effect in myeloma cells, leading to genome-wide elevation of H3K4me3 levels. The selective inhibitor GSK467 exploited unique binding modes, but it lacked cellular potency in the myeloma system. Taken together, these structural leads deliver multiple starting points for further rational and selective inhibitor design.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Headington, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSINE-SPECIFIC DEMETHYLASE 4A
A, B, C, D, E
A, B, C, D, E, F, G, H
360Homo sapiensMutation(s): 0 
EC: 1.14.11.27 (PDB Primary Data), 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens)
Explore O75164 
Go to UniProtKB:  O75164
PHAROS:  O75164
GTEx:  ENSG00000066135 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75164
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMK
Query on MMK

Download Ideal Coordinates CCD File 
FA [auth E]
IA [auth F]
J [auth A]
LA [auth G]
P [auth B]
FA [auth E],
IA [auth F],
J [auth A],
LA [auth G],
P [auth B],
PA [auth H],
U [auth C],
Z [auth D]
2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid
C15 H22 N4 O3
RTKGUAPXWDCFNW-BQYQJAHWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
GA [auth E]
JA [auth F]
K [auth A]
MA [auth G]
AA [auth D],
GA [auth E],
JA [auth F],
K [auth A],
MA [auth G],
Q [auth B],
QA [auth H],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
L [auth A]
M [auth A]
BA [auth D],
CA [auth D],
DA [auth D],
L [auth A],
M [auth A],
N [auth A],
NA [auth G],
R [auth B],
RA [auth H],
S [auth B],
SA [auth H],
TA [auth H],
UA [auth H],
W [auth C],
X [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
EA [auth E]
HA [auth F]
I [auth A]
KA [auth G]
O [auth B]
EA [auth E],
HA [auth F],
I [auth A],
KA [auth G],
O [auth B],
OA [auth H],
T [auth C],
Y [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.346α = 90
b = 103.509β = 106.37
c = 157.103γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-01
    Changes: Database references
  • Version 1.3: 2016-06-29
    Changes: Database references
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description