5F5A | pdb_00005f5a

Crystal Structure of human JMJD2D complexed with KDOAM16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 
    0.165 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.131 (Depositor) 
  • R-Value Observed: 
    0.133 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5F5A

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.

Bavetsias, V.Lanigan, R.M.Ruda, G.F.Atrash, B.McLaughlin, M.G.Tumber, A.Mok, N.Y.Le Bihan, Y.V.Dempster, S.Boxall, K.J.Jeganathan, F.Hatch, S.B.Savitsky, P.Velupillai, S.Krojer, T.England, K.S.Sejberg, J.Thai, C.Donovan, A.Pal, A.Scozzafava, G.Bennett, J.M.Kawamura, A.Johansson, C.Szykowska, A.Gileadi, C.Burgess-Brown, N.A.von Delft, F.Oppermann, U.Walters, Z.Shipley, J.Raynaud, F.I.Westaway, S.M.Prinjha, R.K.Fedorov, O.Burke, R.Schofield, C.J.Westwood, I.M.Bountra, C.Muller, S.van Montfort, R.L.Brennan, P.E.Blagg, J.

(2016) J Med Chem 59: 1388-1409

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01635
  • Primary Citation Related Structures: 
    5F2S, 5F2W, 5F32, 5F37, 5F39, 5F3C, 5F3E, 5F3G, 5F3I, 5F5A, 5F5C, 5F5I, 5FPL

  • PubMed Abstract: 

    We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay.


  • Organizational Affiliation
    • Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , 15 Cotswold Road, London SM2 5NG, U.K.

Macromolecule Content 

  • Total Structure Weight: 41.56 kDa 
  • Atom Count: 3,259 
  • Modeled Residue Count: 330 
  • Deposited Residue Count: 346 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 4D346Homo sapiensMutation(s): 0 
Gene Names: KDM4DJHDM3DJMJD2D
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens)
Explore Q6B0I6 
Go to UniProtKB:  Q6B0I6
PHAROS:  Q6B0I6
GTEx:  ENSG00000186280 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B0I6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5V0

Query on 5V0



Download:Ideal Coordinates CCD File
D [auth A]2-[(furan-2-ylmethylamino)methyl]pyridine-4-carboxylic acid
C12 H12 N2 O3
WAXTXDDUSDCZNA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
R [auth A],
S [auth A],
T [auth A],
U [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
C [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free:  0.165 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.131 (Depositor) 
  • R-Value Observed: 0.133 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.28α = 90
b = 71.28β = 90
c = 150.36γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description