5F2W | pdb_00005f2w

Crystal structure of human KDM4A in complex with compound 16

• PDB DOI: https://doi.org/10.2210/pdb5F2W/pdb

• Classification: Oxidoreductase/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-02 Released: 2016-01-20 
• Deposition Author(s): Le Bihan, Y.-V., Dempster, S., Westwood, I.M., van Montfort, R.L.M.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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

• PubMed: 26741168 
• 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.

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Organizational Affiliation: 
• Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , 15 Cotswold Road, London SM2 5NG, U.K.
Structural Genomics Consortium (SGC), University of Oxford , ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford , NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K.
Botnar Research Centre, NIHR Oxford Biomedical Research Unit , Oxford OX3 7LD, U.K.
Diamond Light Source (DLS), Harwell Science and Innovation Campus , Didcot OX11 0DE, U.K.
Department of Biochemistry, University of Johannesburg , Auckland Park 2006, South Africa.
Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research , London SM2 5NG, U.K.
Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 170.7 kDa 
• Atom Count: 11,386 
• Modeled Residue Count: 1,391 
• Deposited Residue Count: 1,440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B, C, D	360	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 EC: 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5UP	AA [auth C], G [auth A], LA [auth D], N [auth B]	2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide C9 H8 N4 O S YCMAFYWOEDTAQB-UHFFFAOYSA-N
DMS	K [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], JA [auth D], KA [auth D], L [auth B], M [auth B], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], MA [auth D], NA [auth D], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5UP	BindingDB:  5F2W	IC50: 1.04e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.39	α = 90
b = 102.04	β = 99.7
c = 142.15	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Le Bihan, Y.-V., Dempster, S., Westwood, I.M., van Montfort, R.L.M.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C309/A11566

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description