4URA | pdb_00004ura

Crystal structure of human JMJD2A in complex with compound 14a

PDB DOI: https://doi.org/10.2210/pdb4URA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-27 Released: 2015-06-17
Deposition Author(s): Krojer, T., England, K.S., Vollmar, M., Crawley, L., Williams, E., Riesebos, E., Szykowska, A., Burgess-Brown, N., Oppermann, U., Brennan, P.E., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.207 (Depositor), 0.212 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor.

England, K.S., Tumber, A., Krojer, T., Scozzafava, G., Ng, S.S., Daniel, M., Szykowska, A., Che, K., von Delft, F., Burgess-Brown, N.A., Kawamura, A., Schofield, C.J., Brennan, P.E.

(2014) Medchemcomm 5: 1879-1886

PubMed: 26682034 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/C4MD00291A
Primary Citation Related Structures:
4URA

PubMed Abstract:
A potent inhibitor of the JmjC histone lysine demethylase KDM2A (compound 35 , pIC ₅₀ 7.2) with excellent selectivity over representatives from other KDM subfamilies has been developed; the discovery that a triazolopyridine compound binds to the active site of JmjC KDMs was followed by optimisation of the triazole substituent for KDM2A inhibition and selectivity.

Organizational Affiliation

Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK.

Macromolecule Content

Total Structure Weight: 84.59 kDa
Atom Count: 5,767
Modeled Residue Count: 693
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4A	A, B	360	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75164
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LEL Query on LEL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	2-(2H-1,2,3-triazol-4-yl)pyridine-4-carboxylic acid C₈ H₆ N₄ O₂ XGBRXPYFGYDEMS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.207 (Depositor), 0.212 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.04	α = 90
b = 149.66	β = 90
c = 57.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-06-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-17
Type: Initial release
Version 1.1: 2017-01-18
Changes: Database references
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other