2VD7

Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid

PDB DOI: https://doi.org/10.2210/pdb2VD7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-10-01 Released: 2007-11-27
Deposition Author(s): Ng, S.S., von Delft, F., Pilka, E.S., Kavanagh, K.L., McDonough, M.A., Savitsky, P., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.219
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Inhibitor scaffolds for 2-oxoglutarate-dependent histone lysine demethylases.

Rose, N.R., Ng, S.S., Mecinovic, J., Lienard, B.M., Bello, S.H., Sun, Z., McDonough, M.A., Oppermann, U., Schofield, C.J.

(2008) J Med Chem 51: 7053-7056

PubMed: 18942826 Search on PubMed
DOI: https://doi.org/10.1021/jm800936s
Primary Citation of Related Structures:
2VD7

PubMed Abstract:
The dynamic methylation of histone lysyl residues plays an important role in biology by regulating transcription, maintaining genomic integrity, and by contributing to epigenetic effects. Here we describe a variety of inhibitor scaffolds that inhibit the human 2-oxoglutarate-dependent JMJD2 subfamily of histone demethylases. Combined with structural data, these chemical starting points will be useful to generate small-molecule probes to analyze the physiological roles of these enzymes in epigenetic signaling.

Organizational Affiliation

The Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.

Macromolecule Content

Total Structure Weight: 89.23 kDa
Atom Count: 6,009
Modelled Residue Count: 699
Deposited Residue Count: 762
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A	A, B	381	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75164
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PD2 Query on PD2 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	PYRIDINE-2,4-DICARBOXYLIC ACID C₇ H₅ N O₄ MJIVRKPEXXHNJT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
PD2	BindingDB: 2VD7	IC50: 4200 (nM) from 1 assay(s)
PD2	PDBBind: 2VD7	IC50: 4200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.219
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.285	α = 90
b = 149.121	β = 90
c = 57.566	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-11-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-11-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2013-12-11
Changes: Database references, Derived calculations
Version 1.3: 2018-01-24
Changes: Source and taxonomy
Version 1.4: 2018-03-28
Changes: Database references, Source and taxonomy
Version 1.5: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other