3PDQ

Crystal structure of JMJD2A complexed with bipyridyl inhibitor

PDB DOI: https://doi.org/10.2210/pdb3PDQ/pdb

Classification: Oxidoreductase/Oxidoreductase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-10-23 Released: 2011-03-30
Deposition Author(s): King, O.N.F., Chang, K.-H., Rose, N.R., Clifton, I.J., McDonough, M.A., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.207
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds

Chang, K.-H., King, O.N.F., Tumber, A., Woon, E.C., Heightman, T.D., McDonough, M.A., Schofield, C.J., Rose, N.R.

(2011) ChemMedChem 6: 759-764

PubMed: 21412984 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cmdc.201100026
Primary Citation of Related Structures:
3PDQ

Organizational Affiliation

Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom.

Macromolecule Content

Total Structure Weight: 89.7 kDa
Atom Count: 6,360
Modelled Residue Count: 701
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
Lysine-specific demethylase 4A	A, B	381	Homo sapiens	Mutation(s): 0 Gene Names: KDM4A EC: 1.14.11
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KC6 Query on KC6 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B]	E [auth A], M [auth B]	4'-[(2-aminoethyl)carbamoyl]-2,2'-bipyridine-4-carboxylic acid C₁₄ H₁₄ N₄ O₃ RTGDPYNAIULBPL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B]	D [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B]	C [auth A], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B]	F [auth A], G [auth A], H [auth A], J [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B]	I [auth A], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
KC6	PDBBind: 3PDQ	IC50: 180 (nM) from 1 assay(s)
KC6	Binding MOAD: 3PDQ	IC50: 180 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.207
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.77	α = 90
b = 149.44	β = 90
c = 57.3	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-03-26
Changes: Database references
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3PDQ

Crystal structure of JMJD2A complexed with bipyridyl inhibitor

Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)