5FP9 | pdb_00005fp9

Crystal structure of human KDM4D in complex with 3-aminopyridine-4- carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb5FP9/pdb

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

Deposited: 2015-11-27 Released: 2016-01-27
Deposition Author(s): Chung, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.211 (Depositor), 0.223 (DCC)
R-Value Work:
0.157 (Depositor), 0.169 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives.

Westaway, S.M., Preston, A.G.S., Barker, M.D., Brown, F., Brown, J.A., Campbell, M., Chung, C., Diallo, H., Douault, C., Drewes, G., Eagle, R., Gordon, L., Haslam, C., Hayhow, T.G., Humphreys, P.G., Joberty, G., Katso, R., Kruidenier, L., Leveridge, M., Liddle, J., Mosley, J., Muelbaier, M., Randle, R., Rioja, I., Rueger, A., Seal, G.A., Sheppard, R.J., Singh, O., Taylor, J., Thomas, P., Thomson, D., Wilson, D.M., Lee, K., Prinjha, R.K.

(2016) J Med Chem 59: 1357

PubMed: 26771107 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5b01537
Primary Citation Related Structures:
5FP3, 5FP4, 5FP8, 5FP9, 5FPA, 5FPB

PubMed Abstract:
Optimization of KDM6B (JMJD3) HTS hit 12 led to the identification of 3-((furan-2-ylmethyl)amino)pyridine-4-carboxylic acid 34 and 3-(((3-methylthiophen-2-yl)methyl)amino)pyridine-4-carboxylic acid 39 that are inhibitors of the KDM4 (JMJD2) family of histone lysine demethylases. Compounds 34 and 39 possess activity, IC50 ≤ 100 nM, in KDM4 family biochemical (RFMS) assays with ≥ 50-fold selectivity against KDM6B and activity in a mechanistic KDM4C cell imaging assay (IC50 = 6-8 μM). Compounds 34 and 39 are also potent inhibitors of KDM5C (JARID1C) (RFMS IC50 = 100-125 nM).

Organizational Affiliation

Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K.

Macromolecule Content

Total Structure Weight: 39.58 kDa
Atom Count: 3,333
Modeled Residue Count: 327
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN LYSINE-SPECIFIC DEMETHYLASE 4D JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI DOMAIN-CONTAINING PROTEIN 2D, JMJD2D	A	334	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B0I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4SV Query on 4SV Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3-AMINOPYRIDINE-4-CARBOXYLIC ACID C₆ H₆ N₂ O₂ FYEQKMAVRYRMBL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CO Query on CO 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]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX Query on CSX	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
4SV	BindingDB: 5FP9	IC50: 1585 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.211 (Depositor), 0.223 (DCC)
R-Value Work: 0.157 (Depositor), 0.169 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.416	α = 90
b = 71.416	β = 90
c = 150.292	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Chung, C.

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 1.1: 2016-03-09
Changes: Database references
Version 1.2: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary