5FP7

Crystal structure of human KDM4D in complex with 3-4-methylthiophen-2- yl methylaminopyridine-4-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb5FP7/pdb

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


• Deposited: 2015-11-27 Released: 2016-11-09 
• Deposition Author(s): Chung, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 2. Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives.

Westaway, S.M., Preston, A.G., Barker, M.D., Brown, F., Brown, J.A., Campbell, M., Chung, C.W., Drewes, G., Eagle, R., Garton, N., Gordon, L., Haslam, C., Hayhow, T.G., Humphreys, P.G., Joberty, G., Katso, R., Kruidenier, L., Leveridge, M., Pemberton, M., Rioja, I., Seal, G.A., Shipley, T., Singh, O., Suckling, C.J., Taylor, J., Thomas, P., Wilson, D.M., Lee, K., Prinjha, R.K.

(2016) J Med Chem 59: 1370-1387

• PubMed: 26771203 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01538
• Primary Citation of Related Structures:  
  5FP7


• PubMed Abstract: 
  

  Following the discovery of cell penetrant pyridine-4-carboxylate inhibitors of the KDM4 (JMJD2) and KDM5 (JARID1) families of histone lysine demethylases (e.g., 1), further optimization led to the identification of non-carboxylate inhibitors derived from pyrido[3,4-d]pyrimidin-4(3H)-one. A number of exemplars such as compound 41 possess interesting activity profiles in KDM4C and KDM5C biochemical and target-specific, cellular mechanistic assays.

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Organizational Affiliation: 

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.89 kDa 
• Atom Count: 3,276 
• Modelled Residue Count: 330 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4D	A	334	Homo sapiens	Mutation(s): 0  EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens) Explore Q6B0I6  Go to UniProtKB:  Q6B0I6
PHAROS:  Q6B0I6 GTEx:  ENSG00000186280

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YC8	G [auth A]	3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid C16 H16 N2 O3 FLWYUGQMDDTDDS-UHFFFAOYSA-N
SO4	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YC8	BindingDB:  5FP7	IC50: 251 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.41	α = 90
b = 71.41	β = 90
c = 150.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Chung, C.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other