5K4L

Crystal structure of KDM5A in complex with a naphthyridone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5K4L/pdb

• Classification: Oxidoreductase/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-05-20 Released: 2016-08-10 
• Deposition Author(s): Kiefer, J.R., Vinogradova, M.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.257 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors.

Labadie, S.S., Dragovich, P.S., Cummings, R.T., Deshmukh, G., Gustafson, A., Han, N., Harmange, J.C., Kiefer, J.R., Li, Y., Liang, J., Liederer, B.M., Liu, Y., Manieri, W., Mao, W., Murray, L., Ortwine, D.F., Trojer, P., VanderPorten, E., Vinogradova, M., Wen, L.

(2016) Bioorg Med Chem Lett 26: 4492-4496

• PubMed: 27499454 
• DOI: https://doi.org/10.1016/j.bmcl.2016.07.070
• Primary Citation of Related Structures:  
  5K4L


• PubMed Abstract: 
  

  Features from a high throughput screening (HTS) hit and a previously reported scaffold were combined to generate 1,7-naphthyridones as novel KDM5 enzyme inhibitors with nanomolar potencies. These molecules exhibited high selectivity over the related KDM4C and KDM2B isoforms. An X-ray co-crystal structure of a representative molecule bound to KDM5A showed that these inhibitors are competitive with the co-substrate (2-oxoglutarate or 2-OG).

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Organizational Affiliation: 

Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 183.99 kDa 
• Atom Count: 9,348 
• Modelled Residue Count: 1,174 
• Deposited Residue Count: 1,600 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5A	A, B	790	Homo sapiens	Mutation(s): 0  Gene Names: KDM5A, JARID1A, RBBP2, RBP2 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P29375 (Homo sapiens) Explore P29375  Go to UniProtKB:  P29375
PHAROS:  P29375 GTEx:  ENSG00000073614

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Peptide	C [auth F], D [auth G]	10	Homo sapiens	Mutation(s): 0  Gene Names: KDM5A, JARID1A, RBBP2, RBP2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6QN	H [auth A], L [auth B]	~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide C11 H11 N3 O3 RTMUDFJHLBNEDM-UHFFFAOYSA-N
ZN	F [auth A], G [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	E [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.257 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.141	α = 90
b = 159.141	β = 90
c = 92.109	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Kiefer, J.R., Vinogradova, M.V.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Database references
• Version 1.2: 2016-09-07
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary