5K4L | pdb_00005k4l

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free:
0.257 (Depositor), 0.267 (DCC)
R-Value Work:
0.222 (Depositor), 0.232 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2016.07.070
Primary Citation 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).

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29375
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
6QN Query on 6QN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	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		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
6QN	BindingDB: 5K4L	IC50: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.257 (Depositor), 0.267 (DCC)
R-Value Work: 0.222 (Depositor), 0.232 (DCC)
R-Value Observed: 0.224 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Kiefer, J.R.

Vinogradova, M.V.

Revision History (Full details and data files)

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