6BGW

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(4,4-difluoropiperidin-1-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N41)

PDB DOI: https://doi.org/10.2210/pdb6BGW/pdb

Classification: OXIDOREDUCTASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-10-29 Released: 2018-03-28
Deposition Author(s): Horton, J.R., Cheng, X.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.213
R-Value Work: 0.188
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.

Horton, J.R., Liu, X., Wu, L., Zhang, K., Shanks, J., Zhang, X., Rai, G., Mott, B.T., Jansen, D.J., Kales, S.C., Henderson, M.J., Pohida, K., Fang, Y., Hu, X., Jadhav, A., Maloney, D.J., Hall, M.D., Simeonov, A., Fu, H., Vertino, P.M., Yan, Q., Cheng, X.

(2018) J Med Chem 61: 3193-3208

PubMed: 29537847 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.8b00261
Primary Citation of Related Structures:
6BGU, 6BGV, 6BGW, 6BGX, 6BGY, 6BGZ, 6BH0, 6BH1, 6BH2, 6BH3, 6BH4, 6BH5

PubMed Abstract:

Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, namely, ( R)- and ( S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1 H-pyrrolo[3,2- b]pyridine-7-carboxylic acid (compounds N51 and N52) and ( R) - and ( S) -N-(1-(3-isopropyl-1 H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (compounds N54 and N55). In vitro, the S enantiomer of the N51/N52 pair (N52) and the R enantiomer of the N54/N55 pair (N54) exhibited about 4- to 5-fold greater binding affinity. The more potent enzyme inhibition of KDM5A by the R-isoform for the cell-permeable N54/N55 pair translated to differences in growth inhibitory activity. We determined structures of the KDM5A catalytic domain in complex with all 12 inhibitors, which revealed the interactions (or lack thereof) responsible for the differences in binding affinity. These results provide insights to guide improvements in binding potency and avenues for development of cell permeable inhibitors of the KDM5 family.

Related Citations:

Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Horton, J.R., Liu, X., Gale, M., Wu, L., Shanks, J.R., Zhang, X., Webber, P.J., Bell, J.S., Kales, S.C., Mott, B.T., Rai, G., Jansen, D.J., Henderson, M.J., Urban, D.J., Hall, M.D., Simeonov, A., Maloney, D.J., Johns, M.A., Fu, H., Jadhav, A., Vertino, P.M., Yan, Q., Cheng, X.
(2016) Cell Chem Biol 23: 769

Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases.
Horton, J.R., Engstrom, A., Zoeller, E.L., Liu, X., Shanks, J.R., Zhang, X., Johns, M.A., Vertino, P.M., Fu, H., Cheng, X.
(2016) J Biol Chem 291: 2631

Organizational Affiliation:

Department of Biochemistry , Emory University School of Medicine , Atlanta , Georgia 30322 , United States.

Macromolecule Content

Total Structure Weight: 38.99 kDa
Atom Count: 2,731
Modelled Residue Count: 309
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5A, linked KDM5A JMJ domain	A	330	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29375
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DKS (Subject of Investigation/LOI) Query on DKS Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-{(S)-(2-chlorophenyl)[2-(4,4-difluoropiperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid C₂₂ H₂₂ Cl F₂ N₃ O₃ QCUMGQXPGZQHID-FQEVSTJZSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
DKS	Binding MOAD: 6BGW	Kd: 210 (nM) from 1 assay(s)
	BindingDB: 6BGW	Kd: 210 (nM) from 1 assay(s)
	BindingDB: 6BGW	IC50: 4500 (nM) from 1 assay(s)