6DQC | pdb_00006dqc

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N50 i.e. 2-(4-((2-(dimethylamino)ethyl)(ethyl)carbamoyl)-5-(4-methoxyphenyl)-1H-pyrazol-1-yl)isonicotinic acid

PDB DOI: https://doi.org/10.2210/pdb6DQC/pdb

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

Deposited: 2018-06-10 Released: 2019-06-12
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: 1.75 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

To be determined

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

To be published.

Macromolecule Content

Total Structure Weight: 38.7 kDa
Atom Count: 2,682
Modeled Residue Count: 311
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H5Y (Subject of Investigation/LOI) Query on H5Y 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]	2-[4-{[2-(dimethylamino)ethyl](ethyl)carbamoyl}-5-(4-methoxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid C₂₃ H₂₇ N₅ O₄ ICCHWGKLRKRQKD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.215 (Depositor), 0.216 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.135	α = 90
b = 62.033	β = 92.21
c = 46.661	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Horton, J.R.

Cheng, X.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM049245-23

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description