8Y7L

Crystal Structure of Nur77 LBD in complex with N-(2'-(4-hydroxypiperidin-1-yl)-[4,4'-bipyridin]-2-yl)cinnamamide

PDB DOI: https://doi.org/10.2210/pdb8Y7L/pdb

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

Deposited: 2024-02-04 Released: 2024-07-24
Deposition Author(s): Hong, W.B., Lin, T.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.242
R-Value Work: 0.204

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Discovery of a novel exceptionally potent and orally active Nur77 ligand NB1 with a distinct binding mode for cancer therapy

Chen, J., Zhao, T., Hong, W., Li, H., Ao, M., Zhong, Y., Chen, X., Qiu, Y., Wang, X., Wu, Z., Lin, T., Li, B., Chen, X., Fang, M.

(2024) Acta Pharm Sin B

DOI: https://doi.org/10.1016/j.apsb.2024.07.012

Macromolecule Content

Total Structure Weight: 53.41 kDa
Atom Count: 3,721
Modelled Residue Count: 461
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 4immunitygroup A member 1	A, B	238	Homo sapiens	Mutation(s): 0 Gene Names: NR4A1, GFRP1, HMR, NAK1
UniProt & NIH Common Fund Data Resources
Find proteins for P22736 (Homo sapiens) Explore P22736 Go to UniProtKB: P22736
GTEx: ENSG00000123358
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22736
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D59 Query on A1D59 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	(~{E})-~{N}-[4-[2-(4-oxidanylpiperidin-1-yl)pyridin-4-yl]pyridin-2-yl]-3-phenyl-prop-2-enamide C₂₄ H₂₄ N₄ O₂ LLCXZJGKTNDVLE-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.242
R-Value Work: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.781	α = 90
b = 76.125	β = 90
c = 128.813	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.