Macromolecule Content

Total Structure Weight: 82.4 kDa
Atom Count: 4,823
Modelled Residue Count: 645
Deposited Residue Count: 714
Unique protein chains: 1

6A6K

Crystal structure of Estrogen-related Receptor-3 (ERR-gamma) ligand binding domain with DN201000

PDB DOI: https://doi.org/10.2210/pdb6A6K/pdb

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

Deposited: 2018-06-28 Released: 2019-04-10
Deposition Author(s): Yoon, H., Kim, J., Chin, J., Cho, S.J., Song, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.263
R-Value Work: 0.201
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of Potent, Selective, and Orally Bioavailable Estrogen-Related Receptor-gamma Inverse Agonists To Restore the Sodium Iodide Symporter Function in Anaplastic Thyroid Cancer.

Kim, J., Song, J., Ji, H.D., Yoo, E.K., Lee, J.E., Lee, S.B., Oh, J.M., Lee, S., Hwang, J.S., Yoon, H., Kim, D.S., Lee, S.J., Jeong, M., Lee, S., Kim, K.H., Choi, H.S., Lee, S.W., Park, K.G., Lee, I.K., Kim, S.H., Hwang, H., Jeon, Y.H., Chin, J., Cho, S.J.

(2019) J Med Chem 62: 1837-1858

PubMed: 30657313 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.8b01296
Primary Citation of Related Structures:
6A6K

PubMed Abstract:

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen-related receptor gamma	A, B, C	238	Homo sapiens	Mutation(s): 0 Gene Names: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens) Explore P62508 Go to UniProtKB: P62508
PHAROS: P62508
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62508
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9S6 Query on 9S6 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	3-[(~{E})-5-oxidanyl-2-phenyl-1-[4-(4-propan-2-ylpiperazin-1-yl)phenyl]pent-1-enyl]phenol C₃₀ H₃₆ N₂ O₂ MVDJTCFLEZIJEJ-QVIHXGFCSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.263
R-Value Work: 0.201
R-Value Observed: 0.204
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.828	α = 90
b = 78.571	β = 109.19
c = 106.963	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.