5CJ6 | pdb_00005cj6

Crystal Structure of a Selective Androgen Receptor Modulator Bound to the Ligand Binding Domain of the Human Androgen Receptor

PDB DOI: https://doi.org/10.2210/pdb5CJ6/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-07-14 Released: 2016-01-06
Deposition Author(s): Luz, J.G., Saeed, A., Wang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2-Chloro-4-[[(1R,2R)-2-hydroxy-2-methyl-cyclopentyl]amino]-3-methyl-benzonitrile: A Transdermal Selective Androgen Receptor Modulator (SARM) for Muscle Atrophy.

Saeed, A., Vaught, G.M., Gavardinas, K., Matthews, D., Green, J.E., Losada, P.G., Bullock, H.A., Calvert, N.A., Patel, N.J., Sweetana, S.A., Krishnan, V., Henck, J.W., Luz, J.G., Wang, Y., Jadhav, P.

(2016) J Med Chem 59: 750-755

PubMed: 26683992 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5b01168
Primary Citation Related Structures:
5CJ6

PubMed Abstract:
A transdermal SARM has a potential to have therapeutic benefit through anabolic activity in muscle while sparing undesired effects of benign prostate hyperplasia (BPH) and liver-mediated decrease in HDL-C. 2-Chloro-4-[(2-hydroxy-2-methyl-cyclopentyl)amino]-3-methyl-benzonitrile 6 showed the desired muscle and prostate effects in a preclinical ORX rat model. Compound 6 had minimal effect on HDL-C levels in cynomolgus monkeys and showed human cadaver skin permeability, thus making it an effective tool for proof-of-concept studies in a clinical setting.

Organizational Affiliation

Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center, Indianapolis, Indiana 46285, United States.

Macromolecule Content

Total Structure Weight: 34.06 kDa
Atom Count: 2,233
Modeled Residue Count: 254
Deposited Residue Count: 293
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Androgen receptor	A	283	Homo sapiens	Mutation(s): 0 Gene Names: AR, DHTR, NR3C4
UniProt & NIH Common Fund Data Resources
Find proteins for P10275 (Homo sapiens) Explore P10275 Go to UniProtKB: P10275
PHAROS: P10275 GTEx: ENSG00000169083
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10275
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
small peptide	B	10	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10275 (Homo sapiens) Explore P10275 Go to UniProtKB: P10275
PHAROS: P10275 GTEx: ENSG00000169083
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10275
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
51Y Query on 51Y 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]	2-chloro-4-{[(1R,2R)-2-hydroxy-2-methylcyclopentyl]amino}-3-methylbenzonitrile C₁₄ H₁₇ Cl N₂ O CXFSVKGROITHRY-TZMCWYRMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
51Y	BindingDB: 5CJ6	Ki: 2 (nM) from 1 assay(s)
51Y	BindingDB: 5CJ6	EC50: 0.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.222 (Depositor), 0.222 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.803	α = 90
b = 65.997	β = 90
c = 73.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-01-06

Deposition Author(s):

Luz, J.G.

Saeed, A.

Wang, Y.

Revision History (Full details and data files)

Version 1.0: 2016-01-06
Type: Initial release
Version 1.1: 2016-01-20
Changes: Database references
Version 1.2: 2016-02-10
Changes: Database references
Version 1.3: 2024-03-06
Changes: Data collection, Database references, Derived calculations