3OQ1

Crystal Structure of 11beta-Hydroxysteroid Dehydrogenase-1 (11b-HSD1) in Complex with Diarylsulfone Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3OQ1/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-09-02 Released: 2011-07-20
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.308 (Depositor), 0.300 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The synthesis and SAR of novel diarylsulfone 11beta-HSD1 inhibitors

Yan, X., Wang, Z., Sudom, A., Cardozo, M., DeGraffenreid, M., Di, Y., Fan, P., He, X., Jaen, J.C., Labelle, M., Liu, J., Ma, J., McMinn, D., Miao, S., Sun, D., Tang, L., Tu, H., Ursu, S., Walker, N., Ye, Q., Powers, J.P.

(2010) Bioorg Med Chem Lett 20: 7071-7075

PubMed: 20971000 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.09.097
Primary Citation of Related Structures:
3OQ1

PubMed Abstract:
In this communication, human 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) inhibitory activities of a novel series of diarylsulfones are described. Optimization of this series resulted in several highly potent 11β-HSD1 inhibitors with excellent pharmacokinetic (PK) properties. Compound (S)-25 showed excellent efficacy in a non-human primate ex vivo pharmacodynamic model.

Organizational Affiliation

Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA. xueleiy@amgen.com

Macromolecule Content

Total Structure Weight: 131.93 kDa
Atom Count: 8,469
Modelled Residue Count: 1,058
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-dehydrogenase isozyme 1	A, B, C, D	286	Homo sapiens	Mutation(s): 1 Gene Names: HSD11B1, HSD11, HSD11L EC: 1.1.1.146 (PDB Primary Data), 1.1.1.201 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28845 (Homo sapiens) Explore P28845 Go to UniProtKB: P28845
PHAROS: P28845 GTEx: ENSG00000117594
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28845
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
3OQ Query on 3OQ Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain F [auth A] SDF format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C]	F [auth A], H [auth B], I [auth C], K [auth D]	3-(2-fluoroethyl)-4-({4-[(2S)-1,1,1-trifluoro-2-hydroxypropan-2-yl]phenyl}sulfonyl)benzonitrile C₁₈ H₁₅ F₄ N O₃ S HRHAWLGWRWLWQL-KRWDZBQOSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.308 (Depositor), 0.300 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.303	α = 90
b = 153.398	β = 92.4
c = 73.593	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Wang, Z.

Sudom, A.

Walker, N.P.

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2012-12-05
Changes: Non-polymer description
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations