3PDJ | pdb_00003pdj

Crystal Structure of Human 11-beta-Hydroxysteroid Dehydrogenase 1 (11b-HSD1) in Complex with 4,4-Disubstituted Cyclohexylbenzamide Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3PDJ/pdb

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

Deposited: 2010-10-22 Released: 2011-10-05
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.241 (Depositor), 0.234 (DCC)
R-Value Work:
0.211 (Depositor), 0.204 (DCC)
R-Value Observed:
0.212 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Synthesis and Optimization of Novel 4,4-Disubstituted Cyclohexylbenzamide Derivatives as Potent 11beta-HSD1 Inhibitors

Sun, D., Wang, Z., Caille, S., DeGraffenreid, M., Gonzalez-Lopez de Turiso, F., Hungate, R., Jaen, J.C., Jiang, B., Julian, L.D., Kelly, R., McMinn, D.L., Kaizerman, J., Rew, Y., Sudom, A., Tu, H., Ursu, S., Walker, N., Willcockson, M., Yan, X., Ye, Q., Powers, J.P.

(2011) Bioorg Med Chem Lett 21: 405-410

PubMed: 21093258 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.10.129
Primary Citation Related Structures:
3PDJ

PubMed Abstract:
The synthesis and SAR of a series of 4,4-disubstituted cyclohexylbenzamide inhibitors of 11β-HSD1 are described. Optimization rapidly led to potent, highly selective, and orally bioavailable inhibitors demonstrating efficacy in both rat and non-human primate ex vivo pharmacodynamic models.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 62.71 kDa
Atom Count: 4,549
Modeled Residue Count: 544
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-dehydrogenase isozyme 1	A, B	273	Homo sapiens	Mutation(s): 1 Gene Names: HSD11, HSD11B1, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28845
Sequence Annotations Expand
Reference Sequence

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 F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
3PJ Query on 3PJ Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	N-[trans-4-(3-amino-3-oxopropyl)-4-phenylcyclohexyl]-N-cyclopropyl-4-[(1S)-2,2,2-trifluoro-1-hydroxy-1-methylethyl]benzamide C₂₈ H₃₃ F₃ N₂ O₃ GGXWRFSOCBTDDI-YGPDHOBYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.241 (Depositor), 0.234 (DCC)
R-Value Work: 0.211 (Depositor), 0.204 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.044	α = 90
b = 107.044	β = 90
c = 132.918	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-05
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.