4IJU | pdb_00004iju

Crystal structure of 11b-HSD1 double mutant (L262R, F278E) in complex with (1S,4S)-4-[8-(2-fluorophenoxy)[1,2,4]triazolo[4,3-a]pyridin-3-yl]bicyclo[2.2.1]heptan-1-ol

PDB DOI: https://doi.org/10.2210/pdb4IJU/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-12-23 Released: 2014-06-11
Deposition Author(s): Sheriff, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.182 (Depositor), 0.177 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Optimization of 1,2,4-Triazolopyridines as Inhibitors of Human 11 beta-Hydroxysteroid Dehydrogenase Type 1 (11 beta-HSD-1).

Li, J., Kennedy, L.J., Wang, H., Li, J.J., Walker, S.J., Hong, Z., O'Connor, S.P., Nayeem, A., Camac, D.M., Morin, P.E., Sheriff, S., Wang, M., Harper, T., Golla, R., Seethala, R., Harrity, T., Ponticiello, R.P., Morgan, N.N., Taylor, J.R., Zebo, R., Gordon, D.A., Robl, J.A.

(2014) Bioorg Med Chem Lett 5: 803-808

PubMed: 25050169 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ml500144h
Primary Citation Related Structures:
4IJU, 4IJV, 4IJW

PubMed Abstract:
Small alkyl groups and spirocyclic-aromatic rings directly attached to the left side and right side of the 1,2,4-triazolopyridines (TZP), respectively, were found to be potent and selective inhibitors of human 11β-hydroxysteroid dehydrogenase-type 1 (11β-HSD-1) enzyme. 3-(1-(4-Chlorophenyl)cyclopropyl)-8-cyclopropyl-[1,2,4]triazolo[4,3-a]pyridine (9f) was identified as a potent inhibitor of the 11β-HSD-1 enzyme with reduced Pregnane-X receptor (PXR) transactivation activity. The binding orientation of this TZP series was revealed by X-ray crystallography structure studies.

Organizational Affiliation

Department of Medicinal Chemistry, Department of Biology, Lead Evaluation, CADD, Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb , Bldg 13, Princeton, New Jersey 08543-5400, United States.

Macromolecule Content

Total Structure Weight: 129.79 kDa
Atom Count: 9,143
Modeled Residue Count: 1,090
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-dehydrogenase isozyme 1	A, B, C [auth D], D [auth E]	286	Homo sapiens	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28845
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 L [auth E] SDF format, chain I [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth E] MOL2 format, chain I [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth E] mmCIF format, chain I [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], I [auth D], L [auth E]	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 I [auth D] Focus chain L [auth E] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth D] Focus chain L [auth E]
1EO Query on 1EO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth D] SDF format, chain M [auth E] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth D] MOL2 format, chain M [auth E] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth D] mmCIF format, chain M [auth E]	F [auth A], H [auth B], J [auth D], M [auth E]	(1s,4s)-4-[8-(2-fluorophenoxy)[1,2,4]triazolo[4,3-a]pyridin-3-yl]bicyclo[2.2.1]heptan-1-ol C₁₉ H₁₈ F N₃ O₂ WEOITARZWXYXSX-KDURUIRLSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth D] Focus chain M [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth D] Focus chain M [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain N [auth E] MOL2 format, chain K [auth D] MOL2 format, chain N [auth E] mmCIF format, chain K [auth D] mmCIF format, chain N [auth E]	K [auth D], N [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth D] Focus chain N [auth E] Interactions & Density Focus chain K [auth D] Focus chain N [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
1EO	BindingDB: 4IJU	IC50: 5.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.218 (Depositor), 0.219 (DCC)
R-Value Work: 0.182 (Depositor), 0.177 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.4	α = 90
b = 94.2	β = 90
c = 167.8	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-06-11

Deposition Author(s):

Sheriff, S.

Revision History (Full details and data files)

Version 1.0: 2014-06-11
Type: Initial release
Version 1.1: 2014-08-06
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description