2IRW | pdb_00002irw

Human 11-beta-Hydroxysteroid Dehydrogenase (HSD1) with NADP and Adamantane Ether Inhibitor

PDB DOI: https://doi.org/10.2210/pdb2IRW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2006-10-16 Released: 2007-01-23
Deposition Author(s): Longenecker, K.L., Patel, J.R., Russell, J., Qin, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.278 (Depositor), 0.273 (DCC)
R-Value Work:
0.237 (Depositor), 0.230 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Discovery of adamantane ethers as inhibitors of 11beta-HSD-1: Synthesis and biological evaluation.

Patel, J.R., Shuai, Q., Dinges, J., Winn, M., Pliushchev, M., Fung, S., Monzon, K., Chiou, W., Wang, J., Pan, L., Wagaw, S., Engstrom, K., Kerdesky, F.A., Longenecker, K., Judge, R., Qin, W., Imade, H.M., Stolarik, D., Beno, D.W., Brune, M., Chovan, L.E., Sham, H.L., Jacobson, P., Link, J.T.

(2007) Bioorg Med Chem Lett 17: 750-755

PubMed: 17110106 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.10.074
Primary Citation Related Structures:
2IRW

PubMed Abstract:
A novel class of adamantane ethers 11beta-hydroxysteroid hydrogenase type I inhibitors has been discovered. These compounds have excellent HSD-1 potency and selectivity against HSD-2. The structure-activity relationships, selectivity, metabolism, PK, ex vivo pharmacodynamic data, and an X-ray crystal structure of one of these inhibitors bound to h-HSD-1 are discussed.

Organizational Affiliation

Global Pharmaceutical Research & Development, Abbott Laboratories, R43G, AP52, 200 Abbott Park Road, Abbott Park, IL-60064-6217, USA. jyoti.patel@abbott.com

Macromolecule Content

Total Structure Weight: 241.37 kDa
Atom Count: 16,728
Modeled Residue Count: 2,098
Deposited Residue Count: 2,112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-dehydrogenase isozyme 1	A, B, C, D, E A, B, C, D, E, F, G, H	264	Homo sapiens	Mutation(s): 0 Gene Names: HSD11B1 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 I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] MOL2 format, chain O [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H] mmCIF format, chain O [auth D]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
NN4 Query on NN4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain P [auth D] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] SDF format, chain R [auth E] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] MOL2 format, chain R [auth E] MOL2 format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H] mmCIF format, chain R [auth E] mmCIF format, chain N [auth C]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	(1S,3R,4S,5S,7S)-4-{[2-(4-METHOXYPHENOXY)-2-METHYLPROPANOYL]AMINO}ADAMANTANE-1-CARBOXAMIDE C₂₂ H₃₀ N₂ O₄ MNVKIDPRYUGTTG-YINOZDTMSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.278 (Depositor), 0.273 (DCC)
R-Value Work: 0.237 (Depositor), 0.230 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.537	α = 90
b = 184.537	β = 90
c = 558.052	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-01-23
Type: Initial release
Version 1.1: 2007-10-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Refinement description

2IRW | pdb_00002irw

Human 11-beta-Hydroxysteroid Dehydrogenase (HSD1) with NADP and Adamantane Ether Inhibitor

Literature

Discovery of adamantane ethers as inhibitors of 11beta-HSD-1: Synthesis and biological evaluation.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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