2IRW | pdb_00002irw

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.278 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

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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

  • DOI: https://doi.org/10.1016/j.bmcl.2006.10.074
  • Primary Citation of 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

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Corticosteroid 11-beta-dehydrogenase isozyme 1
A, B, C, D, E
A, B, C, D, E, F, G, H
264Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28845
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
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
NN4
Query on NN4
Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.278 (Depositor), 0.270 (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 = 184.537α = 90
b = 184.537β = 90
c = 558.052γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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