9W6V | pdb_00009w6v

Crystal structure of 11betaHSD1 in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-based design, synthesis, and evaluation of tetrahydrotriazolothiazepine derivatives as novel 11 beta-hydroxysteroid dehydrogenase type 1 inhibitors.

Numata, Y.Hasegawa, T.Mori, M.Shinozuka, T.Yamamoto, Y.Honzumi, M.Kanayama, C.Aoyagi, A.Abe, M.Ofune, Y.Suzuki, K.Imamura, Y.Yahara, C.Obuchi, W.Moritomo, A.Takahashi, M.

(2025) Bioorg Med Chem 132: 118418-118418

  • DOI: https://doi.org/10.1016/j.bmc.2025.118418
  • Primary Citation of Related Structures:  
    9W6V

  • PubMed Abstract: 

    11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) is an enzyme that converts cortisone to cortisol, and the therapeutic inhibition of this enzyme has attracted substantial attention for the treatment of various disorders including metabolic syndrome, cognitive decline, skin diseases, liver fibrosis, glaucoma, and osteoporosis. With the aim of developing a novel and potent 11β-HSD1 inhibitor, we designed and synthesized a series of tetrahydrotriazolothiazepine derivatives containing a sulfur atom in the seven-membered ring. An optimization study guided by structure-based drug design led to the discovery of compound 3f as a potent and orally bioavailable 11β-HSD1 inhibitor. The oral administration of 3f demonstrated good pharmacokinetic profiles and in vivo inhibition of 11β-HSD1 in mice and monkeys.


  • Organizational Affiliation
    • R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. Electronic address: yukinobu.numata@daiichisankyo.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
11-beta-hydroxysteroid dehydrogenase 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K
246Homo sapiensMutation(s): 0 
Gene Names: HSD11B1HSD11HSD11LSDR26C1
EC: 1.1.1.146 (PDB Primary Data), 1.1.1.201 (PDB Primary Data)
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 
BA [auth I]
DA [auth J]
FA [auth K]
L [auth A]
N [auth B]
BA [auth I],
DA [auth J],
FA [auth K],
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
A1MBC (Subject of Investigation/LOI)
Query on A1MBC

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
EA [auth J]
GA [auth K]
M [auth A]
AA [auth H],
CA [auth I],
EA [auth J],
GA [auth K],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
3-(1-adamantyl)-6,7,8,9-tetrahydro-5~{H}-[1,2,4]triazolo[4,3-a]azepine
C17 H25 N3
VFTQRHWULYJKCI-ZZNDEYBLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 308.09α = 90
b = 99.37β = 104.14
c = 136.245γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Database references