9W6V | pdb_00009w6v

Crystal structure of 11betaHSD1 in complex with compound 1

PDB DOI: https://doi.org/10.2210/pdb9W6V/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2025-08-05 Released: 2025-10-08
Deposition Author(s): Takahashi, M.
Funding Organization(s): Not funded

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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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 : 118418

DOI: https://doi.org/10.1016/j.bmc.2025.118418

Macromolecule Content

Total Structure Weight: 304.92 kDa
Atom Count: 20,742
Modeled Residue Count: 2,633
Deposited Residue Count: 2,706
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
11-beta-hydroxysteroid dehydrogenase 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	246	Homo sapiens	Mutation(s): 0 Gene Names: HSD11B1, HSD11, HSD11L, SDR26C1 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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 BA [auth I] SDF format, chain DA [auth J] SDF format, chain FA [auth K] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] SDF format, chain T [auth E] SDF format, chain P [auth C] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain T [auth E] MOL2 format, chain P [auth C] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain T [auth E] mmCIF format, chain P [auth C]	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		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]
A1MBC (Subject of Investigation/LOI) Query on A1MBC Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth I] SDF format, chain EA [auth J] SDF format, chain GA [auth K] SDF format, chain O [auth B] SDF format, chain S [auth D] SDF format, chain W [auth F] SDF format, chain Y [auth G] SDF format, chain U [auth E] SDF format, chain Q [auth C] SDF format, chain M [auth A] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain O [auth B] MOL2 format, chain S [auth D] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain U [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain GA [auth K] mmCIF format, chain O [auth B] mmCIF format, chain S [auth D] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain U [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth A]	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		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]