4NMH | pdb_00004nmh

11-beta-HSD1 in complex with a 3,3-Di-methyl-azetidin-2-one

PDB DOI: https://doi.org/10.2210/pdb4NMH/pdb

Classification: oxidoreductase/oxidoreductase INHIBITOR
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-11-15 Released: 2014-03-26
Deposition Author(s): McCoull, W., Augustin, M., Blake, C., Ertan, A., Kilgour, E.K., Krapp, S., Moore, J.E., Newcombe, N.J., Packer, M.J., Rees, A., Revill, J., Scott, J.S., Selmi, N., Gerhardt, S., Ogg, D.J., Steinbacher, S., Whittamore, P.R.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.251 (Depositor), 0.256 (DCC)
R-Value Work:
0.199 (Depositor), 0.203 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification and optimisation of 3,3-dimethyl-azetidin-2-ones as potent and selective inhibitors of 11 beta-hydroxysteroid dehydrogenase type 1 (11-beta-HSD1)

McCoull, W., Augustin, M., Blake, C., Ertan, A., Kilgour, E.K., Krapp, S., Moore, J.E., Newcombe, N.J., Packer, M.J., Rees, A., Revill, J., Scott, J.S., Selmi, N., Gerhardt, S., Ogg, D.J., Steinbacher, S., Whittamore, P.R.O.

To be published.

Macromolecule Content

Total Structure Weight: 136.62 kDa
Atom Count: 8,506
Modeled Residue Count: 1,058
Deposited Residue Count: 1,184
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, D	296	Mus musculus	Mutation(s): 3 Gene Names: Hsd11b1, Hsd11 EC: 1.1.1.146 (PDB Primary Data), 1.1.1.201 (UniProt)
UniProt
Find proteins for P50172 (Mus musculus) Explore P50172 Go to UniProtKB: P50172
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50172
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	F [auth A], I [auth B], M [auth C], Q [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
2KG Query on 2KG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], H [auth B], L [auth C], P [auth D]	(4S)-4-(2-methoxyphenyl)-3,3-dimethyl-1-[3-(methylsulfonyl)phenyl]azetidin-2-one C₁₉ H₂₁ N O₄ S JTEHJTAGXBHCOJ-KRWDZBQOSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain G [auth A]	G [auth A] J [auth B] K [auth B] N [auth C] O [auth C] G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.251 (Depositor), 0.256 (DCC)
R-Value Work: 0.199 (Depositor), 0.203 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.132	α = 90
b = 70.842	β = 91.67
c = 95.653	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description