4YYZ | pdb_00004yyz

11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb4YYZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2015-03-24 Released: 2016-02-03
Deposition Author(s): Branden, G., Boden, C., Ogg, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.267 (Depositor), 0.265 (DCC)
R-Value Work:
0.218 (Depositor)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Design of pyrozolo-pyrimidines as 11beta-HSD1 inhibitors through optimisation of molecular electrostatic potential.

Robb, G.R., Boyd, S., Davies, C.D., Dossiter, A.G., Goldberg, F.W., Kemmitt, P.D., Scott, J.S., Swales, J.G.

(2016) Medchemcomm 6: 926-934

DOI: https://doi.org/10.1039/C5MD00043B

Macromolecule Content

Total Structure Weight: 58.94 kDa
Atom Count: 4,106
Modeled Residue Count: 517
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-dehydrogenase isozyme 1	A, B	259	Homo sapiens	Mutation(s): 0 Gene Names: HSD11B1, HSD11, HSD11L 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 E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B]
4JX Query on 4JX Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-5,7-dimethylpyrazolo[1,5-a]pyrimidine-3-carboxamide C₁₉ H₂₄ N₄ O₂ XAKHQMQFIBQWBI-VTPCDMJMSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.267 (Depositor), 0.265 (DCC)
R-Value Work: 0.218 (Depositor)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.788	α = 90
b = 107.788	β = 90
c = 136.02	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-03
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.