3U2C | pdb_00003u2c

Aldose reductase in complex with NSAID-type inhibitor at 1.0 A resolution

PDB DOI: https://doi.org/10.2210/pdb3U2C/pdb

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

Deposited: 2011-10-03 Released: 2011-11-02
Deposition Author(s): Steuber, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.138 (Depositor), 0.136 (DCC)
R-Value Work:
0.113 (Depositor), 0.113 (DCC)
R-Value Observed:
0.114 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

An old NSAID revisited: crystal structure of aldose reductase in complex with sulindac at 1.0 A supports a novel mechanism for its anticancer and antiproliferative effects.

Steuber, H.

(2011) ChemMedChem 6: 2155-2157

PubMed: 21997888 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.201100374
Primary Citation Related Structures:
3U2C

Organizational Affiliation

Proteros Biostructures GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany. steuber@proteros.com

Macromolecule Content

Total Structure Weight: 37.95 kDa
Atom Count: 3,040
Modeled Residue Count: 315
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0 Gene Names: AKR1B1, aldose reductase, ALDR1 EC: 1.1.1.21 (PDB Primary Data), 1.1.1.372 (UniProt), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens) Explore P15121 Go to UniProtKB: P15121
PHAROS: P15121 GTEx: ENSG00000085662
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SUZ Query on SUZ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	[(1Z)-5-fluoro-2-methyl-1-{4-[methylsulfinyl]benzylidene}-1H-inden-3-yl]acetic acid C₂₀ H₁₇ F O₃ S MLKXDPUZXIRXEP-LQVWSKNFSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain H [auth A]	C [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain H [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
SUZ	BindingDB: 3U2C	IC50: 293 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.138 (Depositor), 0.136 (DCC)
R-Value Work: 0.113 (Depositor), 0.113 (DCC)
R-Value Observed: 0.114 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.095	α = 90
b = 67.207	β = 92.38
c = 49.419	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-11-02

Deposition Author(s):

Steuber, H.

Revision History (Full details and data files)

Version 1.0: 2011-11-02
Type: Initial release
Version 1.1: 2013-07-03
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description