4YU1

Human Aldose Reductase complexed with Schl12134 (3-[5-(3-nitrophenyl)-2-thienyl]propanoic acid) at 1.02 A

PDB DOI: https://doi.org/10.2210/pdb4YU1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-18 Released: 2016-03-23
Deposition Author(s): Rechlin, C., Heine, A., Klebe, G.
Funding Organization(s): European Union/ERC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.02 Å
R-Value Free: 0.150
R-Value Work: 0.133
R-Value Observed: 0.134

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Keys to open the specificity pocket: Biphenylic Inhibitors of the human aldose reductase

Rechlin, C., Heine, A., Ortmann, R., Schlitzer, M., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 36.92 kDa
Atom Count: 3,144
Modelled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0 Gene Names: AKR1B1, 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15121
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 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]
53N Query on 53N Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3-[5-(3-nitrophenyl)thiophen-2-yl]propanoic acid C₁₃ H₁₁ N O₄ S IHKCOKRMJRDWAL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.02 Å
R-Value Free: 0.150
R-Value Work: 0.133
R-Value Observed: 0.134
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.449	α = 90
b = 66.354	β = 92.31
c = 47.429	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-23

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union/ERC		268145-DrugProfilBind

Revision History (Full details and data files)

Version 1.0: 2016-03-23
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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.