4Q7B

Human Aldose Reductase complexed with a ligand with an IDD structure ([2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid) at 1.19 A

PDB DOI: https://doi.org/10.2210/pdb4Q7B/pdb

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

Deposited: 2014-04-24 Released: 2015-06-10
Deposition Author(s): Rechlin, C., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free: 0.160
R-Value Work: 0.138
R-Value Observed: 0.139

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Aldose Reductase: How expensive is the opening of the specificity pocket? IDD ligands under investigation

Rechlin, C., Heine, A., Scheer, F., Toth, P., Diederich, W., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 36.81 kDa
Atom Count: 2,995
Modelled Residue Count: 315
Deposited Residue Count: 315
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	315	Homo sapiens	Mutation(s): 0 Gene Names: AKR1B1, ALDR1 EC: 1.1.1.21
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]	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]
2YZ Query on 2YZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	[2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid C₁₆ H₁₄ F N O₄ RQCSQAIXIUJOJU-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: 1.19 Å
R-Value Free: 0.160
R-Value Work: 0.138
R-Value Observed: 0.139
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.317	α = 90
b = 66.739	β = 92.07
c = 47.254	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Rechlin, C.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4Q7B

Human Aldose Reductase complexed with a ligand with an IDD structure ([2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid) at 1.19 A

Aldose Reductase: How expensive is the opening of the specificity pocket? IDD ligands under investigation

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)