4RPQ

Human Aldose Reductase complexed with a ligand with an IDD structure at 1.20 A (1)

PDB DOI: https://doi.org/10.2210/pdb4RPQ/pdb

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

Deposited: 2014-10-31 Released: 2015-11-18
Deposition Author(s): Rechlin, C., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.165
R-Value Work: 0.142
R-Value Observed: 0.143

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Aldose Reductase: IDD ligands under investigation

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

To be published.

Macromolecule Content

Total Structure Weight: 36.92 kDa
Atom Count: 2,866
Modelled Residue Count: 314
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 C [auth A] MOL2 format, chain C [auth A]	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
3UH Query on 3UH Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	({3-[(3-nitrobenzyl)carbamoyl]biphenyl-4-yl}oxy)acetic acid C₂₂ H₁₈ N₂ O₆ YDJQSGAIAXGWHG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3UH	BindingDB: 4RPQ	Kd: 15 (nM) from 1 assay(s)
		-TΔS: -1.23e+1 (kJ/mol) from 1 assay(s)
		ΔH: -5.58e+1 (kJ/mol) from 1 assay(s)
		ΔG: -4.35e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.165
R-Value Work: 0.142
R-Value Observed: 0.143
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.554	α = 90
b = 66.796	β = 93.08
c = 47.191	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: 2015-11-18

Deposition Author(s):

Rechlin, C.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2015-11-18
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

4RPQ

Human Aldose Reductase complexed with a ligand with an IDD structure at 1.20 A (1)

Aldose Reductase: 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)