4PUW | pdb_00004puw

Human Aldose Reductase complexed with a ligand with an IDD structure (2-[5-fluoro-2-(prop-2-ynylcarbamoyl)phenoxy]acetic acid) at 1.12 A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 
    0.157 (Depositor), 0.157 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.137 (DCC) 
  • R-Value Observed: 
    0.138 (Depositor) 

Starting Model: experimental
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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

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: 37.09 kDa 
  • Atom Count: 3,063 
  • Modeled Residue Count: 316 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aldose reductase316Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP


Download:Ideal Coordinates CCD File
D [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
2WQ

Query on 2WQ


Download:Ideal Coordinates CCD File
B [auth A][5-fluoro-2-(prop-2-yn-1-ylcarbamoyl)phenoxy]acetic acid
C12 H10 F N O4
PZTOBGBKDQCKIG-UHFFFAOYSA-N
CIT

Query on CIT


Download:Ideal Coordinates CCD File
C [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2WQ BindingDB:  4PUW ΔG: min: -4.62e+1, max: 7.99 (kJ/mol) from 8 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free:  0.157 (Depositor), 0.157 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.137 (DCC) 
  • R-Value Observed: 0.138 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.411α = 90
b = 66.688β = 92.02
c = 47.353γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description