4PUU | pdb_00004puu

Human Aldose Reductase complexed with a ligand with an IDD structure (2-(2-carbamoyl-5-fluoro-phenoxy)acetic acid) at 1.14 A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 
    0.156 (Depositor), 0.155 (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

Validation slider image for 4PUU

Ligand Structure Quality Assessment 


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

Literature

Human 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: 36.85 kDa 
  • Atom Count: 3,015 
  • 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP


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

Query on 2WR


Download:Ideal Coordinates CCD File
C [auth A](2-carbamoyl-5-fluorophenoxy)acetic acid
C9 H8 F N O4
PCNZVPHJJYWUKQ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2WR BindingDB:  4PUU ΔG: min: -3.90e+1, max: 29.71 (kJ/mol) from 10 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free:  0.156 (Depositor), 0.155 (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 = 49.289α = 90
b = 66.394β = 91.82
c = 47.245γ = 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