3CV7 | pdb_00003cv7

Crystal structure of porcine aldehyde reductase ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.247 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structure of aldehyde reductase in ternary complex with coenzyme and the potent 20alpha-hydroxysteroid dehydrogenase inhibitor 3,5-dichlorosalicylic acid: Implications for inhibitor binding and selectivity

Carbone, V.Chung, R.Endo, S.Hara, A.El-Kabbani, O.

(2008) Arch Biochem Biophys 479: 82-87

  • DOI: https://doi.org/10.1016/j.abb.2008.08.014
  • Primary Citation Related Structures: 
    3CV7

  • PubMed Abstract: 

    The structure of aldehyde reductase (ALR1) in ternary complex with the coenzyme NADPH and 3,5-dichlorosalicylic acid (DCL), a potent inhibitor of human 20alpha-hydroxysteroid dehydrogenase (AKR1C1), was determined at a resolution of 2.41A. The inhibitor formed a network of hydrogen bonds with the active site residues Trp22, Tyr50, His113, Trp114 and Arg312. Molecular modelling calculations together with inhibitory activity measurements indicated that DCL was a less potent inhibitor of ALR1 (256-fold) when compared to AKR1C1. In AKR1C1, the inhibitor formed a 10-fold stronger binding interaction with the catalytic residue (Tyr55), non-conserved hydrogen bonding interaction with His222, and additional van der Waals contacts with the non-conserved C-terminal residues Leu306, Leu308 and Phe311 that contribute to the inhibitor's selectivity advantage for AKR1C1 over ALR1.


  • Organizational Affiliation
    • Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia.

Macromolecule Content 

  • Total Structure Weight: 37.96 kDa 
  • Atom Count: 2,899 
  • Modeled Residue Count: 322 
  • Deposited Residue Count: 325 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alcohol dehydrogenase325Sus scrofaMutation(s): 0 
EC: 1.1.1.2 (PDB Primary Data), 1.6 (UniProt), 1.1.1.20 (UniProt), 1.1.1.19 (UniProt), 1.1.1.372 (UniProt), 1.1.1.54 (UniProt)
UniProt
Find proteins for P50578 (Sus scrofa)
Explore P50578 
Go to UniProtKB:  P50578
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50578
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
C2U BindingDB:  3CV7 IC50: 1.13e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.385α = 90
b = 67.385β = 90
c = 246.106γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
AUTOMARdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description