1LDE

HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL PIPERDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of formamides to liver alcohol dehydrogenase.

Ramaswamy, S.Scholze, M.Plapp, B.V.

(1997) Biochemistry 36: 3522-3527

  • DOI: 10.1021/bi962491z
  • Primary Citation of Related Structures:  1LDY
  • Also Cited By: 5VN1

  • PubMed Abstract: 
  • Amides are analogs of aldehydes and potent inhibitors of liver alcohol dehydrogenases. They can be used for structural studies and for inhibiting the metabolism of alcohols that form toxic products. We studied N-alkyl amides that bind to the enzyme-N ...

    Amides are analogs of aldehydes and potent inhibitors of liver alcohol dehydrogenases. They can be used for structural studies and for inhibiting the metabolism of alcohols that form toxic products. We studied N-alkyl amides that bind to the enzyme-NADH complex and act as uncompetitive inhibitors against varied concentrations of ethanol (millimolar Kii values, at pH 8 and 25 degrees C): N-propylacetamide (16), delta-valerolactam (1.6), N-formylpiperidine (0.14), N-isobutylformamide (0.028), N-(cyclohexylmethyl)-formamide (0.011), and N-cyclohexylformamide (0.0087). The lower affinity of delta-valerolactam and N-propylacetamide can be explained by steric hindrance with Phe93 of the enzyme. Replacing Phe93 with Ala in the S48T/F93A mutated enzyme, which resembles the natural alpha-isoenzyme of primates, improved binding of delta-valerolactam by 210-fold. The structures of horse liver enzyme complexed with NADH and N-cyclohexylformamide or N-formylpiperidine were determined by X-ray crystallography at 2.5 A resolution. In both complexes, the carbonyl oxygens of the inhibitors bind to the catalytic zinc and form a hydrogen bond to the hydroxyl group of Ser48 of the enzyme. The six-membered rings bind in overlapping, but rotated, positions that optimize hydrophobic interactions. The binding modes of the unreactive formamides appear to resemble the Michaelis complexes of the analogous substrates, with the re face of the carbonyl carbon suitably positioned to accept a hydrogen from NADH.


    Related Citations: 
    • Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution
      Eklund, H.,Nordstrom, B.,Zeppezauer, E.,Soderlund, G.,Ohlsson, I.,Boiwe, T.,Soderberg, B.O.,Tapia, O.,Branden, C.I.,Akeson, A.
      (1976) J.Mol.Biol. 102: 27
    • Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides
      Cho, H.,Ramaswamy, S.,Plapp, B.V.
      (1997) Biochemistry 36: 382
    • Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution
      Eklund, H.,Samma, J.P.,Wallen, L.,Branden, C.I.,Akeson, A.,Jones, T.A.
      (1981) J.Mol.Biol. 146: 561
    • Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Plapp, B.V.,Samama, J.P.,Branden, C.I.
      (1982) J.Biol.Chem. 257: 14349


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIVER ALCOHOL DEHYDROGENASE
A, B, C, D
374Equus caballusEC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Go to UniProtKB:  P00327
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FPI
Query on FPI

Download SDF File 
Download CCD File 
A, B, C, D
N-FORMYLPIPERIDINE
C6 H11 N O
FEWLNYSYJNLUOO-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.930α = 90.00
b = 180.200β = 106.00
c = 86.800γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
ARP/wARPmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance