1BTO

HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND (1S,3R)3-BUTYLTHIOLANE 1-OXIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides.

Cho, H.Ramaswamy, S.Plapp, B.V.

(1997) Biochemistry 36: 382-389

  • DOI: 10.1021/bi9624604
  • Primary Citation of Related Structures:  3BTO
  • Also Cited By: 5VN1

  • PubMed Abstract: 
  • Thiolane 1-oxides are analogs of the carbonyl substrates that bind to the alcohol dehydrogenase-NADH complex and are potent uncompetitive inhibitors against alcohol [Chadha, V. K., et al. (1985) J. Med. Chem. 28, 36-40]. The four stereoisomers of 3-b ...

    Thiolane 1-oxides are analogs of the carbonyl substrates that bind to the alcohol dehydrogenase-NADH complex and are potent uncompetitive inhibitors against alcohol [Chadha, V. K., et al. (1985) J. Med. Chem. 28, 36-40]. The four stereoisomers of 3-butylthiolane 1-oxide (BTO) were separated by chiral phase chromatography. CD and 1H-NMR spectra identified the enantiomeric pairs. 1H-NMR chemical shifts were assigned on the basis of COSY spectra of both diastereoisomers and confirmed by HMQC spectra. Coupling constants were determined through one-dimensional decoupling experiments. NMR with chiral shift reagents, Eu(hfc)3 [europium tris [3-[(heptafluoropropyl)hydroxymethylene]-(+)-camphorate]] or (R)-(-)-N-(3,5-dinitrobenzoyl)-alpha-methylbenzylamine, determined that the most inhibitory isomer is either 1S,3R or 1R,3S. The chemical shifts of protons in the thiolane 1-oxide ring were influenced by the whole structure and were not correlated with the computed Mulliken charges. X-ray crystallography at 2.1 and 1.66 A resolution of the ternary enzyme complexes with NADH demonstrated that the absolute configuration of the most inhibitory (Kii = 0.31 microM) stereoisomer is 1S,3R and the next best inhibitor (Kii = 0.73 microM) is 1S,3S. The thiolane 1-oxide rings bind in the same position, in the substrate binding site, but the geometry of the complexes suggests that the sulfoxides are not transition state analogs. Significantly, the butyl groups of the two isomers are accommodated differently by flexible amino acid side chains adopting alternative rotameric conformations.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Department of Biochemistry, University of Iowa, Iowa City 52242, USA.




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
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
SSB
Query on SSB

Download SDF File 
Download CCD File 
A, B, C, D
3-BUTYLTHIOLANE 1-OXIDE
C8 H16 O S
QVVQIIIFHZDBDL-WPRPVWTQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SSBKi: 310 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • 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
AMoREphasing
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: Version format compliance