1P1R

Horse liver alcohol dehydrogenase complexed with NADH and R-N-1-methylhexylformamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism

Venkataramaiah, T.H.Plapp, B.V.

(2003) J Biol Chem 278: 36699-36706

  • DOI: 10.1074/jbc.M305419200
  • Primary Citation of Related Structures:  
    1P1R

  • PubMed Abstract: 
  • Formamides are unreactive analogues of the aldehyde substrates of alcohol dehydrogenases and are useful for structure-function studies and for specific inhibition of alcohol metabolism. They bind to the enzyme-NADH complex and are uncompetitive inhibitors against varied concentrations of alcohol ...

    Formamides are unreactive analogues of the aldehyde substrates of alcohol dehydrogenases and are useful for structure-function studies and for specific inhibition of alcohol metabolism. They bind to the enzyme-NADH complex and are uncompetitive inhibitors against varied concentrations of alcohol. Fourteen new branched chain and chiral formamides were prepared and tested as inhibitors of purified Class I liver alcohol dehydrogenases: horse (EqADH E), human (HsADH1C*2), and mouse (MmADH1). In general, larger, substituted formamides, such as N-1-ethylheptylformamide, are better inhibitors of HsADH1C*2 and MmADH1 than of EqADH, reflecting a few differences in amino acid residues that change the sizes of the active sites. In contrast, the linear, alkyl (n-propyl and n-butyl) formamides are better inhibitors of EqADH and MmADH1 than of HsADH1C*2, probably because water disrupts van der Waals interactions. These enzymes are also inhibited strongly by sulfoxides and 4-substituted pyrazoles. The structure of EqADH complexed with NADH and (R)-N-1-methylhexylformamide was determined by x-ray crystallography at 1.6 A resolution. The structure resembles the expected Michaelis complex with NADH and aldehyde, and shows for the first time that the reduced nicotinamide ring of NADH is puckered, as predicted for the transition state for hydride transfer. Metabolism of ethanol in mice was inhibited by several formamides. The data were fitted with kinetic simulation to a mechanism that describes the non-linear progress curves and yields estimates of the in vivo inhibition constants and the rate constants for elimination of inhibitors. Some small formamides, such as N-isopropylformamide, may be useful inhibitors in vivo.


    Related Citations: 
    • Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides
      Cho, H., Ramaswamy, S., Plapp, B.V.
      (1997) Biochemistry 36: 382
    • 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
    • SUBSTITUTIONS IN A FLEXIBLE LOOP OF HORSE LIVER ALCOHOL DEHYDROGENASE HINDER THE CONFORMATIONAL CHANGE AND UNMASK HYDROGEN TRANSFER
      Ramaswamy, S., Park, D.H., Plapp, B.V.
      (1999) Biochemistry 38: 13951
    • Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 angstrom resolution
      Al-Karadaghi, S., Cedergren-Zeppezauer, E.S., Hovmoller, S., Petratos, K., Terry, H., Wilson, K.S.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 793
    • STRUCTURE OF A TRICLINIC TERNARY COMPLEX OF HORSE LIVER ALCOHOL DEHYDROGENASE AT 2.9 A RESOLUTION
      Eklund, H., Samama, J.P., Wallen, L., Branden, C.I., Akeson, A., Jones, T.A.
      (1981) J Mol Biol 146: 561
    • 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
    • Structures of horse liver alcohol dehydrogenase complexed with NAD+ and substituted benzyl alcohols
      Ramaswamy, S., Eklund, H., Plapp, B.V.
      (1994) Biochemistry 33: 5230
    • On the enzymatic activation of NADH
      Meijers, R., Morris, R.J., Adolph, H.W., Merli, A., Lamzin, V.S., Cedergren-Zeppezauer, E.S.
      (2001) J Biol Chem 276: 9316
    • Amino acid residues in the Nicotinamide Binding site Contribute to Catalysis by horse liver alcohol dehydrogenase
      Rubach, J.K., Plapp, B.V.
      (2003) Biochemistry 42: 2907
    • Binding of formamides to liver alcohol dehydrogenase
      Ramaswamy, S., Scholze, M., Plapp, B.V.
      (1997) Biochemistry 36: 3522

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alcohol dehydrogenase E chainA, B, C, D374Equus caballusMutation(s): 0 
EC: 1.1.1.1
UniProt
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00327
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
P [auth C],
T [auth D]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
NMH
Query on NMH

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
Q [auth C],
U [auth D]
(R)-N-(1-METHYL-HEXYL)-FORMAMIDE
C8 H17 N O
GFVRKPKAQHTAQK-MRVPVSSYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
M [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
N [auth C],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
N [auth C],
O [auth C],
R [auth D],
S [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NMH Binding MOAD:  1P1R Ki: 1.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.095α = 90
b = 180.34β = 106.36
c = 87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance