1PL6

Human SDH/NADH/inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase.

Pauly, T.A.Ekstrom, J.L.Beebe, D.A.Chrunyk, B.Cunningham, D.Griffor, M.Kamath, A.Lee, S.E.Madura, R.Mcguire, D.Subashi, T.Wasilko, D.Watts, P.Mylari, B.L.Oates, P.J.Adams, P.D.Rath, V.L.

(2003) Structure 11: 1071-1085

  • DOI: 10.1016/s0969-2126(03)00167-9
  • Primary Citation of Related Structures:  
    1PL8, 1PL7, 1PL6

  • PubMed Abstract: 
  • Sorbitol dehydrogenase (hSDH) and aldose reductase form the polyol pathway that interconverts glucose and fructose. Redox changes from overproduction of the coenzyme NADH by SDH may play a role in diabetes-induced dysfunction in sensitive tissues, ma ...

    Sorbitol dehydrogenase (hSDH) and aldose reductase form the polyol pathway that interconverts glucose and fructose. Redox changes from overproduction of the coenzyme NADH by SDH may play a role in diabetes-induced dysfunction in sensitive tissues, making SDH a therapeutic target for diabetic complications. We have purified and determined the crystal structures of human SDH alone, SDH with NAD(+), and SDH with NADH and an inhibitor that is competitive with fructose. hSDH is a tetramer of identical, catalytically active subunits. In the apo and NAD(+) complex, the catalytic zinc is coordinated by His69, Cys44, Glu70, and a water molecule. The inhibitor coordinates the zinc through an oxygen and a nitrogen atom with the concomitant dissociation of Glu70. The inhibitor forms hydrophobic interactions to NADH and likely sterically occludes substrate binding. The structure of the inhibitor complex provides a framework for developing more potent inhibitors of hSDH.


    Organizational Affiliation

    Exploratory Medicinal Sciences, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sorbitol dehydrogenaseABCD356Homo sapiensMutation(s): 8 
Gene Names: SORD
EC: 1.1.1.14 (PDB Primary Data), 1.1.1 (UniProt), 1.1.1.4 (UniProt), 1.1.1.56 (UniProt), 1.1.1.9 (UniProt)
Find proteins for Q00796 (Homo sapiens)
Explore Q00796 
Go to UniProtKB:  Q00796
NIH Common Fund Data Resources
PHAROS  Q00796
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
572
Query on 572

Download CCD File 
A, B, C, D
4-[2-(HYDROXYMETHYL)PYRIMIDIN-4-YL]-N,N-DIMETHYLPIPERAZINE-1-SULFONAMIDE
C11 H19 N5 O3 S
XDTHNROWHAAVPJ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
572IC50:  1000   nM  BindingDB
572Ki:  154   nM  Binding MOAD
572IC50:  240   nM  BindingDB
572IC50:  246   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.814α = 90
b = 134.814β = 90
c = 225.184γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance