Structure of glutamate dehydrogenase complexed with bithionol

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.239 

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Novel Inhibitors Complexed with Glutamate Dehydrogenase: ALLOSTERIC REGULATION BY CONTROL OF PROTEIN DYNAMICS

Li, M.Smith, C.J.Walker, M.T.Smith, T.J.

(2009) J Biol Chem 284: 22988-23000

  • DOI: https://doi.org/10.1074/jbc.M109.020222
  • Primary Citation of Related Structures:  
    3ETD, 3ETE, 3ETG

  • PubMed Abstract: 

    Mammalian glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate using NAD(P)(+) as coenzyme. Unlike its counterparts from other animal kingdoms, mammalian GDH is regulated by a host of ligands. The recently discovered hyperinsulinism/hyperammonemia disorder showed that the loss of allosteric inhibition of GDH by GTP causes excessive secretion of insulin. Subsequent studies demonstrated that wild-type and hyperinsulinemia/hyperammonemia forms of GDH are inhibited by the green tea polyphenols, epigallocatechin gallate and epicatechin gallate. This was followed by high throughput studies that identified more stable inhibitors, including hexachlorophene, GW5074, and bithionol. Shown here are the structures of GDH complexed with these three compounds. Hexachlorophene forms a ring around the internal cavity in GDH through aromatic stacking interactions between the drug and GDH as well as between the drug molecules themselves. In contrast, GW5074 and bithionol both bind as pairs of stacked compounds at hexameric 2-fold axes between the dimers of subunits. The internal core of GDH contracts when the catalytic cleft closes during enzymatic turnover. None of the drugs cause conformational changes in the contact residues, but all bind to key interfaces involved in this contraction process. Therefore, it seems likely that the drugs inhibit enzymatic turnover by inhibiting this transition. Indeed, this expansion/contraction process may play a major role in the inter-subunit communication and allosteric regulation observed in GDH.

  • Organizational Affiliation

    Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUD1 protein
A, B, C, D, E
A, B, C, D, E, F
501Bos taurusMutation(s): 0 
Find proteins for P00366 (Bos taurus)
Explore P00366 
Go to UniProtKB:  P00366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00366
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
BA [auth F]
H [auth A]
L [auth B]
P [auth C]
T [auth D]
BA [auth F],
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
C21 H30 N7 O17 P3
Query on GTP

Download Ideal Coordinates CCD File 
CA [auth F]
I [auth A]
M [auth B]
Q [auth C]
U [auth D]
CA [auth F],
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
C10 H16 N5 O14 P3
Query on B1T

Download Ideal Coordinates CCD File 
DA [auth F]
J [auth A]
N [auth B]
R [auth C]
V [auth D]
DA [auth F],
J [auth A],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
C12 H6 Cl4 O2 S
Query on GLU

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
K [auth B]
O [auth C]
S [auth D]
AA [auth F],
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
C5 H9 N O4
Binding Affinity Annotations 
IDSourceBinding Affinity
B1T Binding MOAD:  3ETD IC50: 4800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.38α = 90
b = 101.3β = 102.46
c = 166.59γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations