2VD4

Structure of small-molecule inhibitor of Glmu from Haemophilus influenzae reveals an allosteric binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a Small-Molecule Inhibitor Complexed with Glmu from Haemophilus Influenzae Reveals an Allosteric Binding Site.

Mochalkin, I.Lightle, S.Narasimhan, L.Bornemeier, D.Melnick, M.Vanderroest, S.Mcdowell, L.

(2008) Protein Sci. 17: 577

  • DOI: 10.1110/ps.073271408

  • PubMed Abstract: 
  • N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine-diphospho-N-acetylglucosamine (UDP-GlcNAc), an i ...

    N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine-diphospho-N-acetylglucosamine (UDP-GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram-negative and Gram-positive bacteria. Here we disclose a 1.9 A resolution crystal structure of a synthetic small-molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high-throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC(50) approximately 18 microM in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc-1-P substrate-binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure-guided design of a new class of mechanism-based inhibitors of GlmU.


    Organizational Affiliation

    Pfizer Inc., Michigan Laboratories, Ann Arbor, Michigan 48105, USA. Igor.Mochalkin@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIFUNCTIONAL PROTEIN GLMU
A
456Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: glmU
Find proteins for P43889 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P43889
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
P21
Query on P21

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Download CCD File 
A
4-chloro-N-(3-methoxypropyl)-N-[(3S)-1-(2-phenylethyl)piperidin-3-yl]benzamide
C24 H31 Cl N2 O2
OOUGHDJEJNMXSV-QHCPKHFHSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P21IC50: 18000 nM BINDINGMOAD
P21IC50: 18000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 108.186α = 90.00
b = 108.186β = 90.00
c = 327.430γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
REFMACphasing
CNXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance