5ELY

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a hydroxamate inhibitor JHU242


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unprecedented Binding Mode of Hydroxamate-Based Inhibitors of Glutamate Carboxypeptidase II: Structural Characterization and Biological Activity.

Novakova, Z.Wozniak, K.Jancarik, A.Rais, R.Wu, Y.Pavlicek, J.Ferraris, D.Havlinova, B.Ptacek, J.Vavra, J.Hin, N.Rojas, C.Majer, P.Slusher, B.S.Tsukamoto, T.Barinka, C.

(2016) J.Med.Chem. 59: 4539-4550

  • DOI: 10.1021/acs.jmedchem.5b01806
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of glutamate carboxypeptidase II (GCPII) is effective in preclinical models of neurological disorders associated with excessive activation of glutamatergic systems. Here we report synthesis, structural characterization, and biological acti ...

    Inhibition of glutamate carboxypeptidase II (GCPII) is effective in preclinical models of neurological disorders associated with excessive activation of glutamatergic systems. Here we report synthesis, structural characterization, and biological activity of new hydroxamic acid-based inhibitors with nanomolar affinity for human GCPII. Crystal structures of GCPII/hydroxamate complexes revealed an unprecedented binding mode in which the putative P1' glutarate occupies the spacious entrance funnel rather than the conserved glutamate-binding S1' pocket. This unique binding mode provides a mechanistic explanation for the structure-activity relationship data, most notably the lack of enantiospecificity and the tolerance for bulky/hydrophobic functions as substituents of a canonical glutarate moiety. The in vivo pharmacokinetics profile of one of the inhibitors will be presented along with analgesic efficacy data from the rat chronic constrictive injury model of neuropathic pain.


    Organizational Affiliation

    Institute of Biotechnology, Academy of Sciences of the Czech Republic, BIOCEV , Prumyslova 595, 252 50 Vestec, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate carboxypeptidase 2
A
696Homo sapiensMutation(s): 0 
Gene Names: FOLH1 (FOLH, NAALAD1, PSM, PSMA)
EC: 3.4.17.21
Find proteins for Q04609 (Homo sapiens)
Go to Gene View: FOLH1
Go to UniProtKB:  Q04609
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
5PU
Query on 5PU

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A
4-[(2~{R})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid
JHU242
C13 H15 N O6
VUDGMYIWOPKVSL-SNVBAGLBSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.060α = 90.00
b = 130.827β = 90.00
c = 158.386γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Helmholtz-Zentrum Berlin and BioStruct-XGermanyN283570

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references