4NGR

Crystal Structure of Glutamate Carboxypeptidase II in a complex with urea-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Rational design of urea-based glutamate carboxypeptidase II (GCPII) inhibitors as versatile tools for specific drug targeting and delivery

Tykvart, J.Schimer, J.Barinkova, J.Pachl, P.Postova-Slavetinska, L.Majer, P.Konvalinka, J.Sacha, P.

(2014) Bioorg.Med.Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate carboxypeptidase 2
A
739Homo 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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
J21
Query on J21

Download SDF File 
Download CCD File 
A
N-{[(1S)-5-({2-[2-(acetylamino)ethoxy]-4-bromobenzoyl}amino)-1-carboxypentyl]carbamoyl}-L-glutamic acid
C23 H31 Br N4 O10
GEZLVAJRFLXCLD-IRXDYDNUSA-N
 Ligand Interaction
BMA
Query on BMA

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

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
J21Ki: 0.3 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.104α = 90.00
b = 130.048β = 90.00
c = 158.454γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XDSdata scaling
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-11-02 
  • Released Date: 2014-06-18 
  • Deposition Author(s): Tykvart, J., Pachl, P.

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release