4P4F

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a phosphoramidate inhibitor NC-2-40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities.

Novakova, Z.Cerny, J.Choy, C.J.Nedrow, J.R.Choi, J.K.Lubkowski, J.Berkman, C.E.Barinka, C.

(2016) Febs J. 283: 130-143

  • DOI: 10.1111/febs.13557
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibitors targeting human glutamate carboxypeptidase II (GCPII) typically consist of a P1' glutamate-derived binding module, which warrants the high affinity and specificity, linked to an effector function that is positioned within the entrance funn ...

    Inhibitors targeting human glutamate carboxypeptidase II (GCPII) typically consist of a P1' glutamate-derived binding module, which warrants the high affinity and specificity, linked to an effector function that is positioned within the entrance funnel of the enzyme. Here we present a comprehensive structural and computational study aimed at dissecting the importance of the effector function for GCPII binding and affinity. To this end we determined crystal structures of human GCPII in complex with a series of phosphoramidate-based inhibitors harboring effector functions of diverse physicochemical characteristics. Our data show that higher binding affinities of phosphoramidates, compared to matching phosphonates, are linked to the presence of additional hydrogen bonds between Glu424 and Gly518 of the enzyme and the amide group of the phosphoramidate. While the positioning of the P1' glutamate-derived module within the S1' pocket of GCPII is invariant, interaction interfaces between effector functions and residues lining the entrance funnel are highly varied, with the positively charged arginine patch defined by Arg463, Arg534 and Arg536 being the only 'hot-spot' common to several studied complexes. This variability stems in part from the fact that the effector/GCPII interfaces generally encompass isolated areas of nonpolar residues within the entrance funnel and resulting van der Waals contacts lack the directionality typical for hydrogen bonding interactions. The presented data unravel a complexity of binding modes of inhibitors within non-prime site(s) of GCPII and can be exploited for the design of novel GCPII-specific compounds.


    Organizational Affiliation

    Department of Chemistry, Washington State University, Pullman, WA, USA.,Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,National Cancer Institute, Center for Cancer Research, Macromolecular Crystallography Laboratory, Frederick, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate carboxypeptidase 2
A
707Homo 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

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 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
BMA
Query on BMA

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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
2GB
Query on 2GB

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A
N-[(S)-(biphenyl-4-ylmethoxy)(hydroxy)phosphoryl]-L-glutamic acid
C18 H20 N O7 P
DATQTWKKBHKLSV-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2GBIC50: 168 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.766α = 90.00
b = 130.612β = 90.00
c = 159.118γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-12 
  • Released Date: 2015-05-20 
  • Deposition Author(s): Barinka, C.

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references
  • Version 1.2: 2016-01-20
    Type: Database references