4NGQ | pdb_00004ngq

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 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 22: 4099-4108

  • DOI: https://doi.org/10.1016/j.bmc.2014.05.061
  • Primary Citation Related Structures: 
    4NGM, 4NGN, 4NGP, 4NGQ, 4NGR, 4NGS, 4NGT

  • PubMed Abstract: 

    Glutamate carboxypeptidase II (GCPII), also known as prostate specific membrane antigen (PSMA), is an established prostate cancer marker and is considered a promising target for specific anticancer drug delivery. Low-molecular-weight inhibitors of GCPII are advantageous specific ligands for this purpose. However, they must be modified with a linker to enable connection of the ligand with an imaging molecule, anticancer drug, and/or nanocarrier. Here, we describe a structure-activity relationship (SAR) study of GCPII inhibitors with linkers suitable for imaging and drug delivery. Structure-assisted inhibitor design and targeting of a specific GCPII exosite resulted in a 7-fold improvement in Ki value compared to the parent structure. X-ray structural analysis of the inhibitor series led to the identification of several inhibitor binding modes. We also optimized the length of the inhibitor linker for effective attachment to a biotin-binding molecule and showed that the optimized inhibitor could be used to target nanoparticles to cells expressing GCPII.


  • Organizational Affiliation
    • Gilead Sciences and IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo n. 2, Prague 6, 166 10 Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, Prague 2, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 87.79 kDa 
  • Atom Count: 6,240 
  • Modeled Residue Count: 694 
  • Deposited Residue Count: 739 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate carboxypeptidase 2739Homo sapiensMutation(s): 0 
Gene Names: FOLHFOLH1GIG27NAALAD1PSMPSMA
EC: 3.4.17.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q04609 (Homo sapiens)
Explore Q04609 
Go to UniProtKB:  Q04609
PHAROS:  Q04609
GTEx:  ENSG00000086205 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04609
Glycosylation
Glycosylation Sites: 7Go to GlyGen: Q04609-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C, D, E
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J37

Query on J37



Download:Ideal Coordinates CCD File
M [auth A]N-({(1S)-6-(4-bromobenzyl)-1-carboxy-7,47-dioxo-52-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-10,13,16,19,22,25,28,31,34,37,40,43-dodecaoxa-6,46-diazadopentacont-1-yl}carbamoyl)-L-glutamic acid
C57 H95 Br N6 O22 S
BWJXSXULCISGDF-CRIRDAMVSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
L [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.088α = 90
b = 130.347β = 90
c = 158.784γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary