4OC0 | pdb_00004oc0

X-ray structure of of human glutamate carboxypeptidase II (GCPII) in a complex with CCIBzL, a urea-based inhibitor N~2~-[(1-carboxycyclopropyl)carbamoyl]-N~6~-(4-iodobenzoyl)-L-lysine

• PDB DOI: https://doi.org/10.2210/pdb4OC0/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2014-01-08 Released: 2014-05-21 
• Deposition Author(s): Pavlicek, J., Ptacek, J., Cerny, J., Byun, Y., Skultetyova, L., Pomper, M., Lubkowski, J., Barinka, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.181 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II.

Pavlicek, J., Ptacek, J., Cerny, J., Byun, Y., Skultetyova, L., Pomper, M.G., Lubkowski, J., Barinka, C.

(2014) Bioorg Med Chem Lett 24: 2340-2345

• PubMed: 24731280 
• DOI: https://doi.org/10.1016/j.bmcl.2014.03.066
• Primary Citation Related Structures: 
  4OC0, 4OC1, 4OC2, 4OC3, 4OC4, 4OC5


• PubMed Abstract: 
  

  Urea-based inhibitors of human glutamate carboxypeptidase II (GCPII) have advanced into clinical trials for imaging metastatic prostate cancer. In parallel efforts, agents with increased lipophilicity have been designed and evaluated for targeting GCPII residing within the neuraxis. Here we report the structural and computational characterization of six complexes between GCPII and P1'-diversified urea-based inhibitors that have the C-terminal glutamate replaced by more hydrophobic moieties. The X-ray structures are complemented by quantum mechanics calculations that provide a quantitative insight into the GCPII/inhibitor interactions. These data can be used for the rational design of novel glutamate-free GCPII inhibitors with tailored physicochemical properties.

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Organizational Affiliation: 
• Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Laboratory of Structural Biology, Vídeňská 1083, 14220 Prague 4, Czech Republic.
Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, 1550 Orleans Street, Baltimore, MD 21231, USA; College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong 339-700, South Korea.
Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, 1550 Orleans Street, Baltimore, MD 21231, USA.
Center for Cancer Research, Frederick National Laboratory for Cancer Research, Macromolecular Crystallography Laboratory, Frederick, MD 21702, USA.
Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Laboratory of Structural Biology, Vídeňská 1083, 14220 Prague 4, Czech Republic. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 83.25 kDa 
• Atom Count: 6,490 
• Modeled Residue Count: 694 
• Deposited Residue Count: 709 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate carboxypeptidase 2	A	709	Homo sapiens	Mutation(s): 0  Gene Names: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA 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
Glycosylation
Glycosylation Sites: 7		Go to GlyGen: Q04609-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2R7	M [auth A]	N~2~-[(1-carboxycyclopropyl)carbamoyl]-N~6~-(4-iodobenzoyl)-L-lysine C18 H22 I N3 O6 VRNHYZLBDDWTFH-ZDUSSCGKSA-N
NAG	F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
2R7	BindingDB:  4OC0	Ki: 318 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.181 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.376	α = 90
b = 129.938	β = 90
c = 158.575	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Pavlicek, J., Ptacek, J., Cerny, J., Byun, Y., Skultetyova, L., Pomper, M., Lubkowski, J., Barinka, C.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary