5OF0 | pdb_00005of0

X-ray structure of human glutamate carboxypeptidase II (GCPII), the E424M inactive mutant, in complex with a inhibitor CFBzOG

• PDB DOI: https://doi.org/10.2210/pdb5OF0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2017-07-10 Released: 2018-08-01 
• Deposition Author(s): Novakova, Z., Motlova, L., Barinka, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.172 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

2-Aminoadipic Acid-C(O)-Glutamate Based Prostate-Specific Membrane Antigen Ligands for Potential Use as Theranostics.

Nakajima, R., Novakova, Z., Tueckmantel, W., Motlova, L., Barinka, C., Kozikowski, A.P.

(2018) ACS Med Chem Lett 9: 1099-1104

• PubMed: 30429952 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00318
• Primary Citation Related Structures: 
  5OF0, 6H7Y, 6H7Z, 6HKJ, 6HKZ


• PubMed Abstract: 
  

  The design and synthesis of prostate specific membrane antigen (PSMA) ligands derived from 2-aminoadipic acid, a building block that has not previously been used to construct PSMA ligands, are reported. The effects of both the linker length and of an N-substituent of our PSMA ligands were probed, and X-ray structures of five of these ligands bound to PSMA were obtained. Among the ligands disclosed herein, 13b showed the highest inhibitory activity for PSMA. As ligand 13b can readily be radiolabeled since its fluorine atom is adjacent to the nitrogen atom of its pyridine ring, the use of this and related compounds as theranostics can be pursued.

---

Organizational Affiliation: 
• Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, United States.
Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
StarWise Therapeutics LLC, 505 South Rosa Road, Suite 27, Madison, Wisconsin 53719-1235, United States.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.64 kDa 
• Atom Count: 6,629 
• Modeled Residue Count: 692 
• Deposited Residue Count: 707 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate carboxypeptidase 2	A	707	Homo sapiens	Mutation(s): 1  Gene Names: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9TB	M [auth A]	(2~{S})-2-[[(2~{S})-6-[(4-fluorophenyl)methylamino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid C19 H24 F N3 O8 ZCBCSGACSCSXNO-KBPBESRZSA-N
NAG	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
9TB	BindingDB:  5OF0	IC50: min: 2.3, max: 1500 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.172 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.467	α = 90
b = 130.461	β = 90
c = 159.574	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
REFMAC	phasing
Coot	model building
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Novakova, Z., Motlova, L., Barinka, C.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary