Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 82.57 kDa 
• Atom Count: 6633 
• Residue Count: 690 
• Unique protein chains: 1

3SJX

X-ray structure of human glutamate carboxypeptidase II (the E424A inactive mutant) in complex with N-acetyl-aspartyl-methionine

• DOI: 10.2210/pdb3SJX/pdb

• Classification: Hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2011-06-22 Released: 2011-10-05 
• Deposition Author(s): Plechanovova, A., Byun, Y., Alquicer, G., Skultetyova, L., Mlcochova, P., Nemcova, A., Kim, H., Navratil, M., Mease, R., Lubkowski, J., Pomper, M., Konvalinka, J., Rulisek, L., Barinka, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Literature

Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity.

Plechanovova, A., Byun, Y., Alquicer, G., Skultetyova, L., Mlcochova, P., Nemcova, A., Kim, H.J., Navratil, M., Mease, R., Lubkowski, J., Pomper, M., Konvalinka, J., Rulisek, L., Barinka, C.

(2011) J Med Chem 54: 7535-7546

• PubMed: 21923190 
• DOI: 10.1021/jm200807m
• Primary Citation of Related Structures:  
  3SJE, 3SJF, 3SJG, 3SJX


• PubMed Abstract: 
  

Virtually all low molecular weight inhibitors of human glutamate carboxypeptidase II (GCPII) are highly polar compounds that have limited use in settings where more lipophilic molecules are desired. Here we report the identification and characterization of GCPII inhibitors with enhanced liphophilicity that are derived from a series of newly identified dipeptidic GCPII substrates featuring nonpolar aliphatic side chains at the C-terminus. To analyze the interactions governing the substrate recognition by GCPII, we determined crystal structures of the inactive GCPII(E424A) mutant in complex with selected dipeptides and complemented the structural data with quantum mechanics/molecular mechanics calculations. Results reveal the importance of nonpolar interactions governing GCPII affinity toward novel substrates as well as formerly unnoticed plasticity of the S1' specificity pocket. On the basis of those data, we designed, synthesized, and evaluated a series of novel GCPII inhibitors with enhanced lipophilicity, with the best candidates having low nanomolar inhibition constants and clogD > -0.3. Our findings offer new insights into the design of more lipophilic inhibitors targeting GCPII.

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Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí, Praha 6, Czech Republic.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate carboxypeptidase 2	A	709	Homo sapiens	Mutation(s): 1  Gene Names: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 EC: 3.4.17.21
Find proteins for Q04609 (Homo sapiens) Explore Q04609  Go to UniProtKB:  Q04609
NIH Common Fund Data Resources
PHAROS  Q04609 GTEx  ENSG00000086205

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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	D	4		N-Glycosylation

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QRG	A	N-acetyl-L-alpha-aspartyl-L-methionine C11 H18 N2 O6 S FGMUBJQYXOPMHD-YUMQZZPRSA-N
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000799 (QRG)	A	N-ACETYL-L-ALPHA-ASPARTYL-L-METHIONINE	Polypeptide /  Enzyme inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.539	α = 90
b = 129.937	β = 90
c = 159.194	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-22 
• Released Date: 2011-10-05 
Deposition Author(s): Plechanovova, A., Byun, Y., Alquicer, G., Skultetyova, L., Mlcochova, P., Nemcova, A., Kim, H., Navratil, M., Mease, R., Lubkowski, J., Pomper, M., Konvalinka, J., Rulisek, L., Barinka, C.

Revision History 

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2011-11-16
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary