6H7Y

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 1-79-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

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

  • DOI: 10.1021/acsmedchemlett.8b00318
  • Primary Citation of Related Structures:  

  • 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 ...

    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: 

    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.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, United States.




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 11 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
EDO
Query on EDO
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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA
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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
FVZ
Query on FVZ
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A
(2~{S})-2-[[(2~{S})-6-[(4-fluorophenyl)amino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid
C18 H22 F N3 O8
CKNIHKIYCHYOOG-STQMWFEESA-N
 Ligand Interaction
PGE
Query on PGE
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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TAM
Query on TAM
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A
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG
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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FVZIC50: 0.35 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.150 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.258α = 90.00
b = 131.376β = 90.00
c = 159.874γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACphasing
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release