6RBC | pdb_00006rbc

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor KB1157


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.191 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RBC

Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Novel beta- and gamma-Amino Acid-Derived Inhibitors of Prostate-Specific Membrane Antigen.

Kim, K.Kwon, H.Barinka, C.Motlova, L.Nam, S.Choi, D.Ha, H.Nam, H.Son, S.H.Minn, I.Pomper, M.G.Yang, X.Kutil, Z.Byun, Y.

(2020) J Med Chem 63: 3261-3273

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b02022
  • Primary Citation Related Structures: 
    6RBC, 6S1X

  • PubMed Abstract: 

    Prostate-specific membrane antigen (PSMA) is an excellent biomarker for the early diagnosis of prostate cancer progression and metastasis. The most promising PSMA-targeted agents in the clinical phase are based on the Lys-urea-Glu motif, in which Lys and Glu are α-(l)-amino acids. In this study, we aimed to determine the effect of β- and γ-amino acids in the S1 pocket on the binding affinity for PSMA. We synthesized and evaluated the β- and γ-amino acid analogues with ( S )- or ( R )-configuration with keeping α-(l)-Glu as the S1'-binding pharmacophore. The structure-activity relationship studies identified that compound 13c , a β-amino acid analogue with ( R )-configuration, exhibited the most potent PSMA inhibitory activity with an IC 50 value of 3.97 nM. The X-ray crystal structure of PSMA in complex with 13c provided a mechanistic basis for the stereochemical preference of PSMA, which can guide the development of future PSMA inhibitors.


  • Organizational Affiliation
    • College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 82.9 kDa 
  • Atom Count: 6,603 
  • Modeled Residue Count: 694 
  • Deposited Residue Count: 707 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate carboxypeptidase 2707Homo sapiensMutation(s): 0 
Gene Names: FOLH1FOLHNAALAD1PSMPSMAGIG27
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
Expand
Reference Sequence

Oligosaccharides

Help  
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
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD 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
D
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JX5

Query on JX5



Download:Ideal Coordinates CCD File
M [auth A](2~{S})-2-[[(2~{R})-2-[4-[(4-iodophenyl)carbonylamino]butanoylamino]-3-oxidanyl-3-oxidanylidene-propyl]carbamoylamino]pentanedioic acid
C20 H25 I N4 O9
AOGSPOQTLUVJFT-UONOGXRCSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
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
K [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
L [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
JX5 BindingDB:  6RBC IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.191 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.551α = 90
b = 130.47β = 90
c = 159.045γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-11-25
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2024-11-13
    Changes: Structure summary