1M51

PEPCK complex with a GTP-competitive inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray Structures of two xanthine inhibitors bound to PEPCK and N-3 modifications of substituted 1,8-Dibenzylxanthines

Foley, L.H.Wang, P.Dunten, P.Ramsey, G.Gubler, M.-L.Wertheimer, S.J.

(2003) Bioorg Med Chem Lett 13: 3871-3874

  • DOI: https://doi.org/10.1016/s0960-894x(03)00723-6
  • Primary Citation of Related Structures:  
    1M51, 1NHX

  • PubMed Abstract: 

    The analysis of the X-ray structures of two xanthine inhibitors bound to PEPCK and a comparison to the X-ray structure of GTP bound to PEPCK are reported. The SAR at N-1, N-7 and developing SAR at C-8 are consistent with information gained from the X-ray structures of compounds 1 and 2 bound to PEPCK. Representative N-3 modifications of compound 2 that led to the discovery of 3-cyclopropylmethyl and its carboxy analogue as optimal N-3 groups are presented.


  • Organizational Affiliation

    Department of Discovery Chemistry, Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA. louf1203@aol.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
phosphoenolpyruvate carboxykinase, cytosolic625Homo sapiensMutation(s): 3 
Gene Names: PCK1
EC: 4.1.1.32
UniProt & NIH Common Fund Data Resources
Find proteins for P35558 (Homo sapiens)
Explore P35558 
Go to UniProtKB:  P35558
PHAROS:  P35558
GTEx:  ENSG00000124253 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35558
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TSX
Query on TSX

Download Ideal Coordinates CCD File 
D [auth A]N-[4-(1-ALLYL-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YLMETHYL)-PHENYL]-ACETAMIDE
C21 H25 N5 O3
XFOWZKUTPKXWIE-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TSX Binding MOAD:  1M51 IC50: 1.88e+4 (nM) from 1 assay(s)
PDBBind:  1M51 IC50: 1.88e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.407α = 88.91
b = 61.067β = 70.21
c = 62.007γ = 72.62
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations