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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  
  • Also Cited By: 2GMV

  • 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 ...

    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.


    Related Citations: 
    • Crystal Structure of Human Cytosolic Phosphoenolpyruvate Carboxykinase Reveals a New GTP-Binding Site
      Dunten, P.,Belunis, C.,Crowther, R.,Hollfelder, K.,Kammlott, U.,Levin, W.,Michel, H.,Ramsey, G.B.,Swain, A.,Weber, D.,Wertheimer, S.J.
      (2002) J.Mol.Biol. 316: 257


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phosphoenolpyruvate carboxykinase, cytosolic
A
625Homo sapiensMutation(s): 0 
Gene Names: PCK1 (PEPCK1)
EC: 4.1.1.32
Find proteins for P35558 (Homo sapiens)
Go to Gene View: PCK1
Go to UniProtKB:  P35558
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
TSX
Query on TSX

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Download CCD File 
A
N-[4-(1-ALLYL-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YLMETHYL)-PHENYL]-ACETAMIDE
1-ALLYL-3-BUTYL-8-(N-ACETYL-4-AMINOBENZYL)-XANTHINE
C21 H25 N5 O3
XFOWZKUTPKXWIE-UHFFFAOYSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TSXIC50: 18800 nM BINDINGMOAD
TSXIC50: 18800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • 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
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance