2GMV

PEPCK complex with a GTP-competitive inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

C-8 Modifications of 3-alkyl-1,8-dibenzylxanthines as inhibitors of human cytosolic phosphoenolpyruvate carboxykinase.

Pietranico, S.L.Foley, L.H.Huby, N.Yun, W.Dunten, P.Vermeulen, J.Wang, P.Toth, K.Ramsey, G.Gubler, M.L.Wertheimer, S.J.

(2007) Bioorg.Med.Chem.Lett. 17: 3835-3839

  • DOI: 10.1016/j.bmcl.2007.05.013

  • PubMed Abstract: 
  • New modifications on the C-8 4-aminobenzyl unit of the previously reported 3-alkyl-1,8-dibenzylxanthine inhibitors of cPEPCK are presented. The most active compound reported here is the 5-chloro-1,3-dimethyl-1H-pyrazole-4-sulfonic acid amide derivati ...

    New modifications on the C-8 4-aminobenzyl unit of the previously reported 3-alkyl-1,8-dibenzylxanthine inhibitors of cPEPCK are presented. The most active compound reported here is the 5-chloro-1,3-dimethyl-1H-pyrazole-4-sulfonic acid amide derivative 2 with an IC(50) of 0.29+/-0.08 microM. An X-ray analysis of a heteroaromatic sulfonamide is presented showing a new pi-pi interaction.


    Related Citations: 
    • 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
    • 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.,Hanspeter, M.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoenolpyruvate carboxykinase, cytosolic
A, B
625Homo sapiensGene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UN8
Query on UN8

Download SDF File 
Download CCD File 
A
N-(4-{[3-BUTYL-1-(2-FLUOROBENZYL)-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YL]METHYL}PHENYL)-1-METHYL-1H-IMIDAZOLE-4-SULFONAMIDE
C27 H28 F N7 O4 S
OWJCXBGUTOMZTE-UHFFFAOYSA-N
 Ligand Interaction
PEP
Query on PEP

Download SDF File 
Download CCD File 
A, B
PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UN8IC50: 630 nM (99) BINDINGDB
UN8IC50: 630 nM BINDINGMOAD
UN8IC50: 630 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 128.011α = 90.00
b = 66.134β = 145.09
c = 137.360γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-04-07 
  • Released Date: 2007-05-29 
  • Deposition Author(s): Dunten, P.

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance