1NHX

PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.173 

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:  1M51
  • 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 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FTB
Query on FTB

Download SDF File 
Download CCD File 
A
N-{4-[1-(2-FLUOROBENZYL)-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YLMETHYL]-PHENYL}-ACETAMIDE
1-(2-FLUOROBENZYL)-3-BUTYL-8-(N-ACETYL-4-AMINOBENZYL)-XANTHINE
C25 H26 F N5 O3
JHSHXKJSPVHPCJ-UHFFFAOYSA-N
 Ligand Interaction
PEP
Query on PEP

Download SDF File 
Download CCD File 
A
PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FTBEC50: 8600 nM (90) BINDINGDB
FTBIC50: 2110 nM (99) BINDINGDB
FTBIC50: ~2110 nM BINDINGMOAD
FTBIC50: 2110 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.173 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.383α = 89.71
b = 61.452β = 70.24
c = 62.265γ = 72.56
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: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance