1NHX

PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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

  • DOI: 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLICA625Homo sapiensMutation(s): 3 
Gene Names: PCK1PEPCK1
EC: 4.1.1.32 (PDB Primary Data), 2.7.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P35558 (Homo sapiens)
Explore P35558 
Go to UniProtKB:  P35558
PHAROS:  P35558
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FTB
Query on FTB

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

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FTBIC50:  2110   nM  Binding MOAD
FTBEC50:  8600   nM  BindingDB
FTBIC50:  2110   nM  BindingDB
FTBIC50 :  2110   nM  PDBBind
PEPKi:  289000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • 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



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance