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 1.3 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 5 Unique
IDChains Name / 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
PEP
Query on PEP

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

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

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

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PEP BindingDB:  1NHX Ki: 2.89e+5 (nM) from 1 assay(s)
FTB BindingDB:  1NHX IC50: 2110 (nM) from 1 assay(s)
EC50: 8600 (nM) from 1 assay(s)
Binding MOAD:  1NHX IC50: 2110 (nM) from 1 assay(s)
PDBBind:  1NHX IC50: 2110 (nM) from 1 assay(s)
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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations