1M51

PEPCK complex with a GTP-competitive inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1M51/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-07-06 Released: 2003-09-30 
• Deposition Author(s): Foley, L.H., Wang, P., Dunten, P., Wertheimer, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.237 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

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

• PubMed: 14552798 
• 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.

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Organizational Affiliation: 

Department of Discovery Chemistry, Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.16 kDa 
• Atom Count: 4,945 
• Modelled Residue Count: 603 
• Deposited Residue Count: 625 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoenolpyruvate carboxykinase, cytosolic	A	625	Homo sapiens	Mutation(s): 3  Gene Names: PCK1 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 GTEx:  ENSG00000124253

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TSX	D [auth A]	N-[4-(1-ALLYL-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YLMETHYL)-PHENYL]-ACETAMIDE C21 H25 N5 O3 XFOWZKUTPKXWIE-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TSX	PDBBind:  1M51	IC50: 1.88e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.237 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.407	α = 88.91
b = 61.067	β = 70.21
c = 62.007	γ = 72.62

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-30 
Deposition Author(s): Foley, L.H., Wang, P., Dunten, P., Wertheimer, S.J.

Revision History  

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-28
  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