2GMV | pdb_00002gmv

PEPCK complex with a GTP-competitive inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2GMV/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.287 (Depositor) 
• R-Value Work: 
  0.217 (Depositor) 

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

• PubMed: 17532214 
• DOI: https://doi.org/10.1016/j.bmcl.2007.05.013
• Primary Citation Related Structures: 
  2GMV


• 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 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.

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Organizational Affiliation: 
• Department of Discovery Chemistry, Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.07 kDa 
• Atom Count: 9,624 
• Modeled Residue Count: 1,204 
• Deposited Residue Count: 1,250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase, cytosolic	A, B	625	Homo sapiens	Mutation(s): 4  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UN8	E [auth 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
PEP	D [auth A], G [auth B]	PHOSPHOENOLPYRUVATE C3 H5 O6 P DTBNBXWJWCWCIK-UHFFFAOYSA-N
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PEP	BindingDB:  2GMV	Ki: 2.89e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.287 (Depositor) 
• R-Value Work:  0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.011	α = 90
b = 66.134	β = 145.09
c = 137.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations