1EXV

HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP-403,700

• PDB DOI: https://doi.org/10.2210/pdb1EXV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2000-05-04 Released: 2000-11-01 
• Deposition Author(s): Rath, V.L., Ammirati, M., Danley, D.E., Ekstrom, J.L., Hynes, T.R., Olson, T.V., Hoover, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.280 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 

Literature

Human liver glycogen phosphorylase inhibitors bind at a new allosteric site.

Rath, V.L., Ammirati, M., Danley, D.E., Ekstrom, J.L., Gibbs, E.M., Hynes, T.R., Mathiowetz, A.M., McPherson, R.K., Olson, T.V., Treadway, J.L., Hoover, D.J.

(2000) Chem Biol 7: 677-682

• PubMed: 10980448 
• DOI: https://doi.org/10.1016/s1074-5521(00)00004-1
• Primary Citation of Related Structures:  
  1EM6, 1EXV


• PubMed Abstract: 
  

  Glycogen phosphorylases catalyze the breakdown of glycogen to glucose-1-phosphate for glycolysis. Maintaining control of blood glucose levels is critical in minimizing the debilitating effects of diabetes, making liver glycogen phosphorylase a potential therapeutic target.

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Organizational Affiliation: 

Department of Exploratory Medicinal Sciences, Global Research and Development, Pfizer Inc., Groton, CT 06340, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 196.58 kDa 
• Atom Count: 13,223 
• Modelled Residue Count: 1,572 
• Deposited Residue Count: 1,694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIVER GLYCOGEN PHOSPHORYLASE	A, B	847	Homo sapiens	Mutation(s): 0  EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens) Explore P06737  Go to UniProtKB:  P06737
PHAROS:  P06737 GTEx:  ENSG00000100504

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
700	E [auth A], I [auth B]	[5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC ACID C22 H20 Cl N3 O4 RONLONYAIBUEKT-IBGZPJMESA-N
PLP	D [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
NBG	C [auth A], G [auth B]	N-acetyl-beta-D-glucopyranosylamine C8 H15 N O6 IBONACLSSOLHFU-JAJWTYFOSA-N
MPD	F [auth A], J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
700	BindingDB:  1EXV	IC50: 45 (nM) from 1 assay(s)
	Binding MOAD:  1EXV	IC50: 45 (nM) from 1 assay(s)
	PDBBind:  1EXV	IC50: 45 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.280 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.629	α = 90
b = 124.629	β = 90
c = 124.064	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-01 
Deposition Author(s): Rath, V.L., Ammirati, M., Danley, D.E., Ekstrom, J.L., Hynes, T.R., Olson, T.V., Hoover, D.J.

Revision History  

• Version 1.0: 2000-11-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary