1XOI

Human Liver Glycogen Phosphorylase A complexed with Chloroindoloyl glycine amide

• PDB DOI: https://doi.org/10.2210/pdb1XOI/pdb

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


• Deposited: 2004-10-06 Released: 2005-04-12 
• Deposition Author(s): Wright, S.W., Rath, V.L., Gibbs, E.M., Treadway, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.206 

Literature

5-Chloroindoloyl glycine amide inhibitors of glycogen phosphorylase: synthesis, in vitro, in vivo, and X-ray crystallographic characterization.

Wright, S.W., Rath, V.L., Genereux, P.E., Hageman, D.L., Levy, C.B., McClure, L.D., McCoid, S.C., McPherson, R.K., Schelhorn, T.M., Wilder, D.E., Zavadoski, W.J., Gibbs, E.M., Treadway, J.L.

(2005) Bioorg Med Chem Lett 15: 459-465

• PubMed: 15603973 
• DOI: https://doi.org/10.1016/j.bmcl.2004.10.048
• Primary Citation of Related Structures:  
  1XOI


• PubMed Abstract: 
  

  The synthesis, in vitro, and in vivo biological characterization of a series of achiral 5-chloroindoloyl glycine amide inhibitors of human liver glycogen phosphorylase A are described. Improved potency over previously reported compounds in cellular and in vivo assays was observed. The allosteric binding site of these compounds was shown by X-ray crystallography to be the same as that reported previously for 5-chloroindoloyl norstatine amides.

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Organizational Affiliation: 

Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA. [e-mail]

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: 195.99 kDa 
• Atom Count: 13,762 
• Modelled Residue Count: 1,608 
• Deposited Residue Count: 1,692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, liver form	A, B	846	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
288	E [auth A], H [auth B]	5-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID{[CYCLOPENTYL-(2-HYDROXY-ETHYL)-CARBAMOYL]-METHYL}-AMIDE C18 H24 Cl N3 O3 VXABTOCIIZSEPD-QGZVFWFLSA-N
PLP	D [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
NBG	C [auth A], F [auth B]	N-acetyl-beta-D-glucopyranosylamine C8 H15 N O6 IBONACLSSOLHFU-JAJWTYFOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
288	Binding MOAD:  1XOI	IC50: 57 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.206 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.906	α = 90
b = 123.906	β = 90
c = 123.103	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Wright, S.W., Rath, V.L., Gibbs, E.M., Treadway, J.L.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Structure summary