Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 197.27 kDa 
• Atom Count: 13826 
• Modelled Residue Count: 1584 
• Deposited Residue Count: 1694 
• Unique protein chains: 1

1L5S

Human liver glycogen phosphorylase complexed with uric acid, N-Acetyl-beta-D-glucopyranosylamine, and CP-403,700

• PDB DOI: 10.2210/pdb1L5S/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-03-07 Released: 2002-12-04 
• Deposition Author(s): Ekstrom, J.L., Pauly, T.A., Carty, M.D., Soeller, W.C., Culp, J., Danley, D.E., Hoover, D.J., Treadway, J.L., Gibbs, E.M., Fletterick, R.J., Day, Y.S.N., Myszka, D.G., Rath, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Literature

Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase.

Ekstrom, J.L., Pauly, T.A., Carty, M.D., Soeller, W.C., Culp, J., Danley, D.E., Hoover, D.J., Treadway, J.L., Gibbs, E.M., Fletterick, R.J., Day, Y.S., Myszka, D.G., Rath, V.L.

(2002) Chem Biol 9: 915-924

• PubMed: 12204691 
• DOI: 10.1016/s1074-5521(02)00186-2
• Primary Citation of Related Structures:  
  1L5Q, 1L5R, 1L5S, 1L7X


• PubMed Abstract: 
  

Human liver glycogen phosphorylase (HLGP) catalyzes the breakdown of glycogen to maintain serum glucose levels and is a therapeutic target for diabetes. HLGP is regulated by multiple interacting allosteric sites, each of which is a potential drug binding site. We used surface plasmon resonance (SPR) to screen for compounds that bind to the purine allosteric inhibitor site. We determined the affinities of a series of compounds and solved the crystal structures of three representative ligands with K(D) values from 17-550 microM. The crystal structures reveal that the affinities are partly determined by ligand-specific water-mediated hydrogen bonds and side chain movements. These effects could not be predicted; both crystallographic and SPR studies were required to understand the important features of binding and together provide a basis for the design of new allosteric inhibitors targeting this site.

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Organizational Affiliation: 

Exploratory Medicinal Sciences, Groton, CT 06340, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, liver form	A, B	847	Homo sapiens	Mutation(s): 0  Gene Names: PYGL 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
700	E [auth A], L [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], K [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
NBG	C [auth A], J [auth B]	N-acetyl-beta-D-glucopyranosylamine C8 H15 N O6 IBONACLSSOLHFU-JAJWTYFOSA-N
URC	F [auth A], M [auth B]	URIC ACID C5 H4 N4 O3 LEHOTFFKMJEONL-UHFFFAOYSA-N
MRD	G [auth A], H [auth A], I [auth A], N [auth B], O [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
700	BindingDB:  1L5S	IC50: 45 (nM) from 1 assay(s)
	Binding MOAD:  1L5S	IC50: 145 (nM) from 1 assay(s)
URC	Binding MOAD:  1L5S	Kd: 5.50e+5 (nM) from 1 assay(s)
	PDBBind:  1L5S	Kd: 5.50e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.03	α = 90
b = 124.03	β = 90
c = 123.3	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-07 
• Released Date: 2002-12-04 
Deposition Author(s): Ekstrom, J.L., Pauly, T.A., Carty, M.D., Soeller, W.C., Culp, J., Danley, D.E., Hoover, D.J., Treadway, J.L., Gibbs, E.M., Fletterick, R.J., Day, Y.S.N., Myszka, D.G., Rath, V.L.

Revision History  

• Version 1.0: 2002-12-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  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: Data collection, Derived calculations, Structure summary