1L7X

Human liver glycogen phosphorylase b complexed with caffeine, N-acetyl-beta-D-glucopyranosylamine, and CP-403,700

Structural Biology Knowledgebase: 1L7X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 1L7X

Classification: TRANSFERASE

Total Structure Weight: 197280.02

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogen phosphorylase, liver form A, B 847 Homo sapiens EC#: 2.4.1.1 IUBMB
Gene Name(s): PYGL Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
700
Query on 700

A, B [5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]- AZETIDINE-3-CARBOXYLIC ACID
CP403700, (S)-1-{2-[(5-CHLORO-1H-INDOLE-2- CARBONYL)-AMINO]-3-PHENYL-PROPIONYL}-AZETIDINE- 3-CARBOXYLATE (Synonym)
C22 H20 Cl N3 O4
RONLONYAIBUEKT-IBGZPJMESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

A, B PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NBG
Query on NBG

A, B 1-N-ACETYL-BETA-D-GLUCOSAMINE
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CFF
Query on CFF

A, B CAFFEINE
3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6- DIONE (Synonym)
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

B (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
700 IC50: 45 nM (100) BindingDB

IC50: 145 nM  BindingMOAD

CFF IC50: 648000 nM (94) BindingDB

Kd: 92000 nM  BindingMOAD
Kd: 92000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.206
  • Space Group: P 31

Unit Cell:

Length (Å) Angle (°)
a = 124.07 α = 90.00
b = 124.07 β = 90.00
c = 122.85 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-03-18
  • 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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update