3V51

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor RM-1-176

Structural Biology Knowledgebase: 3V51 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V51

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 55671.41

Macromolecule Entities
Molecule Chains Length Organism Details
Calmodulin-domain protein kinase 1 A 484 Toxoplasma gondii EC#: 2.7.11.17 IUBMB
Fragment: UNP residues 30-507
Gene Name(s): CDPK1

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
I76
Query on I76

A 3-{6-[(3-chlorobenzyl)oxy]naphthalen-2-yl}- 1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin- 4-amine
C25 H22 Cl N5 O
MGARWHQGMCYTAL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
I76 N/A in BindingDB
N/A in BindingMoad
Ki: 2.8 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.197
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.32 α = 90.00
b = 72.62 β = 103.90
c = 67.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-15
  • Released Date: 2012-03-14
  • Deposition author(s): Merritt, E.A., Larson, E.T.

Revision History

  • 2012-04-18
    Type: Citation | Details: Citation update