2J90

CRYSTAL STRUCTURE OF HUMAN ZIP KINASE IN COMPLEX WITH A TETRACYCLIC PYRIDONE INHIBITOR (PYRIDONE 6)

Structural Biology Knowledgebase: 2J90 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2J90

Classification: TRANSFERASE

Total Structure Weight: 71324.85

Macromolecule Entities
Molecule Chains Length Organism Details
DEATH-ASSOCIATED PROTEIN KINASE 3 A, B 304 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 9-289
Details: DIPHOSPHORYLATED FORM (SER50 AND THR265)
Gene Name(s): DAPK3 Gene View ZIPK

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IZA
Query on IZA

A, B 2-TERT-BUTYL-9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]- IMIDAZ[4,5-F]ISOQUINOLINE-7-ONE
2-(1,1-DIMETHYLETHYL)9-FLUORO-3,6-DIHYDRO- 7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLIN-7-ONE (Synonym)
C18 H16 F N3 O
VNDWQCSOSCCWIP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
SEP
Query on SEP
A, B L-PEPTIDE LINKING C3 H8 N O6 P SER
TPO
Query on TPO
A, B L-PEPTIDE LINKING C4 H10 N O6 P THR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.185
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 95.76 α = 90.00
b = 95.76 β = 90.00
c = 150.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-10-31
  • Released Date: 2006-11-07
  • Deposition author(s): Turnbull, A.P., Berridge, G., Fedorov, O., Pike, A.C.W., Savitsky, P., Eswaran, J., Papagrigoriou, E., Ugochukwa, E., Von Delft, F., Gileadi, O., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Knapp, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor