1OKY

Structure of human PDK1 kinase domain in complex with staurosporine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 1OKY

Classification: TRANSFERASE

Total Structure Weight: 36721.82

Macromolecule Entities
Molecule Chains Length Organism Details
3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 A 310 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: KINASE DOMAIN, RESIDUES 51-360
Gene Name(s): PDPK1 Gene View PDK1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
STU IC50: 5.2 - 6.5 nM (100) BindingDB
Kd: 1.7 nM (100) BindingDB

IC50: 6.5 nM  BindingMOAD
IC50: 6.5 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
SEP
Query on SEP
A L-PEPTIDE LINKING C3 H8 N O6 P SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.219
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 124.17 α = 90.00
b = 124.17 β = 90.00
c = 47.31 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-08-01
  • Released Date: 2004-07-29
  • Deposition author(s): Komander, D., Kular, G.S., Alessi, D.R., Van Aalten, D.M.F.

Revision History

  • Version 1_0: 2004-07-29

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance