3NUN

phosphoinositide-dependent kinase-1 (PDK1) with lead compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 3NUN

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 34956.83

Macromolecule Entities
Molecule Chains Length Organism Details
PkB-like A 292 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: UNP residues 59-350
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
JMZ
Query on JMZ

A 6-(2-aminopyrimidin-4-yl)-1H-indazol-3-amine
C11 H10 N6
QVWIVWPIJUYRRF-UHFFFAOYSA-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 %)
JMZ IC50: 370 - 398 nM (100) BindingDB

N/A in BindingMoad
N/A in 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: 2.2 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.180
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 122.76 α = 90.00
b = 122.76 β = 90.00
c = 47.11 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-07-07
  • Released Date: 2011-06-22
  • Deposition author(s): Campobasso, N., Ward, P.

Revision History

  • Version 1_0: 2011-06-22

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance