2XCH

Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 2XCH

Classification: TRANSFERASE

Total Structure Weight: 36960.03

Macromolecule Entities
Molecule Chains Length Organism Details
3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 A 309 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: KINASE CATALYTIC DOMAIN, RESIDUES 1-309
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
CKG
Query on CKG

A 8-(CYCLOHEXA-2,5-DIEN-1-YLIDENEAMINO)-1-(PIPERIDIN- 4-YLMETHYL)-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE- 3-CARBOXAMIDE
C22 H25 N7 O
NJZDNEMNAJYOMW-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 %)
CKG N/A in BindingDB
IC50: 374 nM  BindingMOAD
IC50: 374 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: 2.0 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.189
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 122.89 α = 90.00
b = 122.89 β = 90.00
c = 47.25 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-04-23
  • Released Date: 2010-07-28
  • Deposition author(s): Angiolini, M., Banfi, P., Casale, E., Casuscelli, F., Fiorelli, C., Saccardo, M.B., Silvagni, M., Zuccotto, F.

Revision History

  • Version 1_0: 2010-07-28

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance