2XCK

CRYSTAL STRUCTURE OF PDK1 IN COMPLEX WITH A PYRAZOLOQUINAZOLINE INHIBITOR

Structural Biology Knowledgebase: 2XCK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 2XCK

Classification: TRANSFERASE

Total Structure Weight: 36610.10

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
Mutation: V96T
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
MH4
Query on MH4

A 1-METHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}- N-[(2-METHYLPYRIDIN-4-YL)METHYL]-4,5-DIHYDRO- 1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE
C29 H33 N9 O
BMPXFYMECYEYOL-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 %)
MH4 N/A in BindingDB
IC50: 713 nM  BindingMOAD
IC50: 713 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: 0.240
  • R-Value Work: 0.193
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 123.11 α = 90.00
b = 123.11 β = 90.00
c = 47.24 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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4