1UU3

STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531

Structural Biology Knowledgebase: 1UU3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 1UU3

Classification: TRANSFERASE

Total Structure Weight: 37376.73

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
LY4
Query on LY4

A (9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11- TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4- H][1,4,13]OXADIAZACYCLOHEXADECINE-18,20-DIONE
LY333531 (Synonym)
C28 H28 N4 O3
ZCBUQCWBWNUWSU-SFHVURJKSA-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 %)
LY4 IC50: 500 - 750 nM (99 - 100) BindingDB
Kd: 700 - 700000 nM (100) BindingDB

IC50: 750 nM  BindingMOAD
IC50: 750 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: 1.7 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.173
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.62 α = 90.00
b = 121.62 β = 90.00
c = 47.88 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-12-15
  • Released Date: 2004-03-04
  • Deposition author(s): Komander, D., Kular, G.S., Schuttelkopf, A.W., Deak, M., Prakash, K.R., Bain, J., Elliot, M., Garrido-Franco, M., Kozikowski, A.P., Alessi, D.R., Van Aalten, D.M.F.

Revision History

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