1UU8

STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1

Structural Biology Knowledgebase: 1UU8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1UU8

Classification: TRANSFERASE

Total Structure Weight: 36844.32

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

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BI1
Query on BI1

A 3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3- YL}-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE
RBT205 INHIBITOR (Synonym)
C25 H24 N4 O2
QMGUOJYZJKLOLH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BI1 IC50: 9000 nM (100) BindingDB

IC50: 9000 nM  BindingMOAD
IC50: 9000 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: 2.5 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.198
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 122.40 α = 90.00
b = 122.40 β = 90.00
c = 48.02 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-12-16
  • 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