Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 36.69 kDa 
• Atom Count: 2,568 
• Modelled Residue Count: 282 
• Deposited Residue Count: 310 
• Unique protein chains: 1

 1UU7

Structure of human PDK1 kinase domain in complex with BIM-2

• PDB DOI: 10.2210/pdb1UU7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2003-12-16 Released: 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.279 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

Literature

Interactions of Ly333531 and Other Bisindolyl Maleimide Inhibitors with Pdk1

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.

(2004) Structure 12: 215

• PubMed: 14962382 
• DOI: 10.1016/j.str.2004.01.005
• Primary Citation of Related Structures:  
  1UU3, 1UU7, 1UU8, 1UU9, 1UVR


• PubMed Abstract: 
  

LY333531, BIM-1, BIM-2, BIM-3, and BIM-8 are bisindolyl maleimide-based, nanomolar protein kinase C inhibitors. LY333531, a PKCbeta-specific inhibitor, is in clinical trials against diabetes and cardiac ventricular hypertrophy complications. Specificity analysis with a panel of 29 protein kinases reveals that these bisindolyl maleimide inhibitors also inhibit PDK1, a key kinase from the insulin signaling pathway, albeit in the lower microM range. To understand the molecular basis of inhibition, the PDK1 kinase domain was cocrystallized with these bisindolyl maleimide inhibitors. The inhibitor complexes represent the first structural description of this class of compounds, revealing their unusual nonplanar conformation within the ATP binding site and also explaining the higher inhibitory potential of LY33331 compared to the BIM compounds toward PDK1. A combination of site-directed mutagenesis and essential dynamics analysis gives further insight into PDK1 and also PKC inhibition by these compounds, and may aid inhibitor design.

---

Organizational Affiliation: 

Division of Biological Chemistry and Molecular Microbiology, University of Dundee, Dundee DD1 5EH, Scotland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1	A	310	Homo sapiens	Mutation(s): 0  Gene Names: PDPK1, PDK1 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens) Explore O15530  Go to UniProtKB:  O15530
PHAROS:  O15530

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BI2	F [auth A]	3-(1H-INDOL-3-YL)-4-(1-{2-[(2S)-1-METHYLPYRROLIDINYL]ETHYL}-1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE C27 H26 N4 O2 LBFDERUQORUFIN-QGZVFWFLSA-N
SO4	G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
BI2	PDBBind:  1UU7	IC50: 1.40e+4 (nM) from 1 assay(s)
	BindingDB:  1UU7	IC50: 1.40e+4 (nM) from 1 assay(s)
	Binding MOAD:  1UU7	IC50: 1.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.279 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.947	α = 90
b = 121.947	β = 90
c = 48.071	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• 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  

• Version 1.0: 2004-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-04-24
  Changes: Data collection, Derived calculations, Other, Source and taxonomy