4XX9

Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.

Rettenmaier, T.J.Fan, H.Karpiak, J.Doak, A.Sali, A.Shoichet, B.K.Wells, J.A.

(2015) J.Med.Chem. 58: 8285-8291

  • DOI: 10.1021/acs.jmedchem.5b01216

  • PubMed Abstract: 
  • Finding small molecules that target allosteric sites remains a grand challenge for ligand discovery. In the protein kinase field, only a handful of highly selective allosteric modulators have been found. Thus, more general methods are needed to disco ...

    Finding small molecules that target allosteric sites remains a grand challenge for ligand discovery. In the protein kinase field, only a handful of highly selective allosteric modulators have been found. Thus, more general methods are needed to discover allosteric modulators for additional kinases. Here, we use virtual screening against an ensemble of both crystal structures and comparative models to identify ligands for an allosteric peptide-binding site on the protein kinase PDK1 (the PIF pocket). We optimized these ligands through an analog-by-catalog search that yielded compound 4, which binds to PDK1 with 8 μM affinity. We confirmed the docking poses by determining a crystal structure of PDK1 in complex with 4. Because the PIF pocket appears to be a recurring structural feature of the kinase fold, known generally as the helix αC patch, this approach may enable the discovery of allosteric modulators for other kinases.


    Organizational Affiliation

    Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94158, United States.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, Matrix No. 07-01, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide-dependent protein kinase 1
A
310Homo sapiensMutation(s): 2 
Gene Names: PDPK1 (PDK1)
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Go to Gene View: PDPK1
Go to UniProtKB:  O15530
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
RF4
Query on RF4

Download SDF File 
Download CCD File 
A
(2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid
C19 H20 N2 O3 S
ZAHFRMHMWCBLOL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RF4Kd: 8000 nM (99) BINDINGDB
RF4EC50: 2000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.129 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.626α = 90.00
b = 44.429β = 101.11
c = 47.639γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
Blu-Icedata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01 CA136779

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations