4XX9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

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This is version 1.3 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
  • Primary Citation of Related Structures:  
    4XX9

  • 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 discover allosteric modulators for additional kinases ...

    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

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A310Homo sapiensMutation(s): 2 
Gene Names: PDPK1PDK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens)
Explore O15530 
Go to UniProtKB:  O15530
PHAROS:  O15530
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
RF4 (Subject of Investigation/LOI)
Query on RF4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A](2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid
C19 H20 N2 O3 S
ZAHFRMHMWCBLOL-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
RF4 BindingDB:  4XX9 Kd: 8000 (nM) from 1 assay(s)
EC50: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.626α = 90
b = 44.429β = 101.11
c = 47.639γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA136779

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence, Database references