3RWP

Discovery of a Novel, Potent and Selective Inhibitor of 3-Phosphoinositide Dependent Kinase (PDK1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Novel, Potent, and Selective Inhibitors of 3-Phosphoinositide-Dependent Kinase (PDK1).

Murphy, S.T.Alton, G.Bailey, S.Baxi, S.M.Burke, B.J.Chappie, T.A.Ermolieff, J.Ferre, R.Greasley, S.Hickey, M.Humphrey, J.Kablaoui, N.Kath, J.Kazmirski, S.Kraus, M.Kupchinsky, S.Li, J.Lingardo, L.Marx, M.A.Richter, D.Tanis, S.P.Tran, K.Vernier, W.Xie, Z.Yin, M.J.Yu, X.H.

(2011) J.Med.Chem. 54: 8490-8500

  • DOI: 10.1021/jm201019k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Analogues substituted with various amines at the 6-position of the pyrazine ring on (4-amino-7-isopropyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrazin-2-ylmethanone were discovered as potent and selective inhibitors of PDK1 with potential as anticancer age ...

    Analogues substituted with various amines at the 6-position of the pyrazine ring on (4-amino-7-isopropyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrazin-2-ylmethanone were discovered as potent and selective inhibitors of PDK1 with potential as anticancer agents. An early lead with 2-pyridine-3-ylethylamine as the pyrazine substituent showed moderate potency and selectivity. Structure-based drug design led to improved potency and selectivity against PI3Kα through a combination of cyclizing the ethylene spacer into a saturated, five-membered ring and substituting on the 4-position of the aryl ring with a fluorine. ADME properties were improved by lowering the lipophilicity with heteroatom replacements in the saturated, five-membered ring. The optimized analogues have a PDK1 Ki of 1 nM and >100-fold selectivity against PI3K/AKT-pathway kinases. The cellular potency of these analogues was assessed by the inhibition of AKT phosphorylation (T308) and by their antiproliferation activity against a number of tumor cell lines.


    Organizational Affiliation

    Pfizer Global Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States. sean.murphy@takedasd.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide-dependent protein kinase 1
A
311Homo sapiensMutation(s): 0 
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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
ABQ
Query on ABQ

Download SDF File 
Download CCD File 
A
[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl](6-{[(3S,4R)-4-(4-fluorophenyl)tetrahydrofuran-3-yl]amino}pyrazin-2-yl)methanone
C24 H24 F N7 O2
YXZBQCQAYNRRFP-IEBWSBKVSA-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 %)
ABQKi: 0.6 nM (100) BINDINGDB
ABQKi: 0.6 nM BINDINGMOAD
ABQKi: 0.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.982α = 90.00
b = 122.982β = 90.00
c = 47.505γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACphasing
REFMACrefinement
WARPmodel building
ARPmodel building
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description