3NAY

PDK1 in complex with inhibitor MP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Selective inhibition of PDK1 using an allosteric kinase inhibitor and RNAi impairs cancer cell migration and anchorage-independent growth of primary tumor lines

Nagashima, K.Shumway, S.D.Sathyanarayanan, S.Chen, A.Dolinski, B.Xu, Y.Keilhack, H.Nguyen, T.Wiznerowicz, M.Li, L.Lutterbach, B.A.Paweletz, C.Allison, T.Yan, Y.Munshi, S.K.Klippel, A.Kraus, M.Bobkova, E.V.Deshmukh, S.Xu, Z.Mueller, U.Szewczak, A.A.Pan, B.-S.Richon, V.Pollock, R.Blume-Jensen, P.Northrup, A.Andersen, J.N.

(2010) J Biol Chem 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A, B311Homo sapiensMutation(s): 0 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MP6
Query on MP6

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]4-(2-cyclopropylethylidene)-9-(1H-pyrazol-4-yl)-6-{[(1R)-1,2,2-trimethylpropyl]amino}benzo[c][1,6]naphthyridin-1(4H)-one
C26 H29 N5 O
LURVNNDHOKNBEC-RIEVCORGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, BL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.677α = 90
b = 89.677β = 90
c = 178γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
CNSrefinement
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Database references