3NAY | pdb_00003nay

PDK1 in complex with inhibitor MP6

• PDB DOI: https://doi.org/10.2210/pdb3NAY/pdb

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


• Deposited: 2010-06-02 Released: 2010-11-24 
• Deposition Author(s): Yan, Y., Munshi, S.K., Allison, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

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 Biological Chem 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.2 kDa 
• Atom Count: 4,757 
• Modeled Residue Count: 558 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoinositide-dependent protein kinase 1	A, B	311	Homo sapiens	Mutation(s): 0  Gene Names: PDPK1, PDK1 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 GTEx:  ENSG00000140992

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MP6	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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.677	α = 90
b = 89.677	β = 90
c = 178	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
CNS	refinement
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Yan, Y., Munshi, S.K., Allison, T.

Revision History  

• 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
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary