3NUY

phosphoinositide-dependent kinase-1 (PDK1) with fragment17

• PDB DOI: https://doi.org/10.2210/pdb3NUY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2010-07-07 Released: 2011-05-25 
• Deposition Author(s): Campobasso, N., Ward, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.183 
• R-Value Observed: 0.187 

Literature

Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery.

Medina, J.R., Blackledge, C.W., Heerding, D.A., Campobasso, N., Ward, P., Briand, J., Wright, L., Axten, J.M.

(2010) ACS Med Chem Lett 1: 439-442

• PubMed: 24900229 
• DOI: https://doi.org/10.1021/ml100136n
• Primary Citation of Related Structures:  
  3NUS, 3NUU, 3NUY


• PubMed Abstract: 
  

  Fragment screening of phosphoinositide-dependent kinase-1 (PDK1) in a biochemical kinase assay afforded hits that were characterized and prioritized based on ligand efficiency and binding interactions with PDK1 as determined by NMR. Subsequent crystallography and follow-up screening led to the discovery of aminoindazole 19, a potent leadlike PDK1 inhibitor with high ligand efficiency. Well-defined structure-activity relationships and protein crystallography provide a basis for further elaboration and optimization of 19 as a PDK1 inhibitor.

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Organizational Affiliation: 

Oncology Research, Signal Transduction DPU Medicinal Chemistry.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.96 kDa 
• Atom Count: 2,373 
• Modelled Residue Count: 277 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PkB-like	A	286	Homo sapiens	Mutation(s): 0  Gene Names: PkB-like 1 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JPZ	I [auth A]	quinazolin-4(1H)-one C8 H6 N2 O QMNUDYFKZYBWQX-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
JPZ	PDBBind:  3NUY	IC50: 3.45e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.183 
• R-Value Observed: 0.187 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.695	α = 90
b = 123.695	β = 90
c = 47.346	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Campobasso, N., Ward, P.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-03-30
  Changes: Other
• Version 1.3: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary