2XCK | pdb_00002xck

Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2XCK/pdb

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


• Deposited: 2010-04-23 Released: 2010-07-28 
• Deposition Author(s): Angiolini, M., Banfi, P., Casale, E., Casuscelli, F., Fiorelli, C., Saccardo, M.B., Silvagni, M., Zuccotto, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.240 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Optimization of Potent Pdk1 Inhibitors.

Angiolini, M., Banfi, P., Casale, E., Casuscelli, F., Fiorelli, C., Saccardo, M.B., Silvagni, M., Zuccotto, F.

(2010) Bioorg Med Chem Lett 20: 4095

• PubMed: 20621725 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.070
• Primary Citation of Related Structures:  
  2XCH, 2XCK


• PubMed Abstract: 
  

  In this Letter is described the structure-based design of potent dihydro-pyrazoloquinazolines as PDK1 inhibitors. Starting from low potency HTS hits with the aid of X-ray crystallography and modeling, a medicinal chemistry activity was carried out to improve potency versus PDK1 and selectivity versus CDK2 protein kinase.

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Organizational Affiliation: 

Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano, Milano, Italy. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.61 kDa 
• Atom Count: 2,468 
• Modelled Residue Count: 276 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1	A	309	Homo sapiens	Mutation(s): 0  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
MH4	B [auth A]	1-METHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-N-[(2-METHYLPYRIDIN-4-YL)METHYL]-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE C29 H33 N9 O BMPXFYMECYEYOL-UHFFFAOYSA-N
SO4	G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.240 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.115	α = 90
b = 123.115	β = 90
c = 47.24	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Angiolini, M., Banfi, P., Casale, E., Casuscelli, F., Fiorelli, C., Saccardo, M.B., Silvagni, M., Zuccotto, F.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary