3IOP | pdb_00003iop

PDK-1 in complex with the inhibitor Compound-8i

• PDB DOI: https://doi.org/10.2210/pdb3IOP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-08-14 Released: 2010-02-16 
• Deposition Author(s): Olland, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

The identification of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7]naphthyridin-4-ylamines as potent inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1).

Nittoli, T., Dushin, R.G., Ingalls, C., Cheung, K., Floyd, M.B., Fraser, H., Olland, A., Hu, Y., Grosu, G., Han, X., Arndt, K., Guo, B., Wissner, A.

(2010) Eur J Med Chem 45: 1379-1386

• PubMed: 20074837 
• DOI: https://doi.org/10.1016/j.ejmech.2009.12.036
• Primary Citation Related Structures: 
  3ION, 3IOP


• PubMed Abstract: 
  

  A series of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7]naphthyridin-4-ylamine-based inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1) has been identified. Several examples appear to be potent and relatively selective inhibitors of PDK-1 over the related AGC kinases PKA, PKB/AKT, and p70S6K. The introduction of a stereochemical center beside the amino substituent on the aminoalkoxy-side chain had little effect upon the inhibitory activity against these enzymes, and X-ray crystallographic analyses of a representative pair of enantiomeric inhibitors bound to the active site of PDK-1 revealed comparable binding modes for each enantiomer.

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Organizational Affiliation: 
• Chemical Sciences, Wyeth Research, 401 N. Middletown Road, Pearl River, NY 10965, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.13 kDa 
• Atom Count: 2,382 
• Modeled Residue Count: 276 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoinositide-dependent protein kinase 1	A	312	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
8I1	B [auth A]	2-(5-{[(2R)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine C28 H27 N5 O3 XNXUJUXYVTYIGP-LJQANCHMSA-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: 2.20 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.874	α = 90
b = 122.874	β = 90
c = 47.16	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Olland, A.M.

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary