3T9I | pdb_00003t9i

Pim1 complexed with a novel 3,6-disubstituted indole at 2.6 Ang Resolution

• PDB DOI: https://doi.org/10.2210/pdb3T9I/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-02 Released: 2011-10-12 
• Deposition Author(s): Bellamacina, C., Shu, W., Le, V., Nishiguchi, G., Bussiere, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.227 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Discovery of novel 3,5-disubstituted indole derivatives as potent inhibitors of Pim-1, Pim-2, and Pim-3 protein kinases.

Nishiguchi, G.A., Atallah, G., Bellamacina, C., Burger, M.T., Ding, Y., Feucht, P.H., Garcia, P.D., Han, W., Klivansky, L., Lindvall, M.

(2011) Bioorg Med Chem Lett 21: 6366-6369

• PubMed: 21945284 
• DOI: https://doi.org/10.1016/j.bmcl.2011.08.105
• Primary Citation Related Structures: 
  3T9I


• PubMed Abstract: 
  

  A series of novel 3,5-disubstituted indole derivatives as potent and selective inhibitors of all three members of the Pim kinase family is described. High throughput screen identified a pan-Pim kinase inhibitor with a promiscuous scaffold. Guided by structure-based drug design, SAR of the series afforded a highly selective indole chemotype that was further developed into a potent set of compounds against Pim-1, 2, and 3 (Pim-1 and Pim-3: IC(50)≤2nM and Pim-2: IC(50)≤100nM).

---

Organizational Affiliation: 
• Global Discovery Chemistry/Oncology and Exploratory Chemistry, Novartis Institutes of BioMedical Research, Emeryville, CA 94608, 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: 37.91 kDa 
• Atom Count: 2,335 
• Modeled Residue Count: 274 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase pim-1	A	328	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3T9	B [auth A]	2-methoxy-4-(3-phenyl-2H-pyrazolo[3,4-b]pyridin-6-yl)phenol C19 H15 N3 O2 CCYHSISZPCXEEF-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: 2.60 Å
• R-Value Free:  0.227 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.215	α = 90
b = 96.215	β = 90
c = 80.245	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Bellamacina, C., Shu, W., Le, V., Nishiguchi, G., Bussiere, D.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary