6AYD | pdb_00006ayd

Pim1 complexed with N-(6-(4-hydroxyphenyl)-1H-indazol-3-yl)cyclopropanecarboxamide

• PDB DOI: https://doi.org/10.2210/pdb6AYD/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-09-08 Released: 2017-12-27 
• Deposition Author(s): Shewchuk, L.M., Henley, Z.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.230 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

From PIM1 to PI3K delta via GSK3 beta : Target Hopping through the Kinome.

Henley, Z.A., Bax, B.D., Inglesby, L.M., Champigny, A., Gaines, S., Faulder, P., Le, J., Thomas, D.A., Washio, Y., Baldwin, I.R.

(2017) ACS Med Chem Lett 8: 1093-1098

• PubMed: 29057057 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00296
• Primary Citation Related Structures: 
  5OY4, 6AYD


• PubMed Abstract: 
  

  Selective inhibitors of phosphoinositide 3-kinase delta are of interest for the treatment of inflammatory diseases. Initial optimization of a 3-substituted indazole hit compound targeting the kinase PIM1 focused on improving selectivity over GSK3β through consideration of differences in the ATP binding pockets. Continued kinase cross-screening showed PI3Kδ activity in a series of 4,6-disubstituted indazole compounds, and subsequent structure-activity relationship exploration led to the discovery of an indole-containing lead compound as a potent PI3Kδ inhibitor with selectivity over the other PI3K isoforms.

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Organizational Affiliation: 
• Refractory Respiratory Inflammation DPU, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, U.K.
Molecular Discovery Research, Biological Sciences, and Computational Chemistry, Platform Technology & Science, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, U.K.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.36 kDa 
• Atom Count: 2,254 
• Modeled Residue Count: 272 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	334	Homo sapiens	Mutation(s): 1  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
C2J	B [auth A]	N-[6-(4-hydroxyphenyl)-2H-indazol-3-yl]cyclopropanecarboxamide C17 H15 N3 O2 RXQXACYMRVINQU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.230 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.3	α = 90
b = 97.3	β = 90
c = 80.221	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Shewchuk, L.M., Henley, Z.A.

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description