3JY0

Discovery of 3H-benzo[4,5]thieno[3,2-d]pyrimidin-4-ones as Potent, Highly Selective and Orally Bioavailable Pim Kinases Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3JY0/pdb

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


• Deposited: 2009-09-21 Released: 2009-11-10 
• Deposition Author(s): Stoll, V.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.257 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Discovery of 3H-benzo[4,5]thieno[3,2-d]pyrimidin-4-ones as Potent, Highly Selective and Orally Bioavailable Pim Kinases Inhibitors

Tao, Z.F., Hasvold, L., Leverson, J., Han, E., Guan, R., Johson, E.F., Stoll, V.S., Stewart, K.D., Stamper, G., Soni, N.

To be published.

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: 34.3 kDa 
• Atom Count: 2,256 
• Modelled Residue Count: 275 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase Pim-1	A	294	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
LYG	B [auth A]	8-chloro-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzothieno[3,2-d]pyrimidin-4(3H)-one C15 H14 Cl N3 O2 S DSUSQUXNJRQJMI-VIFPVBQESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LYG	BindingDB:  3JY0	Ki: 5 (nM) from 1 assay(s)
	PDBBind:  3JY0	Ki: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.257 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.286	α = 90
b = 98.286	β = 90
c = 80.58	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Stoll, V.S.

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations