3FZ1 | pdb_00003fz1

Crystal structure of a benzthiophene inhibitor bound to human Cyclin-dependent Kinase-2 (CDK-2)

• PDB DOI: https://doi.org/10.2210/pdb3FZ1/pdb

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


• Deposited: 2009-01-23 Released: 2009-04-07 
• Deposition Author(s): Kurumbail, R.G., Caspers, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Benzothiophene inhibitors of MK2. Part 2: improvements in kinase selectivity and cell potency.

Anderson, D.R., Meyers, M.J., Kurumbail, R.G., Caspers, N., Poda, G.I., Long, S.A., Pierce, B.S., Mahoney, M.W., Mourey, R.J., Parikh, M.D.

(2009) Bioorg Med Chem Lett 19: 4882-4884

• PubMed: 19616942 
• DOI: https://doi.org/10.1016/j.bmcl.2009.02.017
• Primary Citation Related Structures: 
  3FYJ, 3FYK, 3FZ1


• PubMed Abstract: 
  

  Optimization of kinase selectivity for a set of benzothiophene MK2 inhibitors provided analogs with potencies of less than 500 nM in a cell based assay. The selectivity of the inhibitors can be rationalized by examination of X-ray crystal structures of inhibitors bound to MK2.

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Organizational Affiliation: 
• Pfizer Global Research and Development, St Louis Laboratories, Chesterfield, MO 63017, 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: 34.25 kDa 
• Atom Count: 2,512 
• Modeled Residue Count: 284 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDK2_Human EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B98	B [auth A]	(3R)-3-(aminomethyl)-9-methoxy-1,2,3,4-tetrahydro-5H-[1]benzothieno[3,2-e][1,4]diazepin-5-one C13 H15 N3 O2 S TXYKBKYDFZQOCB-SSDOTTSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.717	α = 90
b = 71.709	β = 90
c = 72.242	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Kurumbail, R.G., Caspers, N.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description