3R22 | pdb_00003r22

Design, synthesis, and biological evaluation of pyrazolopyridine-sulfonamides as potent multiple-mitotic kinase (MMK) inhibitors (Part I)

• PDB DOI: https://doi.org/10.2210/pdb3R22/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2011-03-11 Released: 2011-08-10 
• Deposition Author(s): Zhang, L., Fan, J., Chong, J.-H., Cesana, A., Tam, B., Gilson, C., Boykin, C., Wang, D., Marcotte, D., Le Brazidec, J.-Y., Aivazian, D., Piao, J., Lundgren, K., Hong, K., Vu, K., Nguyen, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.313 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.265 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and biological evaluation of pyrazolopyrimidine-sulfonamides as potent multiple-mitotic kinase (MMK) inhibitors (part I).

Zhang, L., Fan, J., Chong, J.H., Cesena, A., Tam, B.Y., Gilson, C., Boykin, C., Wang, D., Aivazian, D., Marcotte, D., Xiao, G., Le Brazidec, J.Y., Piao, J., Lundgren, K., Hong, K., Vu, K., Nguyen, K., Gan, L.S., Silvian, L., Ling, L., Teng, M., Reff, M., Takeda, N., Timple, N., Wang, Q., Morena, R., Khan, S., Zhao, S., Li, T., Lee, W.C., Taveras, A.G., Chao, J.

(2011) Bioorg Med Chem Lett 21: 5633-5637

• PubMed: 21798738 
• DOI: https://doi.org/10.1016/j.bmcl.2011.06.129
• Primary Citation Related Structures: 
  3R21, 3R22


• PubMed Abstract: 
  

  A novel class of pyrazolopyrimidine-sulfonamides was discovered as selective dual inhibitors of aurora kinase A (AKA) and cyclin-dependent kinase 1 (CDK1). These inhibitors were originally designed based on an early lead (compound I). SAR development has led to the discovery of potent inhibitors with single digit nM IC(50)s towards both AKA and CDK1. An exemplary compound 1a has demonstrated good efficacy in an HCT116 colon cancer xenograft model.

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Organizational Affiliation: 
• Biogen Idec, 5200 Research Place, San Diego, CA 92122, United States. [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: 31.75 kDa 
• Atom Count: 2,061 
• Modeled Residue Count: 255 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 6	A	271	Homo sapiens	Mutation(s): 2  Gene Names: AURKA, AIK, ARK1, AURA, BTAK, STK15, STK6 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens) Explore O14965  Go to UniProtKB:  O14965
PHAROS:  O14965 GTEx:  ENSG00000087586

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D37	B [auth A]	N-{5-[(1-cycloheptyl-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino]pyridin-2-yl}methanesulfonamide C18 H23 N7 O2 S PARUULGUCQEWNM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D37	BindingDB:  3R22	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.313 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.265 (DCC) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.384	α = 90
b = 81.384	β = 90
c = 166.393	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Zhang, L., Fan, J., Chong, J.-H., Cesana, A., Tam, B., Gilson, C., Boykin, C., Wang, D., Marcotte, D., Le Brazidec, J.-Y., Aivazian, D., Piao, J., Lundgren, K., Hong, K., Vu, K., Nguyen, K.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2012-02-29
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description