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Crystal structure of palbociclib isethionate Form B, (C24H30N7O2)(C2H5O4S)

Published online by Cambridge University Press:  18 June 2021

James A. Kaduk Open the ORCID record for James A. Kaduk [Opens in a new window] ,
Amy M. Gindhart  and
Thomas N. Blanton Open the ORCID record for Thomas N. Blanton [Opens in a new window]
James A. Kaduk*
Affiliation:
Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, Illinois60616, USA North Central College, 131 S. Loomis St., Naperville, Illinois60540, USA
Amy M. Gindhart
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, Pennsylvania19073-3273, USA
Thomas N. Blanton
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, Pennsylvania19073-3273, USA
*
a)Author to whom correspondence should be addressed. Electronic mail: kaduk@polycrystallography.com
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Abstract

The crystal structure of palbociclib isethionate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Palbociclib isethionate crystallizes in space group P-1 (#2) with a = 8.71334(4), b = 9.32119(6), c = 17.73725(18) Å, α = 80.0260(5), β = 82.3579(3), γ = 76.1561(1)°, V = 1371.282(4) Å3, and Z = 2. The crystal structure is dominated by cation⋯anion and cation⋯cation hydrogen bonds, which result in layers roughly parallel to the (104) plane. Both hydrogen atoms on the protonated nitrogen atom of the pyrimidine ring participate in strong hydrogen bonds to the anions. One proton binds to the sulfonate group, while the other bonds to the hydroxyl group of the isethionate anion. The hydroxyl group of the anion acts as a donor to a ketone oxygen atom in the cation. There are also strong N–H⋯N hydrogen bonds, which occur in pairs linking the cations into dimers with rings having a graph set R2,2(8). The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Keywords

palbociclib isethionateIbrance®powder diffractionRietveld refinementdensity functional theory
Type
New Diffraction Data
Information
Powder Diffraction , Volume 36 , Issue 3 , September 2021 , pp. 196 - 201
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Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

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References

Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R., Corriero, N., and Falcicchio, A. (2013). “EXPO2013: a kit of tools for phasing crystal structures from powder data,” J. Appl. Crystallogr. 46, 1231–1235.CrossRefGoogle Scholar
Antao, S. M., Hassan, I., Wang, J., Lee, P. L., and Toby, B. H. (2008). “State-of-the-art high-resolution powder X-ray diffraction (HRPXRD) illustrated with rietveld refinement of quartz, sodalite, tremolite, and meionite,” Can. Mineral. 46, 1501–1509.CrossRefGoogle Scholar
Bernstein, J., Davis, R. E., Shimoni, L., and Chang, N. L. (1995). “Patterns in hydrogen bonding: functionality and graph set analysis in crystals,” Angew. Chem. Int. Ed. English 34(15), 1555–1573.CrossRefGoogle Scholar
Beylin, V. G., Blackburn, A. C., Erdman, D. T., and Toogood, P. L. (2008). “Isethionate salt of a selective CDK4 inhibitor,” US Patent 7,345,171 B2.Google Scholar
Beylin, V. G., Blackburn, A. C., Erdman, D. T., and Toogood, P. L. (2011). “Isethionate salt of a selective CDK4 inhibitor,” US Patent 7,863,278 B2.Google Scholar
Bravais, A. (1866). Etudes Cristallographiques (Gauthier Villars, Paris).Google Scholar
Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E., and Orpen, A. G. (2004). “Retrieval of crystallographically-derived molecular geometry information,” J. Chem. Inf. Sci. 44, 2133–2144.CrossRefGoogle ScholarPubMed
Chen, M., Zhang, Y., Yang, C., Zhang, X., Li, J., and Wang, P. (2016). “Salts and crystalline forms of 6-acetyl-8-cyclopentyl-5-methyl-2(5-(piperazin-1-yl)pyridin-2-yl)amino)yrido[2,3-D]pyrimidin-7(8H)-one (palbociclib),” International Patent Application WO 2016/090257 A1.Google Scholar
Chen, M., Zhang, Y., Yang, C., Yang, C, and Zhang, X. (2017). “Novel crystalline form of palbociclib,” International Patent Application WO 2017/067506.Google Scholar
Dassault Systèmes (2020). Materials Studio 2020 (BIOVIA, San Diego, CA).Google Scholar
Donnay, J. D. H., and Harker, D. (1937). “A new law of crystal morphology extending the law of bravais,” Am. Mineral. 22, 446–447.Google Scholar
Dovesi, R., Orlando, R., Erba, A., Zicovich-Wilson, C. M., Civalleri, B., Casassa, S., Maschio, L., Ferrabone, M., De Le Pierre, M., D'Arco, P., Noel, Y., Causa, M., Rerat, M., and Kirtman, B. (2014). “CRYSTAL14: a program for the ab initio investigation of crystalline solids,” Int. J. Quantum Chem. 114, 1287–1317.CrossRefGoogle Scholar
Etter, M. C. (1990). “Encoding and decoding hydrogen-bond patterns of organic compounds,” Acc. Chem. Res. 23(4), 120–126.CrossRefGoogle Scholar
European Medicines Agency (2016). “Assessment report: Ibrance,” EMA/652627/2016.Google Scholar
Friedel, G. (1907). “Etudes sur la loi de bravais,” Bull. Soc. Fr. Mineral. 30, 326–455.Google Scholar
Gates-Rector, S., and Blanton, T. (2019). “The powder diffraction file: a quality materials characterization database,” Powd. Diffr. 39(4), 352–360.CrossRefGoogle Scholar
Gatti, C., Saunders, V. R., and Roetti, C. (1994). “Crystal-field effects on the topological properties of the electron-density in molecular crystals—the case of urea,” J. Chem. Phys. 101, 10686–10696.CrossRefGoogle Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P., and Ward, S. C. (2016). “The cambridge structural database,” Acta Crystallogr. Sect. B: Struct. Sci., Cryst. Eng. Mater. 72, 171–179.CrossRefGoogle ScholarPubMed
Hirshfeld, F. L. (1977). “Bonded-atom fragments for describing molecular charge densities,” Theor. Chem. Acta 44, 129–138.CrossRefGoogle Scholar
Kaduk, J. A., Crowder, C. E., Zhong, K., Fawcett, T. G., and Suchomel, M. R. (2014). “Crystal structure of atomoxetine hydrochloride (Strattera), C17H22NOCl,” Powd. Diffr. 29(3), 269–273.CrossRefGoogle Scholar
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., and Bolton, E. E. (2019). “Pubchem 2019 update: improved access to chemical data,” Nucleic Acids Res. 47(D1), D1102–D1109. doi:10.1093/nar/gky1033.CrossRefGoogle ScholarPubMed
Kresse, G., and Furthmüller, J. (1996). “Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set,” Comput. Mater. Sci. 6, 15–50.CrossRefGoogle Scholar
Lee, P. L., Shu, D., Ramanathan, M., Preissner, C., Wang, J., Beno, M. A., Von Dreele, R. B., Ribaud, L., Kurtz, C., Antao, S. M., Jiao, X., and Toby, B. H. (2008). “A twelve-analyzer detector system for high-resolution powder diffraction,” J. Synch. Rad. 15(5), 427–432.CrossRefGoogle ScholarPubMed
Lengauer, H. and Kluschanzoff, H. (2016). “Modified particles of palbociclib,” International Patent Application WO 2016/156070 A1.Google Scholar
Lukács, G., Márványos, E. L., Berecz, G., Heder, J. L., Milen, M., Peregi, B., Gudor, R., Volk, B., and Tóthné Lauritz, M. (2017). “Palbociclib salts,” International Patent Application WO 2017/072543 A1.Google Scholar
Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M., and Wood, P. A. (2020). “Mercury 4.0; from visualization to design and prediction,” J. Appl. Crystallogr. 53, 226–235.CrossRefGoogle ScholarPubMed
Mane, N. D., Nehate, S. P., Godbole, H. M., and Singh, G. P. (2017). “Modified particles of crystalline palbociclib free base and process for the preparation thereof,” International Patent Application WO 2017/145054 A1.Google Scholar
Materials Design (2016). MedeA 2.20.4 (Materials Design Inc., Angel Fire, NM).Google Scholar
MDI (2019). JADE Pro Version 7.8 (Computer software), Materials Data, Livermore CA, USA.Google Scholar
Peintinger, M. F., Vilela Oliveira, D., and Bredow, T. (2013). “Consistent Gaussian basis sets of triple-Zeta valence with polarization quality for solid-state calculations,” J. Comput. Chem. 34, 451–459.CrossRefGoogle ScholarPubMed
Rammohan, A., and Kaduk, J. A. (2018). “Crystal structures of alkali metal (group 1) citrate salts,” Acta Crystallogr. Sect. B: Cryst. Eng. Mater. 74, 239–252. doi:10.1107/S2052520618002330.CrossRefGoogle ScholarPubMed
Shields, G. P., Raithby, P. R., Allen, F. H., and Motherwell, W. S. (2000). “The assignment and validation of metal oxidation states in the cambridge structural database,” Acta Crystallogr. Sec. B: Struct. Sci. 56(3), 455–465.CrossRefGoogle ScholarPubMed
Silk Scientific (2013). UN-SCAN-IT 7.0 (Silk Scientific Corporation, Orem, UT).Google Scholar
Stefinovic, M. (2016). “Crystalline forms of palbociclib monohydrochloride,” International Patent Application WO 2016/066420 A1.Google Scholar
Sykes, R. A., McCabe, P., Allen, F. H., Battle, G. M., Bruno, I. J., and Wood, P. A. (2011). “New software for statistical analysis of Cambridge structural database data,” J. Appl. Crystallogr. 44, 882–886.CrossRefGoogle ScholarPubMed
Toby, B. H., and Von Dreele, R. B. (2013). “GSAS II: the genesis of a modern open source all purpose crystallography software package,” J. Appl. Crystallogr. 46, 544–549.CrossRefGoogle Scholar
Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D., and Spackman, M. A. (2017). CrystalExplorer17 (University of Western Australia). Available at: http://hirshfeldsurface.net.Google Scholar
van de Streek, J., and Neumann, M. A. (2014). “Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D),” Acta Crystallogr. Sect. B: Struct. Sci., Cryst. Eng. Mater. 70(6), 1020–1032.CrossRefGoogle Scholar
Wang, J., Toby, B. H., Lee, P. L., Ribaud, L., Antao, S. M., Kurtz, C., Ramanathan, M., Von Dreele, R. B., and Beno, M. A. (2008). “A dedicated powder diffraction beamline at the advanced photon source: commissioning and early operational results,” Rev. Sci. Instrum. 79, 085105.CrossRefGoogle Scholar
Wavefunction, Inc. (2020). Spartan ‘18 Version 1.4.5 (Wavefunction Inc., Irvine, CA).Google Scholar
Wheatley, A. M., and Kaduk, J. A. (2019). “Crystal structures of ammonium citrates,” Powder Diffr. 34, 35–43.CrossRefGoogle Scholar
Zvatora, P., Dammer, O., Miksatko, J., and Krejcik, I. (2016). “Solid forms of palbociclib salts,” International Patent Application WO 2016/127963.Google Scholar