Home Crystal structure of 14-O-[(4-(4-hydroxypiperidine-1-yl)-6-methylpyrimidine-2-yl)thioacetyl]-mutilin monohydrate, C32H49N3O6S
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Crystal structure of 14-O-[(4-(4-hydroxypiperidine-1-yl)-6-methylpyrimidine-2-yl)thioacetyl]-mutilin monohydrate, C32H49N3O6S

  • Si-Jie Liu ORCID logo EMAIL logo , Yuan Fan and Ruofeng Shang ORCID logo
Published/Copyright: December 8, 2021
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 237 Issue 1

Abstract

C32H49N3O6S, orthorhombic, P212121 (no. 19), a = 9.2618(2) Å, b = 12.4066(2) Å, c = 27.2256(5) Å, V = 3128.42(12) Å3, Z = 4, R gt (F) = 0.0517, wR ref (F 2) = 0.1355, T = 173.20(2) K.

CCDC no.: 2111927

The molecular structure is shown in the figure (the carbon bound hydrogen atoms are omitted for clarity). Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colorless block
Size: 0.18 × 0.15 × 0.12 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 1.31 mm−1
Diffractometer, scan mode: SuperNova, ω
θ max, completeness: 66.6°, 98%
N(hkl)measured, N(hkl)unique, R int: 9661, 5241, 0.041
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 4775
N(param)refined: 397
Programs: Olex2 [1], SHELX [2], CrysAlisPRO [3]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
S1 −0.12855 (13) −0.43111 (8) −0.13950 (3) 0.0269 (2)
O1 −0.9226 (5) −0.0675 (3) −0.19578 (13) 0.0473 (10)
O2 −0.6185 (4) −0.2359 (3) −0.40201 (10) 0.0302 (7)
H2 −0.700767 −0.230071 −0.412812 0.045*
O3 −0.3779 (4) −0.2201 (2) −0.20234 (9) 0.0258 (6)
O4 −0.3271 (4) −0.3949 (3) −0.21774 (12) 0.0403 (9)
O5 0.0149 (5) 0.1497 (3) 0.00810 (11) 0.0388 (8)
H5 0.043678 0.169810 0.035059 0.058*
N1 0.1182 (5) −0.1675 (3) −0.03142 (13) 0.0329 (9)
N2 0.0100 (4) −0.2957 (3) −0.08025 (12) 0.0255 (8)
N3 0.0126 (5) −0.4842 (3) −0.06024 (13) 0.0300 (8)
C1 −0.2764 (9) −0.3181 (5) −0.3737 (3) 0.065 (2)
H1A −0.256 (9) −0.285 (7) −0.401 (3) 0.08 (3)*
H1B −0.225 (7) −0.385 (6) −0.373 (2) 0.052 (18)*
C2 −0.3687 (5) −0.2942 (3) −0.34063 (15) 0.0286 (9)
H2A −0.382369 −0.345965 −0.316370 0.034*
C3 −0.4593 (5) −0.1926 (3) −0.33547 (14) 0.0231 (8)
C4 −0.3986 (5) −0.1031 (3) −0.36821 (14) 0.0281 (9)
H4A −0.396006 −0.127420 −0.401665 0.042*
H4B −0.302605 −0.085233 −0.357660 0.042*
H4C −0.459054 −0.040452 −0.365819 0.042*
C5 −0.6189 (5) −0.2146 (3) −0.35041 (13) 0.0224 (8)
H5A −0.673578 −0.148010 −0.345063 0.027*
C6 −0.6979 (5) −0.3077 (3) −0.32141 (14) 0.0242 (9)
H6 −0.622497 −0.345356 −0.302918 0.029*
C7 −0.8043 (5) −0.2602 (3) −0.28204 (15) 0.0245 (9)
C8 −0.7534 (5) −0.1614 (3) −0.25153 (14) 0.0242 (9)
H8 −0.713034 −0.109552 −0.274977 0.029*
C9 −0.6355 (5) −0.1810 (3) −0.21214 (13) 0.0226 (8)
C10 −0.4917 (5) −0.2186 (3) −0.23766 (13) 0.0223 (8)
H10 −0.506039 −0.292530 −0.249300 0.027*
C11 −0.4465 (5) −0.1492 (3) −0.28211 (14) 0.0213 (8)
H11A −0.346340 −0.129169 −0.277127 0.026*
H11B −0.502398 −0.083137 −0.280575 0.026*
C12 −0.7659 (6) −0.3903 (4) −0.35360 (16) 0.0364 (11)
H12A −0.812351 −0.443843 −0.333651 0.055*
H12B −0.693088 −0.423825 −0.373479 0.055*
H12C −0.836217 −0.356405 −0.374419 0.055*
C13 −0.9411 (5) −0.2168 (4) −0.30832 (17) 0.0326 (10)
H13A −0.915097 −0.180107 −0.338515 0.039*
H13B −1.006605 −0.275318 −0.316103 0.039*
C14 −1.0110 (5) −0.1385 (4) −0.27232 (18) 0.0389 (11)
H14A −1.040277 −0.073063 −0.289058 0.047*
H14B −1.095403 −0.170935 −0.257265 0.047*
C15 −0.8973 (6) −0.1139 (4) −0.23374 (16) 0.0325 (10)
C16 −0.8516 (5) −0.3471 (4) −0.24431 (15) 0.0288 (9)
H16A −0.941663 −0.324349 −0.229337 0.035*
H16B −0.870175 −0.413855 −0.261740 0.035*
C17 −0.7419 (5) −0.3692 (3) −0.20363 (16) 0.0272 (9)
H17A −0.656507 −0.401842 −0.217878 0.033*
H17B −0.782938 −0.420177 −0.180497 0.033*
C18 −0.6982 (5) −0.2665 (3) −0.17607 (15) 0.0271 (9)
H18 −0.787980 −0.235676 −0.163184 0.033*
C19 −0.6053 (6) −0.2946 (4) −0.13087 (15) 0.0332 (10)
H19A −0.524769 −0.338013 −0.140908 0.050*
H19B −0.662635 −0.333798 −0.107558 0.050*
H19C −0.570645 −0.229360 −0.115998 0.050*
C20 −0.6014 (5) −0.0749 (3) −0.18531 (15) 0.0288 (9)
H20A −0.515813 −0.083831 −0.165835 0.043*
H20B −0.680883 −0.056064 −0.164375 0.043*
H20C −0.586233 −0.018702 −0.208972 0.043*
C21 −0.3053 (5) −0.3114 (3) −0.19607 (14) 0.0252 (9)
C22 −0.1931 (5) −0.2979 (3) −0.15656 (15) 0.0279 (9)
H22A −0.234786 −0.262103 −0.128238 0.034*
H22B −0.113654 −0.254318 −0.168622 0.034*
C23 −0.0217 (5) −0.3981 (3) −0.08732 (14) 0.0232 (8)
C24 0.0880 (6) −0.4604 (4) −0.01980 (17) 0.0333 (11)
C25 0.1277 (6) −0.3573 (4) −0.00738 (15) 0.0324 (10)
H25 0.179876 −0.343606 0.021132 0.039*
C26 0.0866 (5) −0.2722 (4) −0.03939 (15) 0.0271 (9)
C27 0.1285 (8) −0.5551 (4) 0.0121 (2) 0.0506 (15)
H27A 0.042728 −0.593002 0.021774 0.076*
H27B 0.178093 −0.529761 0.040867 0.076*
H27C 0.190520 −0.602776 −0.005938 0.076*
C28 0.1883 (7) −0.1263 (4) 0.01269 (18) 0.0419 (13)
H28A 0.287636 −0.107604 0.005257 0.050*
H28B 0.188982 −0.181752 0.037810 0.050*
C29 0.1094 (6) −0.0276 (4) 0.03170 (16) 0.0364 (11)
H29A 0.160352 0.001030 0.059957 0.044*
H29B 0.013152 −0.048068 0.042186 0.044*
C30 0.0987 (6) 0.0592 (4) −0.00782 (15) 0.0304 (10)
H30 0.195971 0.083615 −0.016566 0.036*
C31 0.0264 (6) 0.0123 (4) −0.05274 (15) 0.0303 (10)
H31A 0.024181 0.066028 −0.078617 0.036*
H31B −0.072394 −0.006902 −0.044833 0.036*
C32 0.1065 (6) −0.0869 (4) −0.07072 (14) 0.0315 (10)
H32A 0.055511 −0.117761 −0.098472 0.038*
H32B 0.202348 −0.066417 −0.081627 0.038*
O6 −0.1157 (5) −0.7014 (3) −0.05776 (15) 0.0516 (10)
H6A −0.064702 −0.645259 −0.061959 0.077*
H6B −0.082198 −0.737619 −0.033828 0.077*

Source of material

Triethylamine (0.73 g, 7.2 mmol), 4-dimethylaminopyridine (0.01 g, 0.1 mmol) and mesitylene-2-sulfonyl chloride (0.50 g, 2.3 mmol) were added to a solution of 14-O-[(4-ol-6-methylpyrimidine-2-yl)thioacetyl] mutilin (0.75 g, 1.5 mmol) in 20 ml dry dichloromethane. After the mixture was stirred at room temperature for 3 h, piperidin-4-ol (0.76 g, 7.5 mmol) and 1-methylpyrrolidine (1.27 g, 15 mmol) were then added in one portion for stirring for 1.5 h at 273.15 K. The mixture was washed with 5% citric acid, followed by drying with Na2SO4 overnight and rotary evaporation to dryness. The crude residue was purified by silica gel column chromatography (petroleum ether: ethyl acetate 1:1–1:10 v/v) to afford the pure product with a yield of 63%. The clear light colorless crystals were obtained by slow evaporation from a solution of dichloromethane and n-hexane (1:1) at room temperature.

Experimental details

All hydrogen atoms were placed in geometrically idealized positions. The U iso values were set to 1.5U eq of the carrier atom for methyl and oxygen H atoms and 1.2 for the remaining H atoms.

Comment

The title compound may possess antibacterial activities against some Gram-positive bacteria, including Staphylococcus aureus, methicillin-resistant Staphylococcus epidermidis (MRSE), methicillin-resistant S. aureus (MRSA), Streptococcus dysgalactiae and Streptococcus agalactiae and merited further drug development as a potential agent [4]. The starting material was pleuromutilin, which was first isolated in a crystalline form from cultures of two species of basidiomycetes, Pleurotus mutilus and Pleurotus  passeckerianus in 1951 [5]. The pleuromutilin class showed high antibacterial activities with no target-specific cross-resistance to other antibiotics with an unique mode of action, which involve inhibtion of protein synthesis by primarily inhibiting ribosomal peptidyl transferase center (PTC) [6, 7]. The molecular modifications of pleuromutilin led to four drugs: tiamulin, valnemulin, retapamulin and lefamulin [8], [9], [10].

The asymmetric unit is composed of a molecule of 14-O-[(4-(4-Hydroxypiperidine-1-yl)-6-methylpyrimidine-2-yl) thioacetyl] mutilin and a molecule of water. The title molecule is comprised of a 5-6-8 tricyclic carbon skeleton and a methyl pyrimidine group, in which all bond lengths are in normal ranges [11, 12]. The six-membered ring (C9, C8, C7, C16–C18) exhibits a chair conformation and the eight-membered ring (C3, C5–C11) exhibits an irregular boat conformation, which were similar as the previous reported pleuromutilin derivative [11]. The structure is stabilized by some intramolecular hydrogen bonds (for example: C10—H10⃛O4, C18–H18⃛O1, C20–H20A⃛O3, C32–H32A⃛N2). Notably, the hydrogen bond of O2–H2⃛O6, O6–H6A⃛N3 and O6–H6B⃛O5 between the target and water molecules are present.

Corresponding author: Si-Jie Liu, College of Chemical Engineering, Shijiazhuang University, 050035, Shijiazhuang, Hebei, People’s Republic of China, E-mail:

Funding source: Quancheng Scholar Construction Project of Jinan

Award Identifier / Grant number: 00252019025

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was financial supported by Quancheng Scholar Construction Project of Jinan (No. 00252019025).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

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Received: 2021-10-16
Accepted: 2021-11-25
Published Online: 2021-12-08
Published in Print: 2022-02-23

© 2021 Si-Jie Liu et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  42. The crystal structure of N′-(2-chloro-6-hydroxybenzylidene)thiophene-2-carbohydrazide monohydrate, C12H11ClN2O3S
  43. Crystal structure of catena-poly[(μ2-1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol)-κ2N:N′)-bis(4-bromobenzoate-κ1O)zinc(II)], C64H44Br4N8O8Zn2
  44. The crystal structure of catena-poly[(1-(4-carboxybenzyl)pyridin-1-ium-4-carboxylato-κ1O)-(μ2-oxalato-κ4 O:O′:O″:O‴)dioxidouranium(VI)], C16H11NO10U
  45. Crystal structure of 3-allyl-4-(2-bromoethyl)-5-(4-methoxyphenyl)-2-phenylfuran, C22H21BrO2
  46. Halogen bonds in the crystal structure of 4,3′:5′,4″-terpyridine — 1,3-diiodotetrafluorobenzene (1/1), C21H11F4I2N3
  47. Crystal structure of 2-(1H-indol-3-yl)ethan-1-aminium 2-(4-acetylphenoxy)acetate, C20H22N2O4
  48. Chalcogen bonds in the crystal structure of 4,7-dibromo-2,1,3-benzoselenadiazole, C6H2Br2N2Se
  49. The crystal structure of 1,4-bis((1H-benzimidazol-2-yl)methyl)-piperazine-2,5-dione dihydrate, C20H22N6O4
  50. The crystal structure of C19H20O8
  51. The crystal structure of KNa3Te8O18·5H2O exhibiting a ∞2[Te4O9]2− layer
  52. Erratum
  53. Erratum to: Crystal structure of (Z)-3-(6-bromo-1H-indol-3-yl)-1,3-diphenylprop-2-en-1-one, C23H16BrNO
https://doi.org/10.1515/ncrs-2021-0403
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of (E)-7-hydroxy-2-((6-methoxypyridin-3-yl)methylene)-3, 4-dihydronaphthalen-1(2H)-one, C17H15NO3
  4. Crystal structure of (E)-7-methoxy-2-((2-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1 (2H)-one, C18H17NO3
  5. The crystal structure of N 6,N 6′-di(pyridin-2-yl)-[2,2′-bipyridine]-6,6′-diamine, C20H16N6
  6. The crystal structure of {N 1,N 2-bis[2,4-dimethyl-6-(4-(tert-butyl)phenyl)(phenyl)methyl]acenaphthylene-1,2-diimino-κ2 N, N′}-dibromido-nickel(II) – dichloromethane(1/2), C64H64Br2Cl4N2Ni
  7. Synthesis and crystal structure of nonacarbonyltris[(2-thia-1,3,5-triaza-7-phosphatricylco[3.3.1.1]decane-κ1 P)-2,2-dioxide]triruthenium(0) – acetonitrile (7/6), C25.71H32.57N9.86O15P3S3Ru3
  8. A new polymorph of 1-(4-nitrophenyl)-1H-benzimidazole (C13H9N3O2)
  9. The crystal structure of 2,2′-((1E,1′E)-(naphthalene-2,3 diylbis(azanylylidene)) bis(methanylylidene))bis(4-methylphenol), C26H22N2O2
  10. The crystal structure of bis(μ2-iodido)-bis(η6-benzene)-bis(iodido)-diosmium(II), C12H12I4Os2
  11. Redetermination of the crystal structure of bis{hydridotris(3,5-dimethylpyrazol-1-yl-κN 3)borato}copper(II), C30H44B2CuN12
  12. Crystal structure of (E)-3-((4-(tert-butyl)phenyl)thio)-4-hydroxypent-3-en-2-one, C15H20O2S
  13. Crystal structure of 2,2′-(p-tolylazanediyl)bis(1-phenylethan-1-one), C23H21NO2
  14. Redetermination of the crystal structure of the crystal sponge the poly[tetrakis(μ3-2,4,6-tris(pyridin-4-yl)-1,3,5-triazine)-dodecaiodidohexazinc(II) nitrobenzene solvate], C72H48I12N24Zn6⋅10(C6H5NO2)
  15. Crystal structure of (4′E)-6′-(diethylamino)-2-[(E)-[(6-methylpyridin-2-yl)methylidene]amino]-4′-{2-[(2E)-1,3,3-trimethyl-2,3-dihydro-1H-indol-2-ylidene]ethylidene}-1′,2,2′,3,3′,4′-hexahydrospiro[isoindole-1,9′-xanthene]-3-one, C44H45N5O2
  16. Crystal structure of (E)-7-fluoro-2-(3-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C17H12F2O1
  17. Crystal structure of tetrabutylammonium sulfanilate – 1-(diaminomethylene)thiourea (1/2)
  18. Crystal structure of [2,2′-{azanediyl)bis[(propane-3,1-diyl)(azanylylidene)methylylidene]} bis(3,5-dichlorophenolato)-κ2O,O′]-isothiocyanato-κN-iron(III), C21H19Cl4FeN4O2S
  19. Crystal structure of (4-chlorophenyl)(4-hydroxyphenyl)methanone, C13H9ClO2
  20. Crystal structure of 6,6′-((pentane-1,3-diylbis(azaneylylidene))bis(methaneylylidene))bis(2,4-dibromolphenolato-κ4 N,N′,O,O′)copper(II),) C19H16Br4CuN2O2
  21. Chlorido-(2,2′-(ethane-bis(5-methoxyphenolato))-κ4 N,N′,O,O′)manganese(III) monohydrate, C19H18Cl2CuN2O2
  22. Crystal structure of 2,6-di-tert-butyl-4-(4-methoxybenzylidene)cyclohexa-2,5-dien-1-one, C22H28O2
  23. Crystal structure of [6,6′-(((2,2-dimethylpropane-1,3-diyl)bis(azanylylidene))bis(methanylylidene))bis(2-chlorophenolato)-κ4N,N′,O,O′]copper(II)
  24. Crystal structure of 2-chloro-3-((thiophen-2-ylmethyl)amino)naphthalene-1,4-dione, C30H20O4N2Cl2S2
  25. Crystal structure of bis{hydridotris(3-trifluoromethyl-5-methylpyrazolyl-1-yl)borato-κN 3}manganese(II), C30H26B2F18MnN12
  26. Crystal structure of 1-(2-methylphenyl)-2-(2-methylbenzo[b]thienyl)-3,3,4,4,5,5-hexafluorocyclopent-ene, C21H14F6S
  27. Crystal structure of 2-(3-((carbamimidoylthio)methyl)benzyl)isothiouronium hexafluorophosphate monohydrate, C10H17F6N4OPS2
  28. Crystal structure of 4,5-diiodo-1,3-dimesityl-1H-1,2,3-triazol-3-ium chloride – chloroform (1/1), C21H23Cl4I2N3
  29. Crystal structure of azido-k1 N-{6,6′-((((methylazanediyl)bis(propane-3,1-diyl))bis(azanylylidene))bis(methanylylidene))bis(2,4-dibromophenolato)k5 N,N′,N″,O,O′}cobalt(III)-methanol (1/1)), C21H23Br4CoN6O3
  30. The crystal structure of 2-(4-((carbamimidoylthio)methyl)benzyl)isothiouronium hexafluorophosphate monohydrate, C10H17F6N4OPS2
  31. Crystal structure of 1,1′-(methane-1,1-diyl)bis(3-methyl-1H-imidazol-3-ium) bis(hexafluoridophosphate), C9H14F12N4P2
  32. Crystal structure of (4′E)-6′-(diethylamino)-2-[(E)-[(pyren-1-yl)methylidene]amino]-4′-{2-[(2E)-1,3,3-trimethyl-2,3-dihydro-1H-indol-2-ylidene]ethylidene}-1′,2,2′,3,3′,4′-hexahydrospiro[isoindole-1,9′-xanthene]-3-one, C54H48N4O2
  33. Crystal structure of poly[bis(μ2-2,6-bis(1-imidazoly)pyridine-κ2 N,N′)-bis(thiocyanato-κ1 N)copper(II)] dithiocyanate, C24H18CuN12S2
  34. Cones with a three-fold symmetry constructed from three hydrogen bonded theophyllinium cations that coat [FeCl4]− anions in the crystal structure of tris(theophyllinium) bis(tetrachloridoferrate(III)) chloride trihydrate, C21H33Cl9Fe2N12O9
  35. Crystal structure of 14-O-[(4-(4-hydroxypiperidine-1-yl)-6-methylpyrimidine-2-yl)thioacetyl]-mutilin monohydrate, C32H49N3O6S
  36. The crystal structure of (E)-3-chloro-2-(2-(4-methylbenzylidene)hydrazinyl)pyridine, C13H12ClN3
  37. The crystal structure of 4-phenyl-4-[2-(pyridine-4-carbonyl)hydrazinylidene]butanoic acid, C16H15N3O3
  38. The crystal structure of 6-amino-5-carboxypyridin-1-ium pentaiodide monohydrate C6H9I5N2O3
  39. Crystal structure of bis(μ3-oxido)-bis(μ2-2-formylbenzoato-k2O:O′)-bis(2-(dimethoxymethyl)-benzoato-κO)-oktakismethyl-tetratin(IV)
  40. Crystal structure of 2-((E)-(((E)-2-hydroxy-4-methylbenzylidene) hydrazineylidene)methyl)-4-methylphenol, C16H16N2O2
  41. Crystal structure of (E)-amino(2-((5-methylfuran-2-yl)methylene)hydrazinyl) methaniminium nitrate monohydrate, C14H26N10O10
  42. The crystal structure of N′-(2-chloro-6-hydroxybenzylidene)thiophene-2-carbohydrazide monohydrate, C12H11ClN2O3S
  43. Crystal structure of catena-poly[(μ2-1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol)-κ2N:N′)-bis(4-bromobenzoate-κ1O)zinc(II)], C64H44Br4N8O8Zn2
  44. The crystal structure of catena-poly[(1-(4-carboxybenzyl)pyridin-1-ium-4-carboxylato-κ1O)-(μ2-oxalato-κ4 O:O′:O″:O‴)dioxidouranium(VI)], C16H11NO10U
  45. Crystal structure of 3-allyl-4-(2-bromoethyl)-5-(4-methoxyphenyl)-2-phenylfuran, C22H21BrO2
  46. Halogen bonds in the crystal structure of 4,3′:5′,4″-terpyridine — 1,3-diiodotetrafluorobenzene (1/1), C21H11F4I2N3
  47. Crystal structure of 2-(1H-indol-3-yl)ethan-1-aminium 2-(4-acetylphenoxy)acetate, C20H22N2O4
  48. Chalcogen bonds in the crystal structure of 4,7-dibromo-2,1,3-benzoselenadiazole, C6H2Br2N2Se
  49. The crystal structure of 1,4-bis((1H-benzimidazol-2-yl)methyl)-piperazine-2,5-dione dihydrate, C20H22N6O4
  50. The crystal structure of C19H20O8
  51. The crystal structure of KNa3Te8O18·5H2O exhibiting a ∞2[Te4O9]2− layer
  52. Erratum
  53. Erratum to: Crystal structure of (Z)-3-(6-bromo-1H-indol-3-yl)-1,3-diphenylprop-2-en-1-one, C23H16BrNO
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