data_CSF
#
_chem_comp.id CSF
_chem_comp.name "CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID"
_chem_comp.type "RNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C20 H30 F N4 O16 P"
_chem_comp.mon_nstd_parent_comp_id C
_chem_comp.pdbx_synonyms CMP-3FNEUAC
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-12-04
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 632.442
_chem_comp.one_letter_code C
_chem_comp.three_letter_code CSF
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
# #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
CSF C5A C5A C 0 1 N N R 22.128 -5.514 11.468 -0.501 -1.002 4.162 C5A CSF 1
CSF C4A C4A C 0 1 N N R 22.005 -4.016 11.206 -1.862 -1.356 3.552 C4A CSF 2
CSF C2A C2A C 0 1 N N S 20.752 -3.803 13.492 -1.574 0.675 2.135 C2A CSF 3
CSF O6A O6A O 0 1 N N N 21.531 -4.968 13.845 -0.384 1.021 2.841 O6A CSF 4
CSF C6A C6A C 0 1 N N R 22.472 -5.670 12.982 0.305 -0.188 3.148 C6A CSF 5
CSF C3A C3A C 0 1 N N R 20.939 -3.255 12.057 -2.533 -0.066 3.068 C3A CSF 6
CSF O4A O4A O 0 1 N N N 21.682 -3.890 9.804 -2.681 -1.986 4.539 O4A CSF 7
CSF N5A N5A N 0 1 N N N 23.114 -6.222 10.755 0.223 -2.232 4.491 N5A CSF 8
CSF C7A C7A C 0 1 N N R 22.363 -7.031 13.677 1.678 0.143 3.736 C7A CSF 9
CSF C8A C8A C 0 1 N N R 22.653 -7.190 15.150 1.499 0.954 5.022 C8A CSF 10
CSF C9A C9A C 0 1 N N N 22.735 -8.635 15.676 2.863 1.175 5.679 C9A CSF 11
CSF O9A O9A O 0 1 N N N 22.997 -8.659 17.056 2.696 1.932 6.880 O9A CSF 12
CSF O8A O8A O 0 1 N N N 23.915 -6.633 15.565 0.911 2.218 4.709 O8A CSF 13
CSF O7A O7A O 0 1 N N N 21.056 -7.596 13.365 2.375 -1.068 4.031 O7A CSF 14
CSF C1A C1A C 0 1 N N N 19.771 -3.135 14.370 -2.238 1.929 1.627 C1A CSF 15
CSF OBA OBA O 0 1 N N N 19.340 -1.877 14.094 -3.378 1.847 0.923 OBA CSF 16
CSF OAA OAA O 0 1 N N N 19.343 -3.747 15.302 -1.744 3.009 1.854 OAA CSF 17
CSF O1A O1A O 0 1 N N N 21.820 -2.911 13.997 -1.242 -0.165 1.028 O1A CSF 18
CSF O2A O2A O 0 1 N N N 24.350 -2.909 13.223 0.883 1.189 0.898 O2A CSF 19
CSF N1 N1 N 0 1 N N N 24.519 2.408 13.595 0.152 -0.817 -6.180 N1 CSF 20
CSF C2 C2 C 0 1 N N N 24.449 3.495 12.635 -0.714 0.211 -6.188 C2 CSF 21
CSF N3 N3 N 0 1 N N N 25.500 3.557 11.621 -1.710 0.264 -7.071 N3 CSF 22
CSF C4 C4 C 0 1 N N N 26.530 2.614 11.565 -1.880 -0.705 -7.959 C4 CSF 23
CSF C5 C5 C 0 1 N N N 26.607 1.476 12.559 -0.992 -1.801 -7.973 C5 CSF 24
CSF C6 C6 C 0 1 N N N 25.593 1.441 13.517 0.018 -1.837 -7.073 C6 CSF 25
CSF "C3'" C3* C 0 1 N N S 21.794 0.562 14.634 2.719 0.529 -3.879 "C3'" CSF 26
CSF "C2'" C2* C 0 1 N N R 21.999 2.000 14.241 2.100 0.442 -5.299 "C2'" CSF 27
CSF "C1'" C1* C 0 1 N N R 23.411 2.334 14.684 1.241 -0.844 -5.201 "C1'" CSF 28
CSF "O4'" O4* O 0 1 N N N 23.748 1.360 15.703 0.718 -0.798 -3.856 "O4'" CSF 29
CSF "C4'" C4* C 0 1 N N R 22.643 0.450 15.913 1.779 -0.327 -3.008 "C4'" CSF 30
CSF PA PA P 0 1 N N R 23.416 -2.715 14.360 -0.243 0.675 0.087 PA CSF 31
CSF "O5'" O5* O 0 1 N N N 23.955 -1.364 14.939 0.325 -0.277 -1.078 "O5'" CSF 32
CSF "C5'" C5* C 0 1 N N N 23.226 -0.887 16.093 1.201 0.523 -1.875 "C5'" CSF 33
CSF "O3'" O3* O 0 1 N N N 20.431 0.286 14.998 4.042 -0.009 -3.877 "O3'" CSF 34
CSF "O2'" O2* O 0 1 N N N 21.135 2.905 14.947 3.118 0.301 -6.290 "O2'" CSF 35
CSF N4 N4 N 0 1 N N N 27.437 2.726 10.635 -2.915 -0.643 -8.863 N4 CSF 36
CSF O2 O2 O 0 1 N N N 23.521 4.387 12.645 -0.579 1.116 -5.381 O2 CSF 37
CSF O3A O3A O 0 1 N N N 23.812 -3.618 15.332 -1.038 1.911 -0.569 O3A CSF 38
CSF C10 C10 C 0 1 N N N 23.054 -7.477 10.270 0.081 -2.792 5.709 C10 CSF 39
CSF O10 O10 O 0 1 N N N 22.051 -8.177 10.425 -0.646 -2.278 6.532 O10 CSF 40
CSF C11 C11 C 0 1 N N N 24.261 -8.009 9.528 0.826 -4.057 6.048 C11 CSF 41
CSF F3A F3A F 0 1 N N N 19.690 -3.497 11.573 -2.839 0.743 4.168 F3A CSF 42
CSF H5A H5A H 0 1 N N N 21.159 -5.951 11.131 -0.649 -0.412 5.067 H5A CSF 43
CSF H4A H4A H 0 1 N N N 22.968 -3.540 11.502 -1.720 -2.032 2.709 H4A CSF 44
CSF H6A H6A H 0 1 N N N 23.528 -5.324 12.896 0.433 -0.773 2.237 H6A CSF 45
CSF H3A H3A H 0 1 N N N 21.306 -2.202 12.029 -3.449 -0.311 2.530 H3A CSF 46
CSF H4 H4 H 0 1 N N N 21.605 -2.957 9.640 -3.524 -2.191 4.113 H4 CSF 47
CSF H3 H3 H 0 1 N N N 24.001 -5.757 10.561 0.805 -2.643 3.833 H3 CSF 48
CSF H7A H7A H 0 1 N N N 23.237 -7.576 13.251 2.251 0.726 3.016 H7A CSF 49
CSF H8A H8A H 0 1 N N N 21.767 -6.654 15.565 0.849 0.410 5.707 H8A CSF 50
CSF H9A1 1H9A H 0 0 N N N 21.817 -9.216 15.422 3.513 1.718 4.994 H9A1 CSF 51
CSF H9A2 2H9A H 0 0 N N N 23.481 -9.236 15.106 3.311 0.210 5.918 H9A2 CSF 52
CSF H9A H9A H 0 1 N N N 23.047 -9.550 17.380 3.576 2.048 7.262 H9A CSF 53
CSF H2 H2 H 0 1 N N N 24.097 -6.733 16.491 1.516 2.666 4.102 H2 CSF 54
CSF H1 H1 H 0 1 N N N 20.988 -8.439 13.796 1.962 -1.444 4.820 H1 CSF 55
CSF HBA HBA H 0 1 N N N 18.708 -1.447 14.659 -3.804 2.652 0.598 HBA CSF 56
CSF H7 H7 H 0 1 N N N 27.382 0.692 12.584 -1.117 -2.599 -8.690 H7 CSF 57
CSF H6 H6 H 0 1 N N N 25.642 0.613 14.244 0.711 -2.665 -7.064 H6 CSF 58
CSF "H3'" H3* H 0 1 N N N 22.056 -0.134 13.804 2.728 1.561 -3.529 "H3'" CSF 59
CSF "H2'" H2* H 0 1 N N N 21.797 2.110 13.149 1.475 1.311 -5.506 "H2'" CSF 60
CSF "H1'" H1* H 0 1 N N N 23.393 3.388 15.045 1.860 -1.730 -5.341 "H1'" CSF 61
CSF "H4'" H4* H 0 1 N N N 22.007 0.667 16.803 2.326 -1.173 -2.594 "H4'" CSF 62
CSF "H5'" 1H5* H 0 1 N N N 23.868 -0.916 17.003 0.645 1.360 -2.297 "H5'" CSF 63
CSF "H5''" 2H5* H 0 0 N N N 22.442 -1.620 16.393 2.013 0.901 -1.255 "H5''" CSF 64
CSF "HO3'" H3T H 0 0 N Y N 20.301 -0.621 15.246 4.565 0.531 -4.484 "HO3'" CSF 65
CSF H8 H8 H 0 1 N N N 21.264 3.812 14.698 3.614 1.131 -6.302 H8 CSF 66
CSF H41 1H4 H 0 1 N N N 28.188 2.037 10.594 -3.524 0.111 -8.851 H41 CSF 67
CSF H42 2H4 H 0 1 N N N 27.847 3.658 10.686 -3.037 -1.354 -9.511 H42 CSF 68
CSF H5 H5 H 0 1 N N N 24.731 -3.505 15.541 -1.762 1.534 -1.088 H5 CSF 69
CSF H111 1H11 H 0 0 N N N 24.211 -9.048 9.126 0.587 -4.358 7.068 H111 CSF 70
CSF H112 2H11 H 0 0 N N N 24.519 -7.308 8.699 0.532 -4.848 5.358 H112 CSF 71
CSF H113 3H11 H 0 0 N N N 25.162 -7.910 10.177 1.899 -3.881 5.962 H113 CSF 72
# #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
CSF C5A C4A SING N N 1
CSF C5A C6A SING N N 2
CSF C5A N5A SING N N 3
CSF C5A H5A SING N N 4
CSF C4A C3A SING N N 5
CSF C4A O4A SING N N 6
CSF C4A H4A SING N N 7
CSF C2A O6A SING N N 8
CSF C2A C3A SING N N 9
CSF C2A C1A SING N N 10
CSF C2A O1A SING N N 11
CSF O6A C6A SING N N 12
CSF C6A C7A SING N N 13
CSF C6A H6A SING N N 14
CSF C3A F3A SING N N 15
CSF C3A H3A SING N N 16
CSF O4A H4 SING N N 17
CSF N5A C10 SING N N 18
CSF N5A H3 SING N N 19
CSF C7A C8A SING N N 20
CSF C7A O7A SING N N 21
CSF C7A H7A SING N N 22
CSF C8A C9A SING N N 23
CSF C8A O8A SING N N 24
CSF C8A H8A SING N N 25
CSF C9A O9A SING N N 26
CSF C9A H9A1 SING N N 27
CSF C9A H9A2 SING N N 28
CSF O9A H9A SING N N 29
CSF O8A H2 SING N N 30
CSF O7A H1 SING N N 31
CSF C1A OBA SING N N 32
CSF C1A OAA DOUB N N 33
CSF OBA HBA SING N N 34
CSF O1A PA SING N N 35
CSF O2A PA DOUB N N 36
CSF N1 C2 SING N N 37
CSF N1 C6 SING N N 38
CSF N1 "C1'" SING N N 39
CSF C2 N3 SING N N 40
CSF C2 O2 DOUB N N 41
CSF N3 C4 DOUB N N 42
CSF C4 C5 SING N N 43
CSF C4 N4 SING N N 44
CSF C5 C6 DOUB N N 45
CSF C5 H7 SING N N 46
CSF C6 H6 SING N N 47
CSF "C3'" "C2'" SING N N 48
CSF "C3'" "C4'" SING N N 49
CSF "C3'" "O3'" SING N N 50
CSF "C3'" "H3'" SING N N 51
CSF "C2'" "C1'" SING N N 52
CSF "C2'" "O2'" SING N N 53
CSF "C2'" "H2'" SING N N 54
CSF "C1'" "O4'" SING N N 55
CSF "C1'" "H1'" SING N N 56
CSF "O4'" "C4'" SING N N 57
CSF "C4'" "C5'" SING N N 58
CSF "C4'" "H4'" SING N N 59
CSF PA "O5'" SING N N 60
CSF PA O3A SING N N 61
CSF "O5'" "C5'" SING N N 62
CSF "C5'" "H5'" SING N N 63
CSF "C5'" "H5''" SING N N 64
CSF "O3'" "HO3'" SING N N 65
CSF "O2'" H8 SING N N 66
CSF N4 H41 SING N N 67
CSF N4 H42 SING N N 68
CSF O3A H5 SING N N 69
CSF C10 O10 DOUB N N 70
CSF C10 C11 SING N N 71
CSF C11 H111 SING N N 72
CSF C11 H112 SING N N 73
CSF C11 H113 SING N N 74
# #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
CSF SMILES ACDLabs 10.04 "FC3C(O)C(NC(=O)C)C(OC3(OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O)C(=O)O)C(O)C(O)CO"
CSF SMILES_CANONICAL CACTVS 3.341 "CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@@](O[C@H]1[C@H](O)[C@H](O)CO)(O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=NC3=O)N)C(O)=O"
CSF SMILES CACTVS 3.341 "CC(=O)N[CH]1[CH](O)[CH](F)[C](O[CH]1[CH](O)[CH](O)CO)(O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=NC3=O)N)C(O)=O"
CSF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)N[C@@H]1[C@H]([C@H](C(O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)F)O"
CSF SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC1C(C(C(OC1C(C(CO)O)O)(C(=O)O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)F)O"
CSF InChI InChI 1.03 "InChI=1S/C20H30FN4O16P/c1-6(27)23-10-13(31)16(21)20(18(33)34,40-15(10)11(29)7(28)4-26)41-42(36,37)38-5-8-12(30)14(32)17(39-8)25-3-2-9(22)24-19(25)35/h2-3,7-8,10-17,26,28-32H,4-5H2,1H3,(H,23,27)(H,33,34)(H,36,37)(H2,22,24,35)/t7-,8-,10-,11-,12-,13-,14-,15-,16-,17-,20-/m1/s1"
CSF InChIKey InChI 1.03 HNJLGUNKGJTPBF-JTKQZVQZSA-N
# #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
CSF "SYSTEMATIC NAME" ACDLabs 10.04 "(2S,3R,4R,5R,6R)-5-(acetylamino)-2-{[(R)-{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)"
CSF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(3R,4R,5R,6R)-5-acetamido-2-[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CSF "Create component" 2003-12-04 RCSB
CSF "Modify descriptor" 2011-06-04 RCSB
CSF "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id CSF
_pdbx_chem_comp_synonyms.name CMP-3FNEUAC
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##