data_B9H # _chem_comp.id B9H _chem_comp.name "2'-methyl, 3-propyl, cytidine-5'-monophosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H24 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-26 _chem_comp.pdbx_modified_date 2019-05-06 _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 381.319 _chem_comp.one_letter_code C _chem_comp.three_letter_code B9H _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6EK0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 B9H C2 C1 C 0 1 N N N 212.115 258.149 295.824 -2.761 0.120 -0.291 C2 B9H 1 B9H C4 C2 C 0 1 N N R 210.174 257.513 297.120 -3.549 -1.238 1.554 C4 B9H 2 B9H C5 C3 C 0 1 N N N 210.005 256.437 296.284 -2.164 -1.123 2.155 C5 B9H 3 B9H C6 C4 C 0 1 N N N 210.875 256.243 295.233 -1.256 -0.426 1.497 C6 B9H 4 B9H C32 C5 C 0 1 N N N 211.199 260.899 297.209 -5.145 -1.827 -1.316 C32 B9H 5 B9H "C1'" C6 C 0 1 N N R 212.885 256.851 293.895 -0.499 0.944 -0.385 "C1'" B9H 6 B9H "C2'" C7 C 0 1 N N R 214.114 256.042 294.309 -0.085 2.175 0.460 "C2'" B9H 7 B9H "C3'" C8 C 0 1 N N R 213.668 254.654 293.928 1.359 2.437 -0.033 "C3'" B9H 8 B9H C31 C9 C 0 1 N N N 211.415 259.524 297.812 -5.093 -0.615 -0.384 C31 B9H 9 B9H C33 C10 C 0 1 N N N 210.971 261.966 298.251 -6.513 -1.888 -1.998 C33 B9H 10 B9H "C4'" C11 C 0 1 N N R 213.132 254.978 292.557 1.797 1.093 -0.648 "C4'" B9H 11 B9H "C5'" C12 C 0 1 N N N 212.307 253.847 292.005 3.050 0.579 0.064 "C5'" B9H 12 B9H N1 N1 N 0 1 N N N 211.920 257.047 294.994 -1.555 0.186 0.290 N1 B9H 13 B9H N3 N2 N 0 1 N N N 211.237 258.396 296.894 -3.783 -0.558 0.269 N3 B9H 14 B9H N4 N3 N 0 1 N N N 209.315 257.710 298.141 -3.845 -2.665 1.370 N4 B9H 15 B9H O2 O1 O 0 1 N N N 213.081 258.891 295.585 -2.940 0.692 -1.349 O2 B9H 16 B9H "O2'" O2 O 0 1 N N N 215.180 256.403 293.452 -0.930 3.293 0.180 "O2'" B9H 17 B9H "O3'" O3 O 0 1 N N N 214.441 253.438 294.115 1.371 3.467 -1.023 "O3'" B9H 18 B9H "O4'" O4 O 0 1 N N N 212.326 256.123 292.806 0.715 0.166 -0.463 "O4'" B9H 19 B9H "O5'" O5 O 0 1 N N N 211.466 253.422 293.048 3.506 -0.614 -0.576 "O5'" B9H 20 B9H OP1 O6 O 0 1 N N N 209.463 252.161 293.816 4.667 -1.770 1.344 OP1 B9H 21 B9H OP2 O7 O 0 1 N N N 210.722 251.435 291.790 4.947 -2.781 -0.951 OP2 B9H 22 B9H P P1 P 0 1 N N N 210.216 252.586 292.597 4.807 -1.429 -0.089 P B9H 23 B9H C21 C13 C 0 1 N N N 215.977 257.462 293.956 -1.102 4.183 1.285 "CO2'" B9H 24 B9H H1 H1 H 0 1 N N N 210.816 256.905 297.775 -4.262 -0.842 2.277 H1 B9H 25 B9H H2 H2 H 0 1 N N N 209.193 255.745 296.450 -1.926 -1.599 3.095 H2 B9H 26 B9H H3 H3 H 0 1 N N N 210.707 255.405 294.572 -0.262 -0.331 1.907 H3 B9H 27 B9H H4 H4 H 0 1 N N N 212.088 261.168 296.620 -4.366 -1.737 -2.073 H4 B9H 28 B9H H5 H5 H 0 1 N N N 210.320 260.859 296.549 -4.987 -2.738 -0.738 H5 B9H 29 B9H H6 H6 H 0 1 N N N 213.226 257.836 293.542 -0.824 1.252 -1.379 H6 B9H 30 B9H H7 H7 H 0 1 N N N 214.340 256.139 295.381 -0.096 1.939 1.524 H7 B9H 31 B9H H8 H8 H 0 1 N N N 212.762 254.495 294.532 2.005 2.704 0.803 H8 B9H 32 B9H H9 H9 H 0 1 N N N 210.702 259.402 298.641 -5.251 0.295 -0.962 H9 B9H 33 B9H H10 H10 H 0 1 N N N 212.442 259.483 298.203 -5.872 -0.705 0.373 H10 B9H 34 B9H H11 H11 H 0 1 N N N 210.821 262.937 297.756 -6.550 -2.751 -2.663 H11 B9H 35 B9H H12 H12 H 0 1 N N N 210.079 261.715 298.843 -7.293 -1.978 -1.242 H12 B9H 36 B9H H13 H13 H 0 1 N N N 211.847 262.024 298.914 -6.672 -0.977 -2.576 H13 B9H 37 B9H H14 H14 H 0 1 N N N 213.961 255.212 291.872 1.999 1.221 -1.711 H14 B9H 38 B9H H15 H15 H 0 1 N N N 211.707 254.195 291.151 3.831 1.338 0.018 H15 B9H 39 B9H H16 H16 H 0 1 N N N 212.960 253.022 291.683 2.814 0.364 1.106 H16 B9H 40 B9H H17 H17 H 0 1 N N N 209.580 258.531 298.646 -3.759 -3.168 2.240 H17 B9H 41 B9H H18 H18 H 0 1 N N N 208.389 257.825 297.780 -4.761 -2.795 0.966 H18 B9H 42 B9H H20 H20 H 0 1 N N N 214.709 253.369 295.024 2.251 3.672 -1.367 H20 B9H 43 B9H H22 H22 H 0 1 N N N 210.468 250.620 292.207 5.711 -3.323 -0.711 H22 B9H 44 B9H H23 H23 H 0 1 N N N 216.782 257.688 293.241 -1.756 5.004 0.992 H23 B9H 45 B9H H24 H24 H 0 1 N N N 215.352 258.356 294.098 -1.549 3.643 2.120 H24 B9H 46 B9H H25 H25 H 0 1 N N N 216.416 257.164 294.920 -0.133 4.580 1.586 H25 B9H 47 B9H OP3 OP3 O 0 1 N Y N 209.406 253.594 291.656 6.119 -0.520 -0.299 OP3 B9H 48 B9H H19 H19 H 0 1 N N N 208.552 253.765 292.035 6.274 -0.258 -1.217 H19 B9H 49 # # 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 B9H OP2 P SING N N 1 B9H "C5'" "C4'" SING N N 2 B9H "C5'" "O5'" SING N N 3 B9H "C4'" "O4'" SING N N 4 B9H "C4'" "C3'" SING N N 5 B9H P "O5'" SING N N 6 B9H P OP1 DOUB N N 7 B9H "O4'" "C1'" SING N N 8 B9H "O2'" C21 SING N N 9 B9H "O2'" "C2'" SING N N 10 B9H "C1'" "C2'" SING N N 11 B9H "C1'" N1 SING N N 12 B9H "C3'" "O3'" SING N N 13 B9H "C3'" "C2'" SING N N 14 B9H N1 C6 SING N N 15 B9H N1 C2 SING N N 16 B9H C6 C5 DOUB N N 17 B9H O2 C2 DOUB N N 18 B9H C2 N3 SING N N 19 B9H C5 C4 SING N N 20 B9H N3 C4 SING N N 21 B9H N3 C31 SING N N 22 B9H C4 N4 SING N N 23 B9H C32 C31 SING N N 24 B9H C32 C33 SING N N 25 B9H C4 H1 SING N N 26 B9H C5 H2 SING N N 27 B9H C6 H3 SING N N 28 B9H C32 H4 SING N N 29 B9H C32 H5 SING N N 30 B9H "C1'" H6 SING N N 31 B9H "C2'" H7 SING N N 32 B9H "C3'" H8 SING N N 33 B9H C31 H9 SING N N 34 B9H C31 H10 SING N N 35 B9H C33 H11 SING N N 36 B9H C33 H12 SING N N 37 B9H C33 H13 SING N N 38 B9H "C4'" H14 SING N N 39 B9H "C5'" H15 SING N N 40 B9H "C5'" H16 SING N N 41 B9H N4 H17 SING N N 42 B9H N4 H18 SING N N 43 B9H "O3'" H20 SING N N 44 B9H OP2 H22 SING N N 45 B9H C21 H23 SING N N 46 B9H C21 H24 SING N N 47 B9H C21 H25 SING N N 48 B9H P OP3 SING N N 49 B9H OP3 H19 SING N N 50 # # 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 B9H InChI InChI 1.03 "InChI=1S/C13H24N3O8P/c1-3-5-15-9(14)4-6-16(13(15)18)12-11(22-2)10(17)8(24-12)7-23-25(19,20)21/h4,6,8-12,17H,3,5,7,14H2,1-2H3,(H2,19,20,21)/t8-,9-,10-,11-,12-/m1/s1" B9H InChIKey InChI 1.03 GQHNKIBEOWBMPQ-LZQZFOIKSA-N B9H SMILES_CANONICAL CACTVS 3.385 "CCCN1[C@@H](N)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2OC)C1=O" B9H SMILES CACTVS 3.385 "CCCN1[CH](N)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2OC)C1=O" B9H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCCN1C(C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC)N" B9H SMILES "OpenEye OEToolkits" 2.0.6 "CCCN1C(C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC)N" # _pdbx_chem_comp_identifier.comp_id B9H _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-3-propyl-4~{H}-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site B9H "Create component" 2017-09-26 EBI B9H "Initial release" 2018-01-24 RCSB B9H "Modify one letter code" 2019-05-06 EBI ##