data_M1Y # _chem_comp.id M1Y _chem_comp.name "(1S)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-xylitol" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-13 _chem_comp.pdbx_modified_date 2017-12-01 _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 338.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code M1Y _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 6AZ1 _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 M1Y C1 C1 C 0 1 N N N 123.500 200.477 169.994 5.447 1.096 -1.681 C1 M1Y 1 M1Y "C1'" C2 C 0 1 N N S 123.033 205.358 170.039 1.080 -1.043 -0.869 "C1'" M1Y 2 M1Y C2 C3 C 0 1 N N N 121.805 201.543 171.537 4.274 1.408 0.426 C2 M1Y 3 M1Y "C2'" C4 C 0 1 N N R 123.854 206.065 171.084 1.014 -2.315 -0.001 "C2'" M1Y 4 M1Y "C3'" C5 C 0 1 N N R 124.937 206.730 170.250 -0.404 -2.277 0.619 "C3'" M1Y 5 M1Y C4 C6 C 0 1 N N N 121.544 203.949 171.593 2.206 0.417 0.873 C4 M1Y 6 M1Y "C4'" C7 C 0 1 N N R 125.057 205.865 168.996 -1.158 -1.334 -0.352 "C4'" M1Y 7 M1Y C5 C8 C 0 1 N N N 122.581 204.062 170.585 2.221 -0.171 -0.414 C5 M1Y 8 M1Y "C5'" C9 C 0 1 N N N 126.287 205.007 168.849 -2.351 -0.681 0.349 "C5'" M1Y 9 M1Y C6 C10 C 0 1 N N N 123.157 202.936 170.133 3.276 0.056 -1.227 C6 M1Y 10 M1Y N1 N1 N 0 1 N N N 122.796 201.684 170.571 4.304 0.850 -0.798 N1 M1Y 11 M1Y N3 N2 N 0 1 N N N 121.181 202.657 172.056 3.239 1.194 1.258 N3 M1Y 12 M1Y O2 O1 O 0 1 N N N 121.482 200.428 171.947 5.198 2.111 0.786 O2 M1Y 13 M1Y "O2'" O2 O 0 1 N N N 123.029 207.055 171.670 1.176 -3.482 -0.809 "O2'" M1Y 14 M1Y "O3'" O3 O 0 1 N N N 126.180 206.986 170.914 -0.370 -1.729 1.939 "O3'" M1Y 15 M1Y O4 O4 O 0 1 N N N 120.980 204.913 172.063 1.268 0.224 1.626 O4 M1Y 16 M1Y "O4'" O5 O 0 1 N N N 123.890 205.019 168.994 -0.166 -0.346 -0.701 "O4'" M1Y 17 M1Y "O5'" O6 O 0 1 N N N 125.931 203.666 168.549 -3.095 0.090 -0.596 "O5'" M1Y 18 M1Y OP1 O7 O 0 1 N N N 128.201 203.393 167.579 -5.398 0.009 0.433 OP1 M1Y 19 M1Y OP2 O8 O 0 1 N N N 126.722 201.334 168.200 -4.032 2.095 0.823 OP2 M1Y 20 M1Y P P1 P 0 1 N N N 126.860 202.731 167.664 -4.420 0.918 -0.204 P M1Y 21 M1Y H1 H1 H 0 1 N N N 123.093 199.562 170.450 5.255 1.982 -2.286 H1 M1Y 22 M1Y H2 H2 H 0 1 N N N 123.342 200.446 168.906 6.343 1.254 -1.079 H2 M1Y 23 M1Y H3 H3 H 0 1 N N N 124.577 200.545 170.206 5.595 0.235 -2.332 H3 M1Y 24 M1Y H4 H4 H 0 1 N N N 122.185 205.978 169.714 1.216 -1.316 -1.916 H4 M1Y 25 M1Y H5 H5 H 0 1 N N N 124.279 205.363 171.816 1.775 -2.284 0.780 H5 M1Y 26 M1Y H6 H6 H 0 1 N N N 124.530 207.698 169.923 -0.853 -3.271 0.625 H6 M1Y 27 M1Y H7 H7 H 0 1 N N N 125.008 206.535 168.125 -1.486 -1.878 -1.238 H7 M1Y 28 M1Y H8 H8 H 0 1 N N N 126.856 205.028 169.790 -2.992 -1.454 0.772 H8 M1Y 29 M1Y H9 H9 H 0 1 N N N 126.910 205.406 168.035 -1.992 -0.030 1.146 H9 M1Y 30 M1Y H10 H10 H 0 1 N N N 123.939 203.018 169.392 3.307 -0.388 -2.211 H10 M1Y 31 M1Y H11 H11 H 0 1 N N N 120.475 202.555 172.757 3.235 1.601 2.139 H11 M1Y 32 M1Y H12 H12 H 0 1 N N N 122.205 206.664 171.937 1.143 -4.311 -0.313 H12 M1Y 33 M1Y H13 H13 H 0 1 N N N 126.025 207.527 171.680 0.167 -2.238 2.562 H13 M1Y 34 M1Y H15 H15 H 0 1 N N N 127.578 201.002 168.445 -3.393 2.730 0.471 H15 M1Y 35 M1Y OP3 OP3 O 0 1 N Y N 126.183 202.742 166.214 -5.067 1.556 -1.533 OP3 M1Y 36 M1Y H17 H17 H 0 1 N N N 126.766 203.165 165.595 -5.870 2.070 -1.372 H17 M1Y 37 # 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 M1Y OP1 P DOUB N N 1 M1Y P OP2 SING N N 2 M1Y P "O5'" SING N N 3 M1Y "O5'" "C5'" SING N N 4 M1Y "C5'" "C4'" SING N N 5 M1Y "O4'" "C4'" SING N N 6 M1Y "O4'" "C1'" SING N N 7 M1Y "C4'" "C3'" SING N N 8 M1Y C1 N1 SING N N 9 M1Y "C1'" C5 SING N N 10 M1Y "C1'" "C2'" SING N N 11 M1Y C6 N1 SING N N 12 M1Y C6 C5 DOUB N N 13 M1Y "C3'" "O3'" SING N N 14 M1Y "C3'" "C2'" SING N N 15 M1Y N1 C2 SING N N 16 M1Y C5 C4 SING N N 17 M1Y "C2'" "O2'" SING N N 18 M1Y C2 O2 DOUB N N 19 M1Y C2 N3 SING N N 20 M1Y C4 N3 SING N N 21 M1Y C4 O4 DOUB N N 22 M1Y C1 H1 SING N N 23 M1Y C1 H2 SING N N 24 M1Y C1 H3 SING N N 25 M1Y "C1'" H4 SING N N 26 M1Y "C2'" H5 SING N N 27 M1Y "C3'" H6 SING N N 28 M1Y "C4'" H7 SING N N 29 M1Y "C5'" H8 SING N N 30 M1Y "C5'" H9 SING N N 31 M1Y C6 H10 SING N N 32 M1Y N3 H11 SING N N 33 M1Y "O2'" H12 SING N N 34 M1Y "O3'" H13 SING N N 35 M1Y OP2 H15 SING N N 36 M1Y P OP3 SING N N 37 M1Y OP3 H17 SING N N 38 # 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 M1Y SMILES ACDLabs 12.01 "CN2C(=O)NC(=O)C(C1C(O)C(O)C(COP(=O)(O)O)O1)=C2" M1Y InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c1-12-2-4(9(15)11-10(12)16)8-7(14)6(13)5(21-8)3-20-22(17,18)19/h2,5-8,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/t5-,6+,7-,8+/m1/s1" M1Y InChIKey InChI 1.03 VORAOZTXNOXTGQ-CWKFCGSDSA-N M1Y SMILES_CANONICAL CACTVS 3.385 "CN1C=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@H](O)[C@H]2O)C(=O)NC1=O" M1Y SMILES CACTVS 3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)NC1=O" M1Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@H](O2)COP(=O)(O)O)O)O" M1Y SMILES "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" # 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 M1Y "SYSTEMATIC NAME" ACDLabs 12.01 "(1S)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-xylitol" M1Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{R},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(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 M1Y "Create component" 2017-09-13 RCSB M1Y "Initial release" 2017-12-06 RCSB #