data_JMC # _chem_comp.id JMC _chem_comp.name "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-3-methyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H20 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-29 _chem_comp.pdbx_modified_date 2020-10-02 _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 353.266 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JMC _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 6ZJ3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 JMC C1 C1 C 0 1 N N N 272.522 209.037 213.945 5.371 1.277 -1.157 C1 JMC 1 JMC "C1'" C2 C 0 1 N N R 275.946 207.626 210.549 1.010 -0.747 -0.503 "C1'" JMC 2 JMC C2 C3 C 0 1 N N N 274.184 208.319 212.271 3.158 0.318 -0.740 C2 JMC 3 JMC "C2'" C4 C 0 1 N N R 277.221 206.903 210.965 0.817 -1.883 0.533 "C2'" JMC 4 JMC C3 C5 C 0 1 N N N 278.578 208.118 209.504 2.131 -3.635 1.509 C3 JMC 5 JMC "C3'" C6 C 0 1 N N R 276.695 205.525 211.337 -0.622 -2.364 0.223 "C3'" JMC 6 JMC C4 C7 C 0 1 N N R 274.599 210.334 213.537 3.929 2.000 0.825 C4 JMC 7 JMC "C4'" C8 C 0 1 N N R 275.536 205.332 210.376 -1.266 -1.175 -0.517 "C4'" JMC 8 JMC C5 C9 C 0 1 N N N 275.798 210.503 212.874 2.622 1.825 1.569 C5 JMC 9 JMC "C5'" C10 C 0 1 N N N 274.449 204.398 210.839 -2.508 -0.702 0.242 "C5'" JMC 10 JMC C6 C11 C 0 1 N N N 276.173 209.577 211.912 1.752 0.948 1.100 C6 JMC 11 JMC N1 N1 N 0 1 N N N 275.417 208.515 211.608 2.021 0.207 -0.040 N1 JMC 12 JMC N3 N2 N 0 1 N N N 273.784 209.237 213.242 4.135 1.173 -0.376 N3 JMC 13 JMC N4 N3 N 0 1 N N N 274.213 211.213 214.474 4.037 3.410 0.426 N4 JMC 14 JMC O2 O1 O 0 1 N N N 273.414 207.368 212.046 3.315 -0.375 -1.727 O2 JMC 15 JMC "O2'" O2 O 0 1 N N N 278.073 206.830 209.837 1.763 -2.933 0.319 "O2'" JMC 16 JMC "O3'" O3 O 0 1 N N N 277.670 204.506 211.218 -0.592 -3.521 -0.615 "O3'" JMC 17 JMC "O4'" O4 O 0 1 N N N 274.987 206.658 210.205 -0.290 -0.121 -0.562 "O4'" JMC 18 JMC "O5'" O5 O 0 1 N N N 274.976 203.151 211.250 -3.163 0.321 -0.510 "O5'" JMC 19 JMC OP1 O6 O 0 1 N N N 275.059 202.781 213.738 -5.710 -0.021 0.047 OP1 JMC 20 JMC OP2 O7 O 0 1 N N N 274.274 200.916 212.101 -4.291 1.618 1.339 OP2 JMC 21 JMC P P1 P 0 1 N N N 274.348 202.368 212.480 -4.509 1.050 -0.010 P JMC 22 JMC O1 O8 O 0 1 N Y N 272.849 202.919 212.558 -4.891 2.232 -1.034 O1 JMC 23 JMC H1 H1 H 0 1 N N N 272.371 209.852 214.668 5.327 0.587 -2.000 H1 JMC 24 JMC H2 H2 H 0 1 N N N 271.695 209.033 213.220 5.482 2.296 -1.527 H2 JMC 25 JMC H3 H3 H 0 1 N N N 272.547 208.075 214.477 6.222 1.025 -0.525 H3 JMC 26 JMC H4 H4 H 0 1 N N N 276.179 208.239 209.666 1.286 -1.155 -1.475 H4 JMC 27 JMC H5 H5 H 0 1 N N N 277.694 207.395 211.828 0.888 -1.499 1.550 H5 JMC 28 JMC H6 H6 H 0 1 N N N 279.236 208.039 208.626 2.578 -2.938 2.218 H6 JMC 29 JMC H7 H7 H 0 1 N N N 277.740 208.792 209.274 1.243 -4.086 1.953 H7 JMC 30 JMC H8 H8 H 0 1 N N N 279.148 208.519 210.355 2.851 -4.415 1.262 H8 JMC 31 JMC H9 H9 H 0 1 N N N 276.303 205.560 212.364 -1.160 -2.576 1.146 H9 JMC 32 JMC H10 H10 H 0 1 N N N 274.086 210.927 212.765 4.741 1.788 1.520 H10 JMC 33 JMC H11 H11 H 0 1 N N N 275.931 204.969 209.416 -1.541 -1.473 -1.529 H11 JMC 34 JMC H12 H12 H 0 1 N N N 276.435 211.345 213.101 2.407 2.400 2.457 H12 JMC 35 JMC H13 H13 H 0 1 N N N 273.919 204.858 211.686 -3.188 -1.542 0.383 H13 JMC 36 JMC H14 H14 H 0 1 N N N 273.744 204.232 210.011 -2.211 -0.307 1.213 H14 JMC 37 JMC H15 H15 H 0 1 N N N 277.108 209.718 211.390 0.813 0.807 1.614 H15 JMC 38 JMC H16 H16 H 0 1 N N N 273.327 210.936 214.846 3.964 4.018 1.228 H16 JMC 39 JMC H17 H17 H 0 1 N N N 274.891 211.236 215.209 4.895 3.578 -0.078 H17 JMC 40 JMC H19 H19 H 0 1 N N N 278.374 204.667 211.836 -1.468 -3.865 -0.841 H19 JMC 41 JMC H20 H20 H 0 1 N N N 275.403 202.011 214.175 -5.909 -0.434 -0.805 H20 JMC 42 JMC H21 H21 H 0 1 N N N 272.242 202.218 212.350 -5.694 2.716 -0.795 H21 JMC 43 # # 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 JMC C3 "O2'" SING N N 1 JMC "O2'" "C2'" SING N N 2 JMC "O4'" "C4'" SING N N 3 JMC "O4'" "C1'" SING N N 4 JMC "C4'" "C5'" SING N N 5 JMC "C4'" "C3'" SING N N 6 JMC "C1'" "C2'" SING N N 7 JMC "C1'" N1 SING N N 8 JMC "C5'" "O5'" SING N N 9 JMC "C2'" "C3'" SING N N 10 JMC "O3'" "C3'" SING N N 11 JMC "O5'" P SING N N 12 JMC N1 C6 SING N N 13 JMC N1 C2 SING N N 14 JMC C6 C5 DOUB N N 15 JMC O2 C2 DOUB N N 16 JMC OP2 P DOUB N N 17 JMC C2 N3 SING N N 18 JMC P OP1 SING N N 19 JMC C5 C4 SING N N 20 JMC N3 C4 SING N N 21 JMC N3 C1 SING N N 22 JMC C4 N4 SING N N 23 JMC P O1 SING N N 24 JMC C1 H1 SING N N 25 JMC C1 H2 SING N N 26 JMC C1 H3 SING N N 27 JMC "C1'" H4 SING N N 28 JMC "C2'" H5 SING N N 29 JMC C3 H6 SING N N 30 JMC C3 H7 SING N N 31 JMC C3 H8 SING N N 32 JMC "C3'" H9 SING N N 33 JMC C4 H10 SING N N 34 JMC "C4'" H11 SING N N 35 JMC C5 H12 SING N N 36 JMC "C5'" H13 SING N N 37 JMC "C5'" H14 SING N N 38 JMC C6 H15 SING N N 39 JMC N4 H16 SING N N 40 JMC N4 H17 SING N N 41 JMC "O3'" H19 SING N N 42 JMC OP1 H20 SING N N 43 JMC O1 H21 SING N N 44 # # 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 JMC InChI InChI 1.03 "InChI=1S/C11H20N3O8P/c1-13-7(12)3-4-14(11(13)16)10-9(20-2)8(15)6(22-10)5-21-23(17,18)19/h3-4,6-10,15H,5,12H2,1-2H3,(H2,17,18,19)/t6-,7-,8-,9-,10-/m1/s1" JMC InChIKey InChI 1.03 BKSKIJTVQSZCSV-VVULQXIFSA-N JMC SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C[C@H](N)N(C)C2=O" JMC SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C[CH](N)N(C)C2=O" JMC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C(C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC)N" JMC SMILES "OpenEye OEToolkits" 2.0.7 "CN1C(C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC)N" # _pdbx_chem_comp_identifier.comp_id JMC _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-3-methyl-2-oxidanylidene-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 JMC "Create component" 2020-06-29 PDBE JMC "Initial release" 2020-10-07 RCSB ##