data_JSP # _chem_comp.id JSP _chem_comp.name "(1R)-1-(4-amino-1-methyl-2-oxo-1,2-dihydropyrimidin-5-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-09-20 _chem_comp.pdbx_modified_date 2019-02-22 _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 321.224 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JSP _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 6MIG _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 JSP C1 C1 C 0 1 N N N 24.934 4.576 -18.790 -2.289 -0.376 0.197 C1 JSP 1 JSP "C1'" C2 C 0 1 N N R 25.096 4.203 -20.300 -1.151 -1.335 0.435 "C1'" JSP 2 JSP C2 C3 C 0 1 N N N 24.306 3.799 -17.883 -2.198 0.607 -0.810 C2 JSP 3 JSP "C2'" C4 C 0 1 N N N 25.222 5.423 -21.198 -0.905 -2.212 -0.818 "C2'" JSP 4 JSP "C3'" C5 C 0 1 N N S 25.840 4.780 -22.439 0.581 -2.612 -0.648 "C3'" JSP 5 JSP C4 C6 C 0 1 N N N 24.678 5.248 -16.232 -4.316 1.354 -0.266 C4 JSP 6 JSP "C4'" C7 C 0 1 N N R 26.787 3.736 -21.841 1.152 -1.547 0.308 "C4'" JSP 7 JSP "C5'" C8 C 0 1 N N N 28.273 4.081 -21.841 2.317 -0.817 -0.363 "C5'" JSP 8 JSP C6 C9 C 0 1 N N N 25.451 5.743 -18.388 -3.417 -0.449 0.943 C6 JSP 9 JSP C7 C10 C 0 1 N N N 25.871 7.356 -16.578 -5.659 0.358 1.501 C7 JSP 10 JSP N2 N1 N 0 1 N N N 23.824 2.700 -18.295 -1.064 0.703 -1.582 N2 JSP 11 JSP N3 N2 N 0 1 N N N 24.204 4.153 -16.670 -3.213 1.438 -1.008 N3 JSP 12 JSP N5 N3 N 0 1 N N N 25.331 6.100 -17.093 -4.433 0.426 0.702 N5 JSP 13 JSP "O3'" O1 O 0 1 N N N 24.882 4.113 -23.265 0.688 -3.914 -0.067 "O3'" JSP 14 JSP O4 O2 O 0 1 N N N 24.552 5.540 -15.061 -5.236 2.129 -0.468 O4 JSP 15 JSP "O4'" O3 O 0 1 N N N 26.312 3.500 -20.486 0.092 -0.618 0.598 "O4'" JSP 16 JSP "O5'" O4 O 0 1 N N N 28.565 5.237 -22.632 2.913 0.087 0.570 "O5'" JSP 17 JSP OP1 O5 O 0 1 N N N 30.742 6.380 -22.145 5.277 0.184 -0.309 OP1 JSP 18 JSP OP2 O6 O 0 1 N N N 28.572 7.715 -22.382 3.737 2.086 -0.925 OP2 JSP 19 JSP P P1 P 0 1 N N N 29.280 6.494 -21.935 4.171 1.023 0.203 P JSP 20 JSP H1 H1 H 0 1 N N N 24.234 3.597 -20.616 -1.352 -1.958 1.307 H1 JSP 21 JSP H2 H2 H 0 1 N N N 25.884 6.185 -20.761 -1.548 -3.092 -0.810 H2 JSP 22 JSP H3 H3 H 0 1 N N N 24.242 5.871 -21.416 -1.050 -1.635 -1.732 H3 JSP 23 JSP H4 H4 H 0 1 N N N 26.413 5.528 -23.007 1.096 -2.579 -1.608 H4 JSP 24 JSP H5 H5 H 0 1 N N N 26.663 2.808 -22.419 1.492 -2.020 1.230 H5 JSP 25 JSP H6 H6 H 0 1 N N N 28.834 3.226 -22.245 3.060 -1.543 -0.691 H6 JSP 26 JSP H7 H7 H 0 1 N N N 28.591 4.272 -20.806 1.949 -0.259 -1.224 H7 JSP 27 JSP H8 H8 H 0 1 N N N 25.957 6.389 -19.090 -3.511 -1.194 1.719 H8 JSP 28 JSP H9 H9 H 0 1 N N N 25.656 7.434 -15.502 -5.557 0.998 2.378 H9 JSP 29 JSP H10 H10 H 0 1 N N N 26.959 7.380 -16.737 -6.503 0.695 0.901 H10 JSP 30 JSP H11 H11 H 0 1 N N N 25.405 8.200 -17.107 -5.828 -0.671 1.820 H11 JSP 31 JSP H12 H12 H 0 1 N N N 23.351 2.091 -17.658 -0.324 0.094 -1.435 H12 JSP 32 JSP H13 H13 H 0 1 N N N 23.917 2.442 -19.257 -1.005 1.381 -2.274 H13 JSP 33 JSP H14 H14 H 0 1 N N N 24.289 4.752 -23.642 0.343 -4.623 -0.626 H14 JSP 34 JSP H16 H16 H 0 1 N N N 29.193 8.315 -22.777 3.014 2.671 -0.658 H16 JSP 35 JSP OP3 OP3 O 0 1 N Y N 28.941 6.286 -20.398 4.658 1.808 1.521 OP3 JSP 36 JSP H15 H15 H 0 1 N Y N 29.744 6.129 -19.915 5.414 2.392 1.374 H15 JSP 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 JSP "O3'" "C3'" SING N N 1 JSP "O5'" P SING N N 2 JSP "O5'" "C5'" SING N N 3 JSP "C3'" "C4'" SING N N 4 JSP "C3'" "C2'" SING N N 5 JSP OP2 P SING N N 6 JSP OP1 P DOUB N N 7 JSP "C4'" "C5'" SING N N 8 JSP "C4'" "O4'" SING N N 9 JSP "C2'" "C1'" SING N N 10 JSP "O4'" "C1'" SING N N 11 JSP "C1'" C1 SING N N 12 JSP C1 C6 DOUB N N 13 JSP C1 C2 SING N N 14 JSP C6 N5 SING N N 15 JSP N2 C2 SING N N 16 JSP C2 N3 DOUB N N 17 JSP N5 C7 SING N N 18 JSP N5 C4 SING N N 19 JSP N3 C4 SING N N 20 JSP C4 O4 DOUB N N 21 JSP "C1'" H1 SING N N 22 JSP "C2'" H2 SING N N 23 JSP "C2'" H3 SING N N 24 JSP "C3'" H4 SING N N 25 JSP "C4'" H5 SING N N 26 JSP "C5'" H6 SING N N 27 JSP "C5'" H7 SING N N 28 JSP C6 H8 SING N N 29 JSP C7 H9 SING N N 30 JSP C7 H10 SING N N 31 JSP C7 H11 SING N N 32 JSP N2 H12 SING N N 33 JSP N2 H13 SING N N 34 JSP "O3'" H14 SING N N 35 JSP OP2 H16 SING N N 36 JSP P OP3 SING N N 37 JSP OP3 H15 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 JSP SMILES ACDLabs 12.01 "C1(=CN(C(=O)N=C1N)C)C2CC(C(COP(=O)(O)O)O2)O" JSP InChI InChI 1.03 "InChI=1S/C10H16N3O7P/c1-13-3-5(9(11)12-10(13)15)7-2-6(14)8(20-7)4-19-21(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" JSP InChIKey InChI 1.03 NSXSEZCKIMJZGT-XLPZGREQSA-N JSP SMILES_CANONICAL CACTVS 3.385 "CN1C=C([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=NC1=O)N" JSP SMILES CACTVS 3.385 "CN1C=C([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=NC1=O)N" JSP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=NC1=O)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" JSP SMILES "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=NC1=O)N)C2CC(C(O2)COP(=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 JSP "SYSTEMATIC NAME" ACDLabs 12.01 "(1R)-1-(4-amino-1-methyl-2-oxo-1,2-dihydropyrimidin-5-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol" JSP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-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 JSP "Create component" 2018-09-20 RCSB JSP "Initial release" 2019-02-27 RCSB ##