data_PDU # _chem_comp.id PDU _chem_comp.name "5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2021-07-21 _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 346.230 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PDU _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 1P3X _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 PDU P P1 P 0 1 N N N 1.020 11.691 3.054 4.635 -1.265 -0.129 P PDU 1 PDU OP2 O1 O 0 1 N N N 1.721 12.834 3.687 5.944 -0.327 -0.153 OP1 PDU 2 PDU OP1 O2 O 0 1 N N N 0.582 11.825 1.647 4.404 -1.754 1.248 OP2 PDU 3 PDU "O5'" O3 O 0 1 N N N 2.048 10.406 3.133 3.357 -0.415 -0.618 "O5'" PDU 4 PDU "C5'" C1 C 0 1 N N N 1.591 9.163 3.678 2.840 0.701 0.109 "C5'" PDU 5 PDU "C4'" C2 C 0 1 N N R 2.528 8.011 4.010 1.630 1.274 -0.631 "C4'" PDU 6 PDU "O4'" O4 O 0 1 N N N 1.717 6.998 4.676 0.537 0.331 -0.627 "O4'" PDU 7 PDU "C3'" C3 C 0 1 N N S 3.183 7.373 2.808 1.054 2.496 0.130 "C3'" PDU 8 PDU "O3'" O5 O 0 1 N N N 4.540 6.989 3.080 1.731 3.697 -0.249 "O3'" PDU 9 PDU "C2'" C4 C 0 1 N N N 2.318 6.165 2.681 -0.417 2.515 -0.352 "C2'" PDU 10 PDU "C1'" C5 C 0 1 N N R 1.906 5.711 4.066 -0.667 1.081 -0.858 "C1'" PDU 11 PDU N1 N1 N 0 1 N N N 0.664 4.890 3.874 -1.779 0.479 -0.119 N1 PDU 12 PDU C2 C6 C 0 1 N N N 0.597 3.545 4.294 -1.646 0.252 1.198 C2 PDU 13 PDU O2 O6 O 0 1 N N N 1.535 2.975 4.847 -0.603 0.551 1.747 O2 PDU 14 PDU N3 N2 N 0 1 N N N -0.614 2.875 4.049 -2.633 -0.297 1.927 N3 PDU 15 PDU C4 C7 C 0 1 N N N -1.721 3.433 3.440 -3.802 -0.640 1.344 C4 PDU 16 PDU O4 O7 O 0 1 N N N -2.740 2.768 3.262 -4.700 -1.137 1.998 O4 PDU 17 PDU C5 C8 C 0 1 N N N -1.557 4.817 3.050 -3.967 -0.399 -0.097 C5 PDU 18 PDU C5A C9 C 0 1 N N N -2.658 5.457 2.396 -5.189 -0.739 -0.762 C5A PDU 19 PDU C5B C10 C 0 1 N N N -3.619 5.948 1.895 -6.190 -1.018 -1.308 C5B PDU 20 PDU C5M C11 C 0 1 N N N -4.841 6.513 1.336 -7.446 -1.368 -1.992 C5M PDU 21 PDU C6 C12 C 0 1 N N N -0.405 5.489 3.266 -2.931 0.167 -0.782 C6 PDU 22 PDU OP3 O8 O 0 1 N Y N -0.326 11.391 3.961 4.855 -2.519 -1.115 O1 PDU 23 PDU HOP2 H1 H 0 1 N N N 1.799 13.544 3.061 6.155 0.030 -1.027 H1 PDU 24 PDU "H5'" H2 H 0 1 N N N 1.075 9.415 4.616 2.537 0.376 1.105 "H5'" PDU 25 PDU "H5''" H3 H 0 0 N N N 0.864 8.764 2.955 3.610 1.467 0.195 "H5''" PDU 26 PDU "H4'" H4 H 0 1 N N N 3.309 8.372 4.695 1.899 1.546 -1.651 "H4'" PDU 27 PDU "H3'" H5 H 0 1 N N N 3.102 8.020 1.922 1.109 2.345 1.208 "H3'" PDU 28 PDU H2 H6 H 0 1 N N N 5.080 7.767 3.159 1.406 4.490 0.200 H2 PDU 29 PDU "H2''" H7 H 0 0 N N N 1.423 6.412 2.091 -1.086 2.750 0.475 "H2''" PDU 30 PDU "H2'" H8 H 0 1 N N N 2.877 5.361 2.180 -0.543 3.233 -1.163 "H2'" PDU 31 PDU "H1'" H9 H 0 1 N N N 2.704 5.128 4.550 -0.894 1.099 -1.924 "H1'" PDU 32 PDU H3 H10 H 0 1 N N N -0.679 1.920 4.338 -2.505 -0.448 2.877 H3 PDU 33 PDU H71 H11 H 0 1 N N N -4.591 7.143 0.470 -8.141 -1.804 -1.275 H71 PDU 34 PDU H72 H12 H 0 1 N N N -5.509 5.699 1.017 -7.887 -0.469 -2.424 H72 PDU 35 PDU H73 H13 H 0 1 N N N -5.346 7.123 2.100 -7.240 -2.088 -2.783 H73 PDU 36 PDU H6 H14 H 0 1 N N N -0.327 6.519 2.952 -3.018 0.358 -1.841 H6 PDU 37 PDU HOP3 H15 H 0 1 N Y N -1.090 11.368 3.397 5.609 -3.076 -0.879 H4 PDU 38 # # 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 PDU C5M C5B SING N N 1 PDU OP1 P DOUB N N 2 PDU C5B C5A TRIP N N 3 PDU C5A C5 SING N N 4 PDU "C2'" "C3'" SING N N 5 PDU "C2'" "C1'" SING N N 6 PDU "C3'" "O3'" SING N N 7 PDU "C3'" "C4'" SING N N 8 PDU C5 C6 DOUB N N 9 PDU C5 C4 SING N N 10 PDU P "O5'" SING N N 11 PDU P OP2 SING N N 12 PDU "O5'" "C5'" SING N N 13 PDU O4 C4 DOUB N N 14 PDU C6 N1 SING N N 15 PDU C4 N3 SING N N 16 PDU "C5'" "C4'" SING N N 17 PDU N1 "C1'" SING N N 18 PDU N1 C2 SING N N 19 PDU "C4'" "O4'" SING N N 20 PDU N3 C2 SING N N 21 PDU "C1'" "O4'" SING N N 22 PDU C2 O2 DOUB N N 23 PDU P OP3 SING N N 24 PDU OP2 HOP2 SING N N 25 PDU "C5'" "H5'" SING N N 26 PDU "C5'" "H5''" SING N N 27 PDU "C4'" "H4'" SING N N 28 PDU "C3'" "H3'" SING N N 29 PDU "O3'" H2 SING N N 30 PDU "C2'" "H2''" SING N N 31 PDU "C2'" "H2'" SING N N 32 PDU "C1'" "H1'" SING N N 33 PDU N3 H3 SING N N 34 PDU C5M H71 SING N N 35 PDU C5M H72 SING N N 36 PDU C5M H73 SING N N 37 PDU C6 H6 SING N N 38 PDU OP3 HOP3 SING N N 39 # # 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 PDU InChI InChI 1.03 "InChI=1S/C12H15N2O8P/c1-2-3-7-5-14(12(17)13-11(7)16)10-4-8(15)9(22-10)6-21-23(18,19)20/h5,8-10,15H,4,6H2,1H3,(H,13,16,17)(H2,18,19,20)/t8-,9+,10+/m0/s1" PDU InChIKey InChI 1.03 NUOBVCABUBRVOG-IVZWLZJFSA-N PDU SMILES_CANONICAL CACTVS 3.385 "CC#CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" PDU SMILES CACTVS 3.385 "CC#CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" PDU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC#CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" PDU SMILES "OpenEye OEToolkits" 2.0.7 "CC#CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id PDU _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~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-prop-1-ynyl-pyrimidin-1-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 PDU "Create component" 1999-07-08 EBI PDU "Modify descriptor" 2011-06-04 RCSB PDU "Other modification" 2021-07-21 RCSB ##