data_DDN # _chem_comp.id DDN _chem_comp.name "3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms "((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-12-14 _chem_comp.pdbx_modified_date 2021-03-13 _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 310.198 _chem_comp.one_letter_code U _chem_comp.three_letter_code DDN _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1VQ2 _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 DDN OP3 O3P O 0 1 N Y N 81.603 5.502 15.525 -3.513 -1.588 -1.240 OP3 DDN 1 DDN P P P 0 1 N N N 81.104 6.559 16.500 -3.914 -1.012 0.063 P DDN 2 DDN OP1 O1P O 0 1 N N N 81.184 6.110 17.930 -4.477 -2.181 1.016 OP1 DDN 3 DDN OP2 O2P O 0 1 N N N 81.744 7.909 16.231 -5.064 0.091 -0.170 OP2 DDN 4 DDN "O5'" O5* O 0 1 N N N 79.511 6.767 16.211 -2.639 -0.318 0.759 "O5'" DDN 5 DDN "C5'" C5* C 0 1 N N N 78.688 7.541 17.107 -2.117 0.623 -0.180 "C5'" DDN 6 DDN "C4'" C4* C 0 1 N N R 77.479 8.062 16.349 -0.896 1.321 0.422 "C4'" DDN 7 DDN "O4'" O4* O 0 1 N N N 76.410 8.400 17.232 0.186 0.378 0.600 "O4'" DDN 8 DDN "C3'" C3* C 0 1 N N S 77.747 9.312 15.493 -0.336 2.380 -0.553 "C3'" DDN 9 DDN "O3'" O3* O 0 1 N N N 76.949 9.301 14.345 -0.802 3.684 -0.198 "O3'" DDN 10 DDN "C2'" C2* C 0 1 N N N 77.415 10.490 16.322 1.196 2.286 -0.377 "C2'" DDN 11 DDN "C1'" C1* C 0 1 N N R 76.539 9.824 17.340 1.384 1.181 0.687 "C1'" DDN 12 DDN N1 N1 N 0 1 N N N 75.921 9.989 18.846 2.566 0.373 0.379 N1 DDN 13 DDN C2 C2 C 0 1 N N N 74.822 10.856 19.020 2.557 -0.367 -0.738 C2 DDN 14 DDN O2 O2 O 0 1 N N N 74.237 11.417 18.093 1.577 -0.340 -1.457 O2 DDN 15 DDN N3 N3 N 0 1 N N N 74.538 11.168 20.353 3.610 -1.132 -1.091 N3 DDN 16 DDN C4 C4 C 0 1 N N R 75.573 10.985 21.525 4.787 -1.152 -0.207 C4 DDN 17 DDN O4 O4 O 0 1 N N N 76.020 12.231 22.079 5.011 -2.504 0.196 O4 DDN 18 DDN C5 C5 C 0 1 N N N 76.840 10.235 21.035 4.729 -0.297 1.042 C5 DDN 19 DDN C6 C6 C 0 1 N N N 76.985 9.896 19.719 3.634 0.408 1.262 C6 DDN 20 DDN H1P H1P H 0 1 N N N 80.873 6.770 18.539 -5.238 -2.569 0.563 H1P DDN 21 DDN H2P H2P H 0 1 N N N 81.433 8.569 16.840 -5.297 0.440 0.701 H2P DDN 22 DDN "H5'" 1H5* H 0 1 N N N 79.259 8.358 17.607 -2.880 1.365 -0.414 "H5'" DDN 23 DDN "H5''" 2H5* H 0 0 N N N 78.401 6.968 18.020 -1.824 0.103 -1.092 "H5''" DDN 24 DDN "H4'" H4* H 0 1 N N N 77.214 7.214 15.675 -1.156 1.785 1.374 "H4'" DDN 25 DDN "H3'" H3* H 0 1 N N N 78.813 9.338 15.167 -0.618 2.141 -1.579 "H3'" DDN 26 DDN H1 H1 H 0 1 N N N 77.115 10.073 13.816 -0.398 4.304 -0.821 H1 DDN 27 DDN "H2'" 1H2* H 0 1 N N N 76.972 11.361 15.785 1.671 1.998 -1.315 "H2'" DDN 28 DDN "H2''" 2H2* H 0 0 N N N 78.279 11.071 16.721 1.598 3.233 -0.019 "H2''" DDN 29 DDN "H1'" H1* H 0 1 N N N 76.274 10.840 16.964 1.474 1.622 1.680 "H1'" DDN 30 DDN HN3 HN3 H 0 1 N N N 73.589 11.524 20.469 3.590 -1.659 -1.905 HN3 DDN 31 DDN H4 H4 H 0 1 N N N 75.028 10.405 22.306 5.650 -0.832 -0.792 H4 DDN 32 DDN HO4 HO4 H 0 1 N N N 76.645 12.121 22.786 5.045 -3.034 -0.612 HO4 DDN 33 DDN H5 H5 H 0 1 N N N 77.692 9.923 21.662 5.558 -0.266 1.732 H5 DDN 34 DDN H6 H6 H 0 1 N N N 77.967 9.545 19.359 3.570 1.025 2.146 H6 DDN 35 # # 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 DDN OP3 P DOUB N N 1 DDN P OP1 SING N N 2 DDN P OP2 SING N N 3 DDN P "O5'" SING N N 4 DDN OP1 H1P SING N N 5 DDN OP2 H2P SING N N 6 DDN "O5'" "C5'" SING N N 7 DDN "C5'" "C4'" SING N N 8 DDN "C5'" "H5'" SING N N 9 DDN "C5'" "H5''" SING N N 10 DDN "C4'" "O4'" SING N N 11 DDN "C4'" "C3'" SING N N 12 DDN "C4'" "H4'" SING N N 13 DDN "O4'" "C1'" SING N N 14 DDN "C3'" "O3'" SING N N 15 DDN "C3'" "C2'" SING N N 16 DDN "C3'" "H3'" SING N N 17 DDN "O3'" H1 SING N N 18 DDN "C2'" "C1'" SING N N 19 DDN "C2'" "H2'" SING N N 20 DDN "C2'" "H2''" SING N N 21 DDN "C1'" N1 SING N N 22 DDN "C1'" "H1'" SING N N 23 DDN N1 C2 SING N N 24 DDN N1 C6 SING N N 25 DDN C2 O2 DOUB N N 26 DDN C2 N3 SING N N 27 DDN N3 C4 SING N N 28 DDN N3 HN3 SING N N 29 DDN C4 O4 SING N N 30 DDN C4 C5 SING N N 31 DDN C4 H4 SING N N 32 DDN O4 HO4 SING N N 33 DDN C5 C6 DOUB N N 34 DDN C5 H5 SING N N 35 DDN C6 H6 SING N N 36 # # 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 DDN SMILES ACDLabs 10.04 "O=C1NC(O)C=CN1C2OC(C(O)C2)COP(=O)(O)O" DDN SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C[C@@H](O)NC2=O" DDN SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C[CH](O)NC2=O" DDN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C[C@H](NC2=O)O)COP(=O)(O)O)O" DDN SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(NC2=O)O)COP(=O)(O)O)O" DDN InChI InChI 1.03 "InChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-8,12-13H,3-4H2,(H,10,14)(H2,15,16,17)/t5-,6+,7+,8+/m0/s1" DDN InChIKey InChI 1.03 ILSIYJVILUIVPM-LXGUWJNJSA-N # # 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 DDN "SYSTEMATIC NAME" ACDLabs 10.04 "(4R)-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one" DDN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-[(4R)-4-hydroxy-2-oxo-3,4-dihydropyrimidin-1-yl]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 DDN "Create component" 2004-12-14 RCSB DDN "Modify descriptor" 2011-06-04 RCSB DDN "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DDN _pdbx_chem_comp_synonyms.name "((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##