data_5DB # _chem_comp.id 5DB _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1H)-one" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 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 2015-09-08 _chem_comp.pdbx_modified_date 2016-08-05 _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 336.235 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 5DLF _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 5DB P P1 P 0 1 N N N 27.769 -59.537 19.709 4.398 -1.142 -0.168 P 5DB 1 5DB OP1 O1 O 0 1 N N N 28.397 -58.283 20.278 3.873 -2.310 0.807 OP1 5DB 2 5DB "O5'" O2 O 0 1 N N N 26.296 -59.196 19.159 3.180 -0.152 -0.525 "O5'" 5DB 3 5DB "C5'" C1 C 0 1 N N N 25.623 -60.043 18.224 2.523 0.658 0.452 "C5'" 5DB 4 5DB "C4'" C2 C 0 1 N N R 24.471 -59.251 17.625 1.418 1.474 -0.221 "C4'" 5DB 5 5DB "C3'" C3 C 0 1 N N S 24.927 -58.162 16.662 0.696 2.374 0.814 "C3'" 5DB 6 5DB "O3'" O3 O 0 1 N N N 23.930 -58.063 15.648 1.380 3.618 0.974 "O3'" 5DB 7 5DB "C2'" C4 C 0 1 N N N 24.951 -56.869 17.451 -0.687 2.585 0.152 "C2'" 5DB 8 5DB "C1'" C5 C 0 1 N N R 23.850 -57.151 18.454 -0.812 1.415 -0.844 "C1'" 5DB 9 5DB "O4'" O4 O 0 1 N N N 23.854 -58.556 18.704 0.369 0.607 -0.703 "O4'" 5DB 10 5DB N1 N1 N 0 1 N N N 24.061 -56.501 19.735 -2.001 0.618 -0.530 N1 5DB 11 5DB C6 C6 C 0 1 N N N 25.218 -56.652 20.396 -3.030 0.557 -1.420 C6 5DB 12 5DB C5 C7 C 0 1 N N N 25.393 -56.028 21.626 -4.124 -0.184 -1.117 C5 5DB 13 5DB C7 C8 C 0 1 N N N 26.695 -56.171 22.387 -5.278 -0.272 -2.081 C7 5DB 14 5DB C4 C9 C 0 1 N N N 24.259 -55.224 22.168 -4.165 -0.870 0.111 C4 5DB 15 5DB N3 N2 N 0 1 N N N 23.113 -55.119 21.455 -3.141 -0.781 0.946 N3 5DB 16 5DB C2 C10 C 0 1 N N N 22.991 -55.740 20.256 -2.069 -0.054 0.634 C2 5DB 17 5DB O2 O5 O 0 1 N N N 21.931 -55.655 19.581 -1.136 0.008 1.418 O2 5DB 18 5DB O4 O6 O 0 1 N N N 24.368 -54.581 23.378 -5.245 -1.615 0.437 O4 5DB 19 5DB OP2 O7 O 0 1 N N N 28.604 -60.151 18.613 5.471 -0.379 0.510 OP2 5DB 20 5DB C1 C11 C 0 1 N N N 23.201 -54.266 24.141 -5.215 -2.282 1.701 C1 5DB 21 5DB H1 H1 H 0 1 N N N 29.218 -58.109 19.832 3.167 -2.851 0.428 H1 5DB 22 5DB H2 H2 H 0 1 N N N 25.236 -60.935 18.738 2.087 0.020 1.220 H2 5DB 23 5DB H3 H3 H 0 1 N N N 26.319 -60.351 17.429 3.246 1.334 0.909 H3 5DB 24 5DB H4 H4 H 0 1 N N N 23.765 -59.929 17.123 1.826 2.073 -1.035 H4 5DB 25 5DB H5 H5 H 0 1 N N N 25.921 -58.392 16.252 0.595 1.862 1.771 H5 5DB 26 5DB H6 H6 H 0 1 N N N 23.906 -58.870 15.147 0.920 4.250 1.543 H6 5DB 27 5DB H7 H7 H 0 1 N N N 25.921 -56.710 17.944 -1.480 2.536 0.899 H7 5DB 28 5DB H8 H8 H 0 1 N N N 24.714 -56.001 16.819 -0.716 3.539 -0.375 H8 5DB 29 5DB H9 H9 H 0 1 N N N 22.885 -56.840 18.028 -0.879 1.799 -1.861 H9 5DB 30 5DB H10 H10 H 0 1 N N N 26.009 -57.255 19.975 -2.975 1.092 -2.356 H10 5DB 31 5DB H11 H11 H 0 1 N N N 26.634 -55.606 23.329 -5.124 -1.114 -2.757 H11 5DB 32 5DB H12 H12 H 0 1 N N N 26.876 -57.233 22.607 -6.205 -0.417 -1.526 H12 5DB 33 5DB H13 H13 H 0 1 N N N 27.521 -55.777 21.777 -5.341 0.650 -2.658 H13 5DB 34 5DB H15 H15 H 0 1 N N N 23.496 -53.757 25.070 -4.367 -2.967 1.730 H15 5DB 35 5DB H16 H16 H 0 1 N N N 22.546 -53.606 23.553 -5.115 -1.546 2.498 H16 5DB 36 5DB H17 H17 H 0 1 N N N 22.662 -55.193 24.386 -6.139 -2.843 1.837 H17 5DB 37 5DB OP3 OP3 O 0 1 N Y N ? ? ? 4.976 -1.792 -1.522 OP3 5DB 38 5DB H19 H19 H 0 1 N Y N ? ? ? 5.714 -2.401 -1.383 H19 5DB 39 # 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 5DB "O3'" "C3'" SING N N 1 5DB "C3'" "C2'" SING N N 2 5DB "C3'" "C4'" SING N N 3 5DB "C2'" "C1'" SING N N 4 5DB "C4'" "C5'" SING N N 5 5DB "C4'" "O4'" SING N N 6 5DB "C5'" "O5'" SING N N 7 5DB "C1'" "O4'" SING N N 8 5DB "C1'" N1 SING N N 9 5DB OP2 P DOUB N N 10 5DB "O5'" P SING N N 11 5DB O2 C2 DOUB N N 12 5DB P OP1 SING N N 13 5DB N1 C2 SING N N 14 5DB N1 C6 SING N N 15 5DB C2 N3 SING N N 16 5DB C6 C5 DOUB N N 17 5DB N3 C4 DOUB N N 18 5DB C5 C4 SING N N 19 5DB C5 C7 SING N N 20 5DB C4 O4 SING N N 21 5DB O4 C1 SING N N 22 5DB OP1 H1 SING N N 23 5DB "C5'" H2 SING N N 24 5DB "C5'" H3 SING N N 25 5DB "C4'" H4 SING N N 26 5DB "C3'" H5 SING N N 27 5DB "O3'" H6 SING N N 28 5DB "C2'" H7 SING N N 29 5DB "C2'" H8 SING N N 30 5DB "C1'" H9 SING N N 31 5DB C6 H10 SING N N 32 5DB C7 H11 SING N N 33 5DB C7 H12 SING N N 34 5DB C7 H13 SING N N 35 5DB C1 H15 SING N N 36 5DB C1 H16 SING N N 37 5DB C1 H17 SING N N 38 5DB P OP3 SING N N 39 5DB OP3 H19 SING N N 40 # 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 5DB SMILES ACDLabs 12.01 "P(O)(O)(OCC1OC(CC1O)N2C(N=C(C(=C2)C)OC)=O)=O" 5DB InChI InChI 1.03 "InChI=1S/C11H17N2O8P/c1-6-4-13(11(15)12-10(6)19-2)9-3-7(14)8(21-9)5-20-22(16,17)18/h4,7-9,14H,3,5H2,1-2H3,(H2,16,17,18)/t7-,8+,9+/m0/s1" 5DB InChIKey InChI 1.03 ZEXYXJZBCLRLBU-DJLDLDEBSA-N 5DB SMILES_CANONICAL CACTVS 3.385 "COC1=NC(=O)N(C=C1C)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" 5DB SMILES CACTVS 3.385 "COC1=NC(=O)N(C=C1C)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" 5DB SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)N=C1OC)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 5DB SMILES "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)N=C1OC)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 5DB "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1H)-one" 5DB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,5R)-5-(4-methoxy-5-methyl-2-oxidanylidene-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 5DB "Create component" 2015-09-08 RCSB 5DB "Initial release" 2016-08-10 RCSB #