data_B7C # _chem_comp.id B7C _chem_comp.name "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3H)-one" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H16 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-04-30 _chem_comp.pdbx_modified_date 2011-06-04 _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 345.245 _chem_comp.one_letter_code ? _chem_comp.three_letter_code B7C _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 3GJH _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 B7C OP3 OP3 O 0 1 N Y N 19.181 2.403 28.704 5.964 0.289 0.041 OP3 B7C 1 B7C P P P 0 1 N N N 20.049 2.573 30.031 4.650 1.213 0.135 P B7C 2 B7C OP1 OP1 O 0 1 N N N 21.166 3.506 29.725 4.867 2.343 1.261 OP1 B7C 3 B7C OP2 OP2 O 0 1 N N N 20.334 1.228 30.591 4.409 1.862 -1.174 OP2 B7C 4 B7C "O5'" "O5'" O 0 1 N N N 19.019 3.310 30.978 3.380 0.303 0.525 "O5'" B7C 5 B7C N1 N1 N 0 1 N N N 15.243 1.274 32.198 -1.812 -0.507 0.257 N1 B7C 6 B7C C6 C6 C 0 1 N N N 16.164 0.316 31.874 -2.868 -0.476 1.120 C6 B7C 7 B7C C2 C2 C 0 1 N N N 13.889 0.941 32.323 -1.846 0.151 -0.913 C2 B7C 8 B7C O2 O2 O 0 1 N N N 13.085 1.828 32.656 -0.870 0.103 -1.644 O2 B7C 9 B7C N3 N3 N 0 1 N N N 13.493 -0.334 32.081 -2.910 0.855 -1.306 N3 B7C 10 B7C C4 C4 C 0 1 N N N 14.397 -1.255 31.741 -3.972 0.928 -0.533 C4 B7C 11 B7C N4 N4 N 0 1 N N N 13.971 -2.503 31.466 -5.118 1.620 -0.864 N4 B7C 12 B7C C5 C5 C 0 1 N N N 15.788 -0.946 31.639 -3.970 0.237 0.764 C5 B7C 13 B7C C7 C7 C 0 1 N N N 16.710 -1.964 31.173 -5.165 0.361 1.620 C7 B7C 14 B7C C8 C8 C 0 1 N N N 16.285 -3.227 31.165 -6.315 0.743 1.064 C8 B7C 15 B7C C9 C9 C 0 1 N N N 14.964 -3.530 31.830 -6.390 1.016 -0.419 C9 B7C 16 B7C "C2'" "C2'" C 0 1 N N N 16.856 2.922 33.262 -0.414 -2.450 -0.356 "C2'" B7C 17 B7C "C5'" "C5'" C 0 1 N N N 18.079 4.217 30.424 2.866 -0.721 -0.327 "C5'" B7C 18 B7C "C4'" "C4'" C 0 1 N N R 16.884 4.327 31.333 1.663 -1.387 0.344 "C4'" B7C 19 B7C "O4'" "O4'" O 0 1 N N N 15.978 3.220 31.135 0.568 -0.453 0.455 "O4'" B7C 20 B7C "C1'" "C1'" C 0 1 N N R 15.639 2.676 32.399 -0.613 -1.268 0.618 "C1'" B7C 21 B7C "C3'" "C3'" C 0 1 N N S 17.244 4.319 32.814 1.118 -2.531 -0.540 "C3'" B7C 22 B7C "O3'" "O3'" O 0 1 N N N 16.443 5.282 33.478 1.611 -3.793 -0.087 "O3'" B7C 23 B7C HOP3 HOP3 H 0 0 N N N 18.259 2.369 28.930 6.183 -0.168 0.865 HOP3 B7C 24 B7C HOP1 HOP1 H 0 0 N N N 21.168 3.705 28.796 5.617 2.929 1.091 HOP1 B7C 25 B7C H6 H6 H 0 1 N N N 17.209 0.582 31.807 -2.830 -1.005 2.061 H6 B7C 26 B7C HN4 HN4 H 0 1 N N N 13.081 -2.710 31.060 -5.090 2.453 -1.360 HN4 B7C 27 B7C H7 H7 H 0 1 N N N 17.706 -1.707 30.844 -5.109 0.147 2.677 H7 B7C 28 B7C H8 H8 H 0 1 N N N 16.867 -4.008 30.698 -7.197 0.857 1.676 H8 B7C 29 B7C H9 H9 H 0 1 N N N 15.099 -3.535 32.922 -7.210 1.704 -0.622 H9 B7C 30 B7C H9A H9A H 0 1 N N N 14.607 -4.514 31.494 -6.556 0.081 -0.954 H9A B7C 31 B7C "H2'" "H2'" H 0 1 N N N 16.626 2.874 34.337 -0.795 -3.373 0.080 "H2'" B7C 32 B7C "H2'A" "H2'A" H 0 0 N N N 17.652 2.172 33.145 -0.903 -2.247 -1.309 "H2'A" B7C 33 B7C "H5'" "H5'" H 0 1 N N N 18.547 5.206 30.314 2.556 -0.283 -1.276 "H5'" B7C 34 B7C "H5'A" "H5'A" H 0 0 N N N 17.755 3.850 29.439 3.640 -1.467 -0.508 "H5'A" B7C 35 B7C "H4'" "H4'" H 0 1 N N N 16.425 5.291 31.070 1.940 -1.766 1.328 "H4'" B7C 36 B7C "H1'" "H1'" H 0 1 N N N 14.776 3.129 32.909 -0.688 -1.630 1.643 "H1'" B7C 37 B7C "H3'" "H3'" H 0 1 N N N 18.298 4.554 33.022 1.386 -2.367 -1.584 "H3'" B7C 38 B7C "HO3'" "HO3'" H 0 0 N Y N 16.264 4.989 34.364 1.254 -4.551 -0.570 "HO3'" B7C 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 B7C OP3 P SING N N 1 B7C P OP1 SING N N 2 B7C P OP2 DOUB N N 3 B7C P "O5'" SING N N 4 B7C "O5'" "C5'" SING N N 5 B7C N1 C6 SING N N 6 B7C N1 C2 SING N N 7 B7C N1 "C1'" SING N N 8 B7C C6 C5 DOUB N N 9 B7C C2 O2 DOUB N N 10 B7C C2 N3 SING N N 11 B7C N3 C4 DOUB N N 12 B7C C4 N4 SING N N 13 B7C C4 C5 SING N N 14 B7C N4 C9 SING N N 15 B7C C5 C7 SING N N 16 B7C C7 C8 DOUB N N 17 B7C C8 C9 SING N N 18 B7C "C2'" "C1'" SING N N 19 B7C "C2'" "C3'" SING N N 20 B7C "C5'" "C4'" SING N N 21 B7C "C4'" "O4'" SING N N 22 B7C "C4'" "C3'" SING N N 23 B7C "O4'" "C1'" SING N N 24 B7C "C3'" "O3'" SING N N 25 B7C OP3 HOP3 SING N N 26 B7C OP1 HOP1 SING N N 27 B7C C6 H6 SING N N 28 B7C N4 HN4 SING N N 29 B7C C7 H7 SING N N 30 B7C C8 H8 SING N N 31 B7C C9 H9 SING N N 32 B7C C9 H9A SING N N 33 B7C "C2'" "H2'" SING N N 34 B7C "C2'" "H2'A" SING N N 35 B7C "C5'" "H5'" SING N N 36 B7C "C5'" "H5'A" SING N N 37 B7C "C4'" "H4'" SING N N 38 B7C "C1'" "H1'" SING N N 39 B7C "C3'" "H3'" SING N N 40 B7C "O3'" "HO3'" SING N N 41 # 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 B7C SMILES ACDLabs 10.04 "O=C1N=C3C(=CN1C2OC(C(O)C2)COP(=O)(O)O)C=CCN3" B7C SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C3C=CCNC3=NC2=O" B7C SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C3C=CCNC3=NC2=O" B7C SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C=CC2=CN(C(=O)N=C2N1)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" B7C SMILES "OpenEye OEToolkits" 1.5.0 "C1C=CC2=CN(C(=O)N=C2N1)C3CC(C(O3)COP(=O)(O)O)O" B7C InChI InChI 1.03 "InChI=1S/C12H16N3O7P/c16-8-4-10(22-9(8)6-21-23(18,19)20)15-5-7-2-1-3-13-11(7)14-12(15)17/h1-2,5,8-10,16H,3-4,6H2,(H,13,14,17)(H2,18,19,20)/t8-,9+,10+/m0/s1" B7C InChIKey InChI 1.03 TVIUKNIUQVYWKE-IVZWLZJFSA-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 B7C "SYSTEMATIC NAME" ACDLabs 10.04 "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3H)-one" B7C "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(2-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-3-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 B7C "Create component" 2009-04-30 PDBJ B7C "Modify descriptor" 2011-06-04 RCSB #