data_EDC # _chem_comp.id EDC _chem_comp.name "N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H14 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 331.219 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EDC _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 3UBY _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 EDC OP3 OP3 O 0 1 N Y N 3.262 1.316 35.492 -4.900 2.099 -1.289 OP3 EDC 1 EDC P P P 0 1 N N N 2.260 1.465 34.267 -4.513 1.125 -0.067 P EDC 2 EDC N1 N1 N 0 1 N N N 0.733 -0.643 30.679 2.019 -0.380 -0.095 N1 EDC 3 EDC C2 C2 C 0 1 N N N 0.949 -0.198 29.354 3.100 -0.163 -0.864 C2 EDC 4 EDC O2 O2 O 0 1 N N N 1.642 -0.892 28.572 3.114 -0.586 -2.003 O2 EDC 5 EDC N3 N3 N 0 1 Y N N 0.427 0.971 28.931 4.165 0.511 -0.399 N3 EDC 6 EDC C4 C4 C 0 1 Y N N -0.316 1.735 29.755 4.164 0.996 0.887 C4 EDC 7 EDC N4 N4 N 0 1 Y N N -0.711 2.830 29.087 5.308 1.611 1.096 N4 EDC 8 EDC C5 C5 C 0 1 N N N -0.554 1.323 31.066 2.987 0.759 1.727 C5 EDC 9 EDC C6 C6 C 0 1 N N N -0.016 0.115 31.504 1.950 0.081 1.198 C6 EDC 10 EDC C7 C7 C 0 1 Y N N -0.217 2.768 27.834 6.056 1.543 -0.015 C7 EDC 11 EDC C8 C8 C 0 1 Y N N 0.497 1.591 27.744 5.369 0.867 -0.956 C8 EDC 12 EDC "C1'" "C1'" C 0 1 N N R 1.297 -1.931 31.130 0.884 -1.122 -0.651 "C1'" EDC 13 EDC "C2'" "C2'" C 0 1 N N N 2.814 -1.931 31.308 0.703 -2.450 0.110 "C2'" EDC 14 EDC "C3'" "C3'" C 0 1 N N S 3.024 -2.598 32.654 -0.739 -2.372 0.669 "C3'" EDC 15 EDC "O3'" "O3'" O 0 1 N N N 3.234 -3.995 32.416 -1.402 -3.632 0.545 "O3'" EDC 16 EDC "C4'" "C4'" C 0 1 N N R 1.715 -2.407 33.406 -1.390 -1.312 -0.256 "C4'" EDC 17 EDC "O4'" "O4'" O 0 1 N N N 0.719 -2.322 32.386 -0.325 -0.363 -0.482 "O4'" EDC 18 EDC "C5'" "C5'" C 0 1 N N N 1.700 -1.153 34.294 -2.572 -0.639 0.444 "C5'" EDC 19 EDC "O5'" "O5'" O 0 1 N N N 2.262 -0.025 33.620 -3.224 0.247 -0.468 "O5'" EDC 20 EDC OP1 OP1 O 0 1 N N N 2.960 2.350 33.256 -4.204 1.936 1.131 OP1 EDC 21 EDC OP2 OP2 O 0 1 N N N 0.856 1.768 34.726 -5.751 0.146 0.252 OP2 EDC 22 EDC HOP3 HOP3 H 0 0 N Y N 4.056 1.807 35.314 -5.669 2.658 -1.118 HOP3 EDC 23 EDC H5 H5 H 0 1 N N N -1.147 1.932 31.732 2.949 1.124 2.743 H5 EDC 24 EDC H6 H6 H 0 1 N N N -0.201 -0.217 32.515 1.066 -0.104 1.791 H6 EDC 25 EDC H7 H7 H 0 1 N N N -0.354 3.499 27.051 7.044 1.962 -0.135 H7 EDC 26 EDC H8 H8 H 0 1 N N N 1.021 1.232 26.870 5.703 0.645 -1.959 H8 EDC 27 EDC "H1'" "H1'" H 0 1 N N N 1.052 -2.695 30.377 1.054 -1.321 -1.709 "H1'" EDC 28 EDC "H2'" "H2'" H 0 1 N N N 3.302 -2.505 30.507 0.803 -3.296 -0.570 "H2'" EDC 29 EDC "H2''" "H2''" H 0 0 N N N 3.207 -0.904 31.315 1.424 -2.525 0.924 "H2''" EDC 30 EDC "H3'" "H3'" H 0 1 N N N 3.861 -2.136 33.197 -0.737 -2.035 1.705 "H3'" EDC 31 EDC "HO3'" "HO3'" H 0 0 N Y N 3.369 -4.441 33.244 -0.977 -4.350 1.036 "HO3'" EDC 32 EDC "H4'" "H4'" H 0 1 N N N 1.536 -3.289 34.038 -1.708 -1.765 -1.195 "H4'" EDC 33 EDC "H5'" "H5'" H 0 1 N N N 0.660 -0.923 34.569 -3.277 -1.400 0.778 "H5'" EDC 34 EDC "H5''" "H5''" H 0 0 N N N 2.285 -1.353 35.204 -2.211 -0.075 1.304 "H5''" EDC 35 EDC HOP2 HOP2 H 0 0 N N N 0.542 2.551 34.289 -6.008 -0.417 -0.491 HOP2 EDC 36 # # 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 EDC P OP3 SING N N 1 EDC OP3 HOP3 SING N N 2 EDC OP1 P DOUB N N 3 EDC "O5'" P SING N N 4 EDC P OP2 SING N N 5 EDC C2 N1 SING N N 6 EDC N1 "C1'" SING N N 7 EDC N1 C6 SING N N 8 EDC O2 C2 DOUB N N 9 EDC N3 C2 SING N N 10 EDC C8 N3 SING Y N 11 EDC N3 C4 SING Y N 12 EDC N4 C4 DOUB Y N 13 EDC C4 C5 SING N N 14 EDC C7 N4 SING Y N 15 EDC C5 C6 DOUB N N 16 EDC C5 H5 SING N N 17 EDC C6 H6 SING N N 18 EDC C8 C7 DOUB Y N 19 EDC C7 H7 SING N N 20 EDC C8 H8 SING N N 21 EDC "C1'" "C2'" SING N N 22 EDC "C1'" "O4'" SING N N 23 EDC "C1'" "H1'" SING N N 24 EDC "C2'" "C3'" SING N N 25 EDC "C2'" "H2'" SING N N 26 EDC "C2'" "H2''" SING N N 27 EDC "O3'" "C3'" SING N N 28 EDC "C3'" "C4'" SING N N 29 EDC "C3'" "H3'" SING N N 30 EDC "O3'" "HO3'" SING N N 31 EDC "O4'" "C4'" SING N N 32 EDC "C4'" "C5'" SING N N 33 EDC "C4'" "H4'" SING N N 34 EDC "O5'" "C5'" SING N N 35 EDC "C5'" "H5'" SING N N 36 EDC "C5'" "H5''" SING N N 37 EDC OP2 HOP2 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 EDC SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(N2C(=O)n1c(ncc1)C=C2)CC3O" EDC InChI InChI 1.03 "InChI=1S/C11H14N3O7P/c15-7-5-10(21-8(7)6-20-22(17,18)19)14-3-1-9-12-2-4-13(9)11(14)16/h1-4,7-8,10,15H,5-6H2,(H2,17,18,19)/t7-,8+,10+/m0/s1" EDC InChIKey InChI 1.03 GFTHJCBXWZWVBW-QXFUBDJGSA-N EDC SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=Cc3nccn3C2=O" EDC SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=Cc3nccn3C2=O" EDC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cn2c(n1)C=CN(C2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" EDC SMILES "OpenEye OEToolkits" 1.7.6 "c1cn2c(n1)C=CN(C2=O)C3CC(C(O3)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 EDC "SYSTEMATIC NAME" ACDLabs 12.01 "6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one" EDC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-3-oxidanyl-5-(5-oxidanylideneimidazo[1,2-c]pyrimidin-6-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 EDC "Create component" 1999-07-08 RCSB EDC "Modify descriptor" 2011-06-04 RCSB EDC "Other modification" 2011-12-19 RCSB EDC "Other modification" 2012-01-09 RCSB EDC "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id EDC _pdbx_chem_comp_synonyms.name "6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##