data_6F7 # _chem_comp.id 6F7 _chem_comp.name ;3'-deoxy-5-methyluridine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 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 2016-03-29 _chem_comp.pdbx_modified_date 2016-12-09 _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 322.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6F7 _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 5J02 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 6F7 N1 N1 N 0 1 N N N 211.660 215.681 234.089 2.217 -0.268 -0.282 N1 6F7 1 6F7 C2 C1 C 0 1 N N N 212.634 214.753 233.749 2.184 0.423 0.872 C2 6F7 2 6F7 N3 N2 N 0 1 N N N 213.585 215.068 232.810 3.188 1.255 1.208 N3 6F7 3 6F7 C4 C2 C 0 1 N N N 213.540 216.309 232.232 4.247 1.409 0.388 C4 6F7 4 6F7 C5 C3 C 0 1 N N N 212.530 217.266 232.587 4.293 0.687 -0.829 C5 6F7 5 6F7 C5M C4 C 0 1 N N N 212.441 218.641 231.978 5.466 0.841 -1.763 C5M 6F7 6 6F7 C6 C5 C 0 1 N N N 211.603 216.942 233.510 3.276 -0.144 -1.139 C6 6F7 7 6F7 O2 O1 O 0 1 N N N 212.652 213.657 234.279 1.236 0.294 1.622 O2 6F7 8 6F7 O4 O2 O 0 1 N N N 214.399 216.558 231.403 5.152 2.165 0.689 O4 6F7 9 6F7 "C1'" C6 C 0 1 N N R 210.643 215.323 235.100 1.110 -1.167 -0.621 "C1'" 6F7 10 6F7 "C2'" C7 C 0 1 N N R 211.116 215.751 236.494 1.049 -2.328 0.391 "C2'" 6F7 11 6F7 "O2'" O3 O 0 1 N N N 211.053 214.652 237.392 1.216 -3.581 -0.276 "O2'" 6F7 12 6F7 "C3'" C8 C 0 1 N N N 210.145 216.847 236.922 -0.369 -2.224 1.003 "C3'" 6F7 13 6F7 "C4'" C9 C 0 1 N N S 208.931 216.591 236.040 -1.127 -1.404 -0.071 "C4'" 6F7 14 6F7 "O4'" O4 O 0 1 N N N 209.440 216.017 234.819 -0.138 -0.459 -0.534 "O4'" 6F7 15 6F7 "C5'" C10 C 0 1 N N N 208.211 217.871 235.732 -2.322 -0.677 0.549 "C5'" 6F7 16 6F7 "O5'" O5 O 0 1 N N N 209.017 218.656 234.820 -3.069 -0.025 -0.479 "O5'" 6F7 17 6F7 P P1 P 0 1 N N N 208.297 219.835 233.962 -4.397 0.838 -0.185 P 6F7 18 6F7 OP1 O6 O 0 1 N N N 207.497 220.739 234.856 -5.552 -0.131 0.381 OP1 6F7 19 6F7 OP2 O7 O 0 1 N N N 209.301 220.615 233.169 -4.094 1.883 0.817 OP2 6F7 20 6F7 O1 O8 O 0 1 N Y N 207.302 219.052 232.966 -4.899 1.531 -1.549 O1 6F7 21 6F7 H1 H1 H 0 1 N N N 214.292 214.409 232.555 3.148 1.746 2.044 H1 6F7 22 6F7 H2 H2 H 0 1 N N N 211.586 219.180 232.412 6.179 1.547 -1.338 H2 6F7 23 6F7 H3 H3 H 0 1 N N N 213.368 219.195 232.186 5.950 -0.126 -1.901 H3 6F7 24 6F7 H4 H4 H 0 1 N N N 212.304 218.552 230.890 5.116 1.213 -2.727 H4 6F7 25 6F7 H5 H5 H 0 1 N N N 210.834 217.646 233.793 3.294 -0.703 -2.063 H5 6F7 26 6F7 H6 H6 H 0 1 N N N 210.476 214.236 235.094 1.247 -1.559 -1.628 H6 6F7 27 6F7 H7 H7 H 0 1 N N N 212.135 216.159 236.431 1.809 -2.201 1.163 H7 6F7 28 6F7 H8 H8 H 0 1 N N N 211.348 214.928 238.252 1.186 -4.347 0.314 H8 6F7 29 6F7 H9 H9 H 0 1 N N N 210.567 217.845 236.734 -0.813 -3.211 1.124 H9 6F7 30 6F7 H10 H10 H 0 1 N N N 209.887 216.753 237.987 -0.344 -1.691 1.954 H10 6F7 31 6F7 H11 H11 H 0 1 N N N 208.249 215.891 236.545 -1.453 -2.049 -0.887 H11 6F7 32 6F7 H12 H12 H 0 1 N N N 208.049 218.436 236.662 -2.960 -1.398 1.061 H12 6F7 33 6F7 H13 H13 H 0 1 N N N 207.240 217.646 235.266 -1.965 0.064 1.265 H13 6F7 34 6F7 H14 H14 H 0 1 N N N 207.788 221.636 234.742 -5.801 -0.841 -0.225 H14 6F7 35 6F7 H15 H15 H 0 1 N N N 207.544 219.236 232.066 -5.697 2.068 -1.447 H15 6F7 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 6F7 O4 C4 DOUB N N 1 6F7 C5M C5 SING N N 2 6F7 C4 C5 SING N N 3 6F7 C4 N3 SING N N 4 6F7 C5 C6 DOUB N N 5 6F7 N3 C2 SING N N 6 6F7 OP2 P DOUB N N 7 6F7 C6 N1 SING N N 8 6F7 C2 N1 SING N N 9 6F7 C2 O2 DOUB N N 10 6F7 P "O5'" SING N N 11 6F7 P OP1 SING N N 12 6F7 N1 "C1'" SING N N 13 6F7 "O4'" "C1'" SING N N 14 6F7 "O4'" "C4'" SING N N 15 6F7 "O5'" "C5'" SING N N 16 6F7 "C1'" "C2'" SING N N 17 6F7 "C5'" "C4'" SING N N 18 6F7 "C4'" "C3'" SING N N 19 6F7 "C2'" "C3'" SING N N 20 6F7 "C2'" "O2'" SING N N 21 6F7 P O1 SING N N 22 6F7 N3 H1 SING N N 23 6F7 C5M H2 SING N N 24 6F7 C5M H3 SING N N 25 6F7 C5M H4 SING N N 26 6F7 C6 H5 SING N N 27 6F7 "C1'" H6 SING N N 28 6F7 "C2'" H7 SING N N 29 6F7 "O2'" H8 SING N N 30 6F7 "C3'" H9 SING N N 31 6F7 "C3'" H10 SING N N 32 6F7 "C4'" H11 SING N N 33 6F7 "C5'" H12 SING N N 34 6F7 "C5'" H13 SING N N 35 6F7 OP1 H14 SING N N 36 6F7 O1 H15 SING N N 37 # 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 6F7 SMILES ACDLabs 12.01 "N2(C1C(CC(O1)COP(O)(O)=O)O)C(=O)NC(C(=C2)C)=O" 6F7 InChI InChI 1.03 "InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-8(5)14)9-7(13)2-6(20-9)4-19-21(16,17)18/h3,6-7,9,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,9+/m0/s1" 6F7 InChIKey InChI 1.03 NZONAJJJGMXZKE-LKEWCRSYSA-N 6F7 SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)C[C@H]2O)C(=O)NC1=O" 6F7 SMILES CACTVS 3.385 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)C[CH]2O)C(=O)NC1=O" 6F7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H](C[C@H](O2)COP(=O)(O)O)O" 6F7 SMILES "OpenEye OEToolkits" 2.0.4 "CC1=CN(C(=O)NC1=O)C2C(CC(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 6F7 "SYSTEMATIC NAME" ACDLabs 12.01 ;3'-deoxy-5-methyluridine 5'-(dihydrogen phosphate) ; 6F7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(2~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-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 6F7 "Create component" 2016-03-29 EBI 6F7 "Initial release" 2016-12-14 RCSB #