data_B7A # _chem_comp.id B7A _chem_comp.name "2'-deoxy-5-formyluridine 5'-(tetrahydrogen triphosphate)" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N2 O15 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms 5-FodUTP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-08-03 _chem_comp.pdbx_modified_date 2021-03-01 _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 496.152 _chem_comp.one_letter_code ? _chem_comp.three_letter_code B7A _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 5WO0 _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 B7A C10 C1 C 0 1 N N R -12.645 6.279 64.412 1.824 2.131 0.816 C10 B7A 1 B7A C26 C2 C 0 1 N N N -8.821 7.580 62.052 4.670 -0.134 -0.949 C26 B7A 2 B7A C01 C3 C 0 1 N N N -7.236 6.546 65.889 6.775 -2.975 1.316 C01 B7A 3 B7A O02 O1 O 0 1 N N N -7.860 6.704 66.917 7.469 -3.798 0.756 O02 B7A 4 B7A C03 C4 C 0 1 N N N -7.772 6.898 64.604 6.040 -1.983 0.533 C03 B7A 5 B7A C04 C5 C 0 1 N N N -9.111 6.865 64.334 5.241 -1.035 1.151 C04 B7A 6 B7A N05 N1 N 0 1 N N N -9.631 7.211 63.096 4.575 -0.131 0.390 N05 B7A 7 B7A C06 C6 C 0 1 N N R -11.057 7.121 62.875 3.731 0.872 1.044 C06 B7A 8 B7A C07 C7 C 0 1 N N N -11.546 5.751 62.418 4.254 2.297 0.745 C07 B7A 9 B7A C08 C8 C 0 1 N N S -11.989 5.077 63.708 2.970 3.143 0.592 C08 B7A 10 B7A O09 O2 O 0 1 N N N -12.908 4.029 63.417 2.928 4.173 1.582 O09 B7A 11 B7A C11 C9 C 0 1 N N N -12.823 6.102 65.924 0.650 2.441 -0.115 C11 B7A 12 B7A O12 O3 O 0 1 N N N -11.500 5.846 66.416 -0.428 1.545 0.163 O12 B7A 13 B7A P13 P1 P 0 1 N N N -11.366 4.708 67.572 -1.828 1.585 -0.630 P13 B7A 14 B7A O14 O4 O 0 1 N N N -12.530 4.850 68.529 -1.581 1.201 -2.174 O14 B7A 15 B7A O15 O5 O 0 1 N N N -9.978 4.815 68.162 -2.404 2.945 -0.546 O15 B7A 16 B7A O16 O6 O 0 1 N N N -11.442 3.286 66.776 -2.849 0.528 0.029 O16 B7A 17 B7A P17 P2 P 0 1 N N N -12.627 2.222 66.613 -4.438 0.296 -0.073 P17 B7A 18 B7A O18 O7 O 0 1 N N N -12.610 1.769 65.167 -4.859 0.377 -1.489 O18 B7A 19 B7A O19 O8 O 0 1 N N N -13.984 2.658 67.054 -5.202 1.429 0.780 O19 B7A 20 B7A O20 O9 O 0 1 N N N -12.116 0.952 67.496 -4.807 -1.157 0.514 O20 B7A 21 B7A P21 P3 P 0 1 N N N -12.306 0.657 69.059 -6.069 -2.143 0.347 P21 B7A 22 B7A O22 O10 O 0 1 N N N -10.900 0.273 69.630 -7.307 -1.581 1.210 O22 B7A 23 B7A O23 O11 O 0 1 N N N -13.297 -0.528 69.115 -6.454 -2.215 -1.080 O23 B7A 24 B7A O24 O12 O 0 1 N N N -12.856 1.907 69.755 -5.674 -3.614 0.871 O24 B7A 25 B7A O25 O13 O 0 1 N N N -11.757 7.390 64.093 2.397 0.845 0.492 O25 B7A 26 B7A O27 O14 O 0 1 N N N -9.248 7.866 60.957 4.056 0.701 -1.583 O27 B7A 27 B7A N28 N2 N 0 1 N N N -7.482 7.612 62.340 5.426 -1.026 -1.611 N28 B7A 28 B7A C29 C10 C 0 1 N N N -6.852 7.290 63.540 6.126 -1.963 -0.938 C29 B7A 29 B7A O30 O15 O 0 1 N N N -5.634 7.352 63.629 6.813 -2.773 -1.533 O30 B7A 30 B7A H1 H1 H 0 1 N N N -13.632 6.453 63.960 1.499 2.150 1.856 H1 B7A 31 B7A H2 H2 H 0 1 N N N -6.242 6.126 65.942 6.700 -2.976 2.394 H2 B7A 32 B7A H3 H3 H 0 1 N N N -9.791 6.558 65.115 5.150 -1.015 2.227 H3 B7A 33 B7A H4 H4 H 0 1 N N N -11.351 7.860 62.115 3.699 0.697 2.120 H4 B7A 34 B7A H5 H5 H 0 1 N N N -12.388 5.849 61.717 4.857 2.665 1.576 H5 B7A 35 B7A H6 H6 H 0 1 N N N -10.734 5.185 61.938 4.830 2.306 -0.180 H6 B7A 36 B7A H7 H7 H 0 1 N N N -11.120 4.722 64.281 2.911 3.571 -0.409 H7 B7A 37 B7A H8 H8 H 0 1 N N N -12.769 3.309 64.021 3.659 4.803 1.525 H8 B7A 38 B7A H9 H9 H 0 1 N N N -13.235 7.016 66.376 0.320 3.467 0.046 H9 B7A 39 B7A H10 H10 H 0 1 N N N -13.489 5.253 66.140 0.966 2.319 -1.151 H10 B7A 40 B7A H11 H11 H 0 1 N N N -12.202 4.993 69.409 -1.204 0.320 -2.305 H11 B7A 41 B7A H12 H12 H 0 1 N N N -14.596 2.569 66.333 -4.974 1.434 1.719 H12 B7A 42 B7A H13 H13 H 0 1 N N N -10.909 -0.634 69.913 -7.125 -1.507 2.157 H13 B7A 43 B7A H14 H14 H 0 1 N N N -13.722 1.723 70.100 -6.388 -4.261 0.801 H14 B7A 44 B7A H15 H15 H 0 1 N N N -6.881 7.903 61.595 5.469 -0.995 -2.580 H15 B7A 45 # # 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 B7A O27 C26 DOUB N N 1 B7A C26 N28 SING N N 2 B7A C26 N05 SING N N 3 B7A N28 C29 SING N N 4 B7A C07 C06 SING N N 5 B7A C07 C08 SING N N 6 B7A C06 N05 SING N N 7 B7A C06 O25 SING N N 8 B7A N05 C04 SING N N 9 B7A O09 C08 SING N N 10 B7A C29 O30 DOUB N N 11 B7A C29 C03 SING N N 12 B7A C08 C10 SING N N 13 B7A O25 C10 SING N N 14 B7A C04 C03 DOUB N N 15 B7A C10 C11 SING N N 16 B7A C03 C01 SING N N 17 B7A O18 P17 DOUB N N 18 B7A C01 O02 DOUB N N 19 B7A C11 O12 SING N N 20 B7A O12 P13 SING N N 21 B7A P17 O16 SING N N 22 B7A P17 O19 SING N N 23 B7A P17 O20 SING N N 24 B7A O16 P13 SING N N 25 B7A O20 P21 SING N N 26 B7A P13 O15 DOUB N N 27 B7A P13 O14 SING N N 28 B7A P21 O23 DOUB N N 29 B7A P21 O22 SING N N 30 B7A P21 O24 SING N N 31 B7A C10 H1 SING N N 32 B7A C01 H2 SING N N 33 B7A C04 H3 SING N N 34 B7A C06 H4 SING N N 35 B7A C07 H5 SING N N 36 B7A C07 H6 SING N N 37 B7A C08 H7 SING N N 38 B7A O09 H8 SING N N 39 B7A C11 H9 SING N N 40 B7A C11 H10 SING N N 41 B7A O14 H11 SING N N 42 B7A O19 H12 SING N N 43 B7A O22 H13 SING N N 44 B7A O24 H14 SING N N 45 B7A N28 H15 SING N N 46 # # 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 B7A SMILES ACDLabs 12.01 "C2(COP(=O)(O)OP(O)(OP(=O)(O)O)=O)C(CC(N1C(NC(C(C=O)=C1)=O)=O)O2)O" B7A InChI InChI 1.03 "InChI=1S/C10H15N2O15P3/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(25-8)4-24-29(20,21)27-30(22,23)26-28(17,18)19/h2-3,6-8,14H,1,4H2,(H,20,21)(H,22,23)(H,11,15,16)(H2,17,18,19)/t6-,7+,8+/m0/s1" B7A InChIKey InChI 1.03 YCOXPTBWJXOXAV-XLPZGREQSA-N B7A SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C=O)C(=O)NC2=O" B7A SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C=O)C(=O)NC2=O" B7A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" B7A SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=C(C(=O)NC2=O)C=O)COP(=O)(O)OP(=O)(O)OP(=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 B7A "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5-formyluridine 5'-(tetrahydrogen triphosphate)" B7A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},5~{R})-5-[5-methanoyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 B7A "Create component" 2017-08-03 RCSB B7A "Modify synonyms" 2017-08-03 RCSB B7A "Initial release" 2017-09-13 RCSB B7A "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id B7A _pdbx_chem_comp_synonyms.name 5-FodUTP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##