data_92F # _chem_comp.id 92F _chem_comp.name "7-amino-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-2-oxo-2,3-dihydropyrido[2,3-d]pyrimidine-6-carbonitrile" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H14 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-12-01 _chem_comp.pdbx_modified_date 2022-06-13 _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 383.253 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 92F _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 5YTC _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 92F P P1 P 0 1 N N N -26.366 -2.819 22.644 -5.277 1.472 -0.193 P 92F 1 92F OP1 O1 O 0 1 N N N -26.534 -4.296 22.938 -6.459 0.714 0.276 OP1 92F 2 92F OP2 O2 O 0 1 N N N -25.121 -2.251 23.269 -4.747 2.426 0.991 OP2 92F 3 92F "O5'" O3 O 0 1 N N N -26.409 -2.506 21.059 -4.113 0.444 -0.616 "O5'" 92F 4 92F "C5'" C1 C 0 1 N N N -27.252 -3.269 20.183 -3.606 -0.562 0.263 "C5'" 92F 5 92F "C4'" C2 C 0 1 N N R -27.423 -2.492 18.878 -2.513 -1.360 -0.451 "C4'" 92F 6 92F "O4'" O4 O 0 1 N N N -26.256 -2.563 18.044 -1.345 -0.541 -0.669 "O4'" 92F 7 92F "C3'" C3 C 0 1 N N S -28.579 -2.986 18.028 -1.993 -2.505 0.455 "C3'" 92F 8 92F "C2'" C4 C 0 1 N N N -28.154 -2.705 16.618 -0.572 -2.745 -0.110 "C2'" 92F 9 92F "C1'" C5 C 0 1 N N R -26.645 -2.750 16.673 -0.234 -1.435 -0.854 "C1'" 92F 10 92F N1 N1 N 0 1 N N N -26.207 -4.049 16.133 0.982 -0.842 -0.292 N1 92F 11 92F C6 C6 C 0 1 N N N -25.825 -5.047 16.961 2.083 -0.748 -1.060 C6 92F 12 92F C2 C7 C 0 1 N N N -26.204 -4.241 14.712 0.969 -0.400 0.975 C2 92F 13 92F O2 O5 O 0 1 N N N -26.561 -3.303 13.956 -0.061 -0.509 1.620 O2 92F 14 92F N3 N2 N 0 1 N N N -25.793 -5.422 14.168 2.027 0.149 1.560 N3 92F 15 92F C4 C8 C 0 1 N N N -25.387 -6.444 14.954 3.174 0.286 0.888 C4 92F 16 92F C5 C9 C 0 1 N N N -25.401 -6.255 16.433 3.226 -0.182 -0.506 C5 92F 17 92F C20 C10 C 0 1 N N N -24.999 -7.282 17.271 4.427 -0.045 -1.226 C20 92F 18 92F N23 N3 N 0 1 N N N -24.978 -7.628 14.434 4.256 0.832 1.442 N23 92F 19 92F C22 C11 C 0 1 N N N -24.575 -8.663 15.236 5.382 0.960 0.768 C22 92F 20 92F N26 N4 N 0 1 N N N -24.173 -9.841 14.669 6.469 1.531 1.390 N26 92F 21 92F C21 C12 C 0 1 N N N -24.575 -8.494 16.726 5.510 0.531 -0.575 C21 92F 22 92F C24 C13 C 0 1 N N N -24.199 -9.449 17.508 6.755 0.692 -1.263 C24 92F 23 92F N25 N5 N 0 1 N N N -23.757 -10.311 18.158 7.744 0.821 -1.809 N25 92F 24 92F "O3'" O6 O 0 1 N N N -29.765 -2.240 18.280 -2.802 -3.675 0.314 "O3'" 92F 25 92F H2 H2 H 0 1 N N N -24.662 -2.936 23.741 -3.972 2.954 0.753 H2 92F 26 92F H3 H3 H 0 1 N N N -28.234 -3.424 20.654 -3.188 -0.090 1.153 H3 92F 27 92F H4 H4 H 0 1 N N N -26.787 -4.244 19.976 -4.415 -1.232 0.554 H4 92F 28 92F H5 H5 H 0 1 N N N -27.616 -1.440 19.135 -2.885 -1.757 -1.396 H5 92F 29 92F H6 H6 H 0 1 N N N -28.734 -4.064 18.180 -1.949 -2.188 1.497 H6 92F 30 92F H7 H7 H 0 1 N N N -28.504 -1.713 16.295 0.137 -2.918 0.700 H7 92F 31 92F H8 H8 H 0 1 N N N -28.543 -3.472 15.932 -0.573 -3.587 -0.802 H8 92F 32 92F H9 H9 H 0 1 N N N -26.239 -1.938 16.052 -0.093 -1.637 -1.916 H9 92F 33 92F H10 H10 H 0 1 N N N -25.850 -4.903 18.031 2.079 -1.103 -2.080 H10 92F 34 92F H13 H13 H 0 1 N N N -25.014 -7.145 18.342 4.503 -0.376 -2.251 H13 92F 35 92F H14 H14 H 0 1 N N N -24.174 -9.943 13.674 6.399 1.832 2.310 H14 92F 36 92F H15 H15 H 0 1 N N N -23.878 -10.600 15.249 7.306 1.633 0.909 H15 92F 37 92F H16 H16 H 0 1 N N N -30.057 -2.400 19.170 -2.516 -4.419 0.861 H16 92F 38 92F OP3 OP3 O 0 1 N Y N -27.661 -2.040 23.210 -5.687 2.372 -1.464 OP3 92F 39 92F H1 H1 H 0 1 N Y N -28.257 -2.663 23.608 -6.385 3.015 -1.282 H1 92F 40 # 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 92F O2 C2 DOUB N N 1 92F N3 C2 SING N N 2 92F N3 C4 DOUB N N 3 92F N23 C4 SING N N 4 92F N23 C22 DOUB N N 5 92F N26 C22 SING N N 6 92F C2 N1 SING N N 7 92F C4 C5 SING N N 8 92F C22 C21 SING N N 9 92F N1 "C1'" SING N N 10 92F N1 C6 SING N N 11 92F C5 C6 DOUB N N 12 92F C5 C20 SING N N 13 92F "C2'" "C1'" SING N N 14 92F "C2'" "C3'" SING N N 15 92F "C1'" "O4'" SING N N 16 92F C21 C20 DOUB N N 17 92F C21 C24 SING N N 18 92F C24 N25 TRIP N N 19 92F "C3'" "O3'" SING N N 20 92F "C3'" "C4'" SING N N 21 92F "O4'" "C4'" SING N N 22 92F "C4'" "C5'" SING N N 23 92F "C5'" "O5'" SING N N 24 92F "O5'" P SING N N 25 92F P OP1 DOUB N N 26 92F P OP2 SING N N 27 92F OP2 H2 SING N N 28 92F "C5'" H3 SING N N 29 92F "C5'" H4 SING N N 30 92F "C4'" H5 SING N N 31 92F "C3'" H6 SING N N 32 92F "C2'" H7 SING N N 33 92F "C2'" H8 SING N N 34 92F "C1'" H9 SING N N 35 92F C6 H10 SING N N 36 92F C20 H13 SING N N 37 92F N26 H14 SING N N 38 92F N26 H15 SING N N 39 92F "O3'" H16 SING N N 40 92F P OP3 SING N N 41 92F OP3 H1 SING N N 42 # 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 92F SMILES ACDLabs 12.01 "P(=O)(O)(O)OCC1OC(CC1O)N2C=C3C(=NC2=O)N=C(C(=C3)C#N)N" 92F InChI InChI 1.03 "InChI=1S/C13H14N5O7P/c14-3-6-1-7-4-18(13(20)17-12(7)16-11(6)15)10-2-8(19)9(25-10)5-24-26(21,22)23/h1,4,8-10,19H,2,5H2,(H2,21,22,23)(H2,15,16,17,20)/t8-,9+,10+/m0/s1" 92F InChIKey InChI 1.03 PQSYAYGDMFQUTR-IVZWLZJFSA-N 92F SMILES_CANONICAL CACTVS 3.385 "NC1=NC2=NC(=O)N(C=C2C=C1C#N)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" 92F SMILES CACTVS 3.385 "NC1=NC2=NC(=O)N(C=C2C=C1C#N)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" 92F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=C3C=C(C(=NC3=NC2=O)N)C#N)COP(=O)(O)O)O" 92F SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=C3C=C(C(=NC3=NC2=O)N)C#N)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 92F "SYSTEMATIC NAME" ACDLabs 12.01 "7-amino-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-2-oxo-2,3-dihydropyrido[2,3-d]pyrimidine-6-carbonitrile" 92F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-(7-azanyl-6-cyano-2-oxidanylidene-pyrido[2,3-d]pyrimidin-3-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 92F "Create component" 2017-12-01 PDBJ 92F "Modify linking type" 2017-12-01 PDBJ 92F "Modify leaving atom flag" 2017-12-04 PDBJ 92F "Initial release" 2018-11-21 RCSB 92F "Modify parent residue" 2022-06-13 RCSB #