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 
# 
