data_5FC # _chem_comp.id 5FC _chem_comp.name "5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "2'-DEOXY-5-FORMYLCYTIDINE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-04-06 _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 335.207 _chem_comp.one_letter_code C _chem_comp.three_letter_code 5FC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1VE8 _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 5FC P P P 0 1 N N N -7.079 2.228 3.659 -3.968 -1.665 3.118 P 5FC 1 5FC OP2 O2P O 0 1 N N N -7.965 3.403 3.848 -3.912 -2.311 1.636 OP2 5FC 2 5FC OP1 O1P O 0 1 N N N -7.590 1.027 2.948 -4.406 -2.599 4.208 OP1 5FC 3 5FC "O5'" O5* O 0 1 N N N -5.764 2.718 2.915 -2.493 -1.028 3.315 "O5'" 5FC 4 5FC N1 N1 N 0 1 N N N -2.139 1.245 1.123 1.164 -2.047 0.989 N1 5FC 5 5FC C6 C6 C 0 1 N N N -3.061 0.288 1.392 0.010 -2.813 0.936 C6 5FC 6 5FC C2 C2 C 0 1 N N N -0.845 0.875 0.808 2.348 -2.526 0.380 C2 5FC 7 5FC O2 O2 O 0 1 N N N -0.031 1.755 0.506 3.389 -1.869 0.412 O2 5FC 8 5FC N3 N3 N 0 1 N N N -0.500 -0.440 0.834 2.319 -3.754 -0.256 N3 5FC 9 5FC C4 C4 C 0 1 N N N -1.385 -1.409 1.156 1.226 -4.473 -0.303 C4 5FC 10 5FC N4 N4 N 0 1 N N N -0.899 -2.643 1.336 1.261 -5.687 -0.952 N4 5FC 11 5FC C5 C5 C 0 1 N N N -2.743 -1.001 1.424 -0.040 -4.000 0.328 C5 5FC 12 5FC "C2'" C2* C 0 1 N N N -3.620 3.154 0.326 0.710 0.360 0.754 "C2'" 5FC 13 5FC "C5'" C5* C 0 1 N N N -4.953 3.738 3.487 -2.005 -0.136 2.327 "C5'" 5FC 14 5FC "C4'" C4* C 0 1 N N R -3.801 4.049 2.564 -0.611 0.328 2.728 "C4'" 5FC 15 5FC "O4'" O4* O 0 1 N N N -2.891 2.930 2.531 0.247 -0.829 2.764 "O4'" 5FC 16 5FC "C1'" C1* C 0 1 N N R -2.474 2.679 1.203 1.157 -0.778 1.657 "C1'" 5FC 17 5FC "C3'" C3* C 0 1 N N S -4.220 4.309 1.121 0.008 1.286 1.720 "C3'" 5FC 18 5FC "O3'" O3* O 0 1 N N N -3.698 5.574 0.727 0.965 2.121 2.368 "O3'" 5FC 19 5FC C5A C5A C 0 1 N N N -3.780 -2.066 1.593 -1.315 -4.719 0.336 C5A 5FC 20 5FC O5A O5A O 0 1 N N N -3.473 -3.256 1.626 -1.460 -5.814 -0.196 O5A 5FC 21 5FC OP3 O3P O 0 1 N Y N ? ? ? -4.901 -0.360 2.920 OP3 5FC 22 5FC HOP2 2HOP H 0 0 N N N -7.638 4.170 4.302 -4.684 -2.823 1.313 HOP2 5FC 23 5FC H6 H6 H 0 1 N N N -4.108 0.568 1.592 -0.855 -2.377 1.426 H6 5FC 24 5FC HN41 1HN4 H 0 0 N N N -1.567 -3.374 1.579 1.671 -5.721 -1.853 HN41 5FC 25 5FC HN42 2HN4 H 0 0 N N N -0.155 -2.616 2.033 0.874 -6.473 -0.489 HN42 5FC 26 5FC "H2'" 1H2* H 0 1 N N N -3.326 3.414 -0.717 -0.003 -0.001 0.003 "H2'" 5FC 27 5FC "H2''" 2H2* H 0 0 N N N -4.348 2.357 0.046 1.556 0.818 0.232 "H2''" 5FC 28 5FC "H5'" 1H5* H 0 1 N N N -5.542 4.648 3.744 -1.971 -0.654 1.366 "H5'" 5FC 29 5FC "H5''" 2H5* H 0 0 N N N -4.608 3.474 4.514 -2.683 0.718 2.254 "H5''" 5FC 30 5FC "H4'" H4* H 0 1 N N N -3.335 4.976 2.972 -0.644 0.753 3.736 "H4'" 5FC 31 5FC "H1'" H1* H 0 1 N N N -1.558 3.215 0.860 2.163 -0.604 2.054 "H1'" 5FC 32 5FC "H3'" H3* H 0 1 N N N -5.322 4.351 0.962 -0.722 1.941 1.236 "H3'" 5FC 33 5FC "HO3'" H3T H 0 0 N Y N -4.071 6.293 1.222 0.754 3.041 2.131 "HO3'" 5FC 34 5FC H5A H5A H 0 1 N N N -4.872 -1.964 1.703 -2.141 -4.204 0.856 H5A 5FC 35 5FC HOP3 3HOP H 0 0 N N N 0.567 -0.752 -0.121 -5.874 -0.475 2.871 HOP3 5FC 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 5FC P OP2 SING N N 1 5FC P OP1 DOUB N N 2 5FC P "O5'" SING N N 3 5FC P OP3 SING N N 4 5FC OP2 HOP2 SING N N 5 5FC "O5'" "C5'" SING N N 6 5FC N1 C6 SING N N 7 5FC N1 C2 SING N N 8 5FC N1 "C1'" SING N N 9 5FC C6 C5 DOUB N N 10 5FC C6 H6 SING N N 11 5FC C2 O2 DOUB N N 12 5FC C2 N3 SING N N 13 5FC N3 C4 DOUB N N 14 5FC C4 N4 SING N N 15 5FC C4 C5 SING N N 16 5FC N4 HN41 SING N N 17 5FC N4 HN42 SING N N 18 5FC C5 C5A SING N N 19 5FC "C2'" "C1'" SING N N 20 5FC "C2'" "C3'" SING N N 21 5FC "C2'" "H2'" SING N N 22 5FC "C2'" "H2''" SING N N 23 5FC "C5'" "C4'" SING N N 24 5FC "C5'" "H5'" SING N N 25 5FC "C5'" "H5''" SING N N 26 5FC "C4'" "O4'" SING N N 27 5FC "C4'" "C3'" SING N N 28 5FC "C4'" "H4'" SING N N 29 5FC "O4'" "C1'" SING N N 30 5FC "C1'" "H1'" SING N N 31 5FC "C3'" "O3'" SING N N 32 5FC "C3'" "H3'" SING N N 33 5FC "O3'" "HO3'" SING N N 34 5FC C5A O5A DOUB N N 35 5FC C5A H5A SING N N 36 5FC OP3 HOP3 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 5FC SMILES ACDLabs 10.04 "O=CC=1C(=NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O)N" 5FC SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1C=O)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" 5FC SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1C=O)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" 5FC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)C=O)COP(=O)(O)O)O" 5FC SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=NC2=O)N)C=O)COP(=O)(O)O)O" 5FC InChI InChI 1.03 "InChI=1S/C10H14N3O8P/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(21-8)4-20-22(17,18)19/h2-3,6-8,15H,1,4H2,(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1" 5FC InChIKey InChI 1.03 HDFNXAHZEYLDBJ-XLPZGREQSA-N # # 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 5FC "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5-formylcytidine 5'-(dihydrogen phosphate)" 5FC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-5-methanoyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 5FC "Create component" 2004-04-06 RCSB 5FC "Modify descriptor" 2011-06-04 RCSB 5FC "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 5FC _pdbx_chem_comp_synonyms.name "2'-DEOXY-5-FORMYLCYTIDINE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##