data_A1MA9 # _chem_comp.id A1MA9 _chem_comp.name ;8-CF3-2'F-riboguanosine monophosphate ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H12 F4 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms "[(2~{R},3~{R},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-8-(trifluoromethyl)-1~{H}-purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-07-25 _chem_comp.pdbx_modified_date 2026-02-13 _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 433.210 _chem_comp.one_letter_code G _chem_comp.three_letter_code A1MA9 _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 9VZW _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1MA9 P P1 P 0 1 N N N N N N -0.112 5.497 -4.119 4.977 0.505 1.072 P A1MA9 1 A1MA9 OP2 O1 O 0 1 N N N N N N 0.645 4.572 -5.094 4.894 1.898 0.270 OP2 A1MA9 2 A1MA9 "O5'" O2 O 0 1 N N N N N N 0.956 6.283 -3.312 3.576 -0.276 0.938 "O5'" A1MA9 3 A1MA9 "C2'" C1 C 0 1 N N R N N N 0.809 6.244 1.446 -0.337 -1.805 -1.322 "C2'" A1MA9 4 A1MA9 "C5'" C2 C 0 1 N N N N N N 1.552 5.645 -2.180 3.076 -0.770 -0.306 "C5'" A1MA9 5 A1MA9 "C4'" C3 C 0 1 N N R N N N 1.131 6.398 -0.922 1.728 -1.457 -0.077 "C4'" A1MA9 6 A1MA9 "O4'" O3 O 0 1 N N N N N N -0.236 6.212 -0.657 0.732 -0.488 0.332 "O4'" A1MA9 7 A1MA9 "C1'" C4 C 0 1 N N R N N N -0.477 6.551 0.690 -0.541 -1.105 0.040 "C1'" A1MA9 8 A1MA9 "C3'" C5 C 0 1 N N R N N N 1.812 5.960 0.362 1.188 -2.041 -1.402 "C3'" A1MA9 9 A1MA9 "O3'" O4 O 0 1 N N N N N N 2.985 6.736 0.540 1.476 -3.438 -1.487 "O3'" A1MA9 10 A1MA9 OP1 O5 O 0 1 N N N N N N -0.928 6.578 -4.867 6.062 -0.327 0.505 OP1 A1MA9 11 A1MA9 N9 N1 N 0 1 Y N N N N N -1.670 5.800 1.144 -1.589 -0.087 -0.062 N9 A1MA9 12 A1MA9 C4 C6 C 0 1 Y N N N N N -1.733 4.416 1.160 -2.846 -0.163 0.474 C4 A1MA9 13 A1MA9 N3 N2 N 0 1 N N N N N N -0.824 3.465 0.874 -3.498 -1.080 1.197 N3 A1MA9 14 A1MA9 C2 C7 C 0 1 N N N N N N -1.105 2.145 0.996 -4.737 -0.883 1.588 C2 A1MA9 15 A1MA9 N2 N3 N 0 1 N N N N N N -0.161 1.245 0.745 -5.365 -1.853 2.329 N2 A1MA9 16 A1MA9 N1 N4 N 0 1 N N N N N N -2.366 1.783 1.378 -5.417 0.257 1.279 N1 A1MA9 17 A1MA9 C6 C8 C 0 1 N N N N N N -3.377 2.655 1.659 -4.824 1.229 0.550 C6 A1MA9 18 A1MA9 O6 O6 O 0 1 N N N N N N -4.489 2.233 1.976 -5.424 2.252 0.268 O6 A1MA9 19 A1MA9 C5 C9 C 0 1 Y N N N N N -3.041 4.046 1.566 -3.490 1.030 0.124 C5 A1MA9 20 A1MA9 N7 N5 N 0 1 Y N N N N N -3.764 5.200 1.809 -2.610 1.765 -0.598 N7 A1MA9 21 A1MA9 C8 C10 C 0 1 Y N N N N N -2.889 6.204 1.584 -1.489 1.113 -0.705 C8 A1MA9 22 A1MA9 C C11 C 0 1 N N N N N N -3.264 7.652 1.798 -0.265 1.608 -1.431 C A1MA9 23 A1MA9 "F2'" F1 F 0 1 N N N N N N 1.195 7.338 2.217 -1.023 -3.023 -1.355 "F2'" A1MA9 24 A1MA9 F11 F2 F 0 1 N N N N N N -3.539 8.163 0.609 -0.141 0.933 -2.650 F11 A1MA9 25 A1MA9 F12 F3 F 0 1 N N N N N N -2.240 8.268 2.359 -0.387 2.981 -1.669 F12 A1MA9 26 A1MA9 F13 F4 F 0 1 N N N N N N -4.321 7.712 2.590 0.870 1.369 -0.648 F13 A1MA9 27 A1MA9 HOP2 H1 H 0 0 N N N N N N 0.468 4.841 -5.988 4.203 2.495 0.589 HOP2 A1MA9 28 A1MA9 "H2'" H2 H 0 1 N N N N N N 0.666 5.346 2.065 -0.667 -1.160 -2.136 "H2'" A1MA9 29 A1MA9 "H5'" H3 H 0 1 N N N N N N 1.210 4.601 -2.120 2.948 0.059 -1.001 "H5'" A1MA9 30 A1MA9 "H5''" H4 H 0 0 N N N N N N 2.648 5.667 -2.276 3.783 -1.487 -0.722 "H5''" A1MA9 31 A1MA9 "H4'" H5 H 0 1 N N N N N N 1.339 7.467 -1.076 1.825 -2.241 0.673 "H4'" A1MA9 32 A1MA9 "H1'" H6 H 0 1 N N N N N N -0.680 7.629 0.775 -0.794 -1.836 0.808 "H1'" A1MA9 33 A1MA9 "H3'" H7 H 0 1 N N N N N N 2.039 4.884 0.323 1.614 -1.511 -2.254 "H3'" A1MA9 34 A1MA9 H3 H8 H 0 1 N N N N N N 3.422 6.472 1.341 1.159 -3.856 -2.299 H3 A1MA9 35 A1MA9 H21 H10 H 0 1 N N N N N N 0.752 1.543 0.467 -4.894 -2.670 2.557 H21 A1MA9 36 A1MA9 H22 H11 H 0 1 N N N N N N -0.364 0.270 0.834 -6.280 -1.721 2.624 H22 A1MA9 37 A1MA9 H1 H12 H 0 1 N N N N N N -2.563 0.806 1.458 -6.331 0.372 1.583 H1 A1MA9 38 A1MA9 OP3 OP3 O 0 1 N Y N N N N -1.018 4.633 -3.188 5.282 0.798 2.626 OP3 A1MA9 39 A1MA9 HOP3 HOP3 H 0 0 N Y N N N N -1.917 4.934 -3.252 6.113 1.267 2.782 HOP3 A1MA9 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 A1MA9 OP2 P SING N N 1 A1MA9 OP1 P DOUB N N 2 A1MA9 P "O5'" SING N N 3 A1MA9 "O5'" "C5'" SING N N 4 A1MA9 "C5'" "C4'" SING N N 5 A1MA9 "C4'" "O4'" SING N N 6 A1MA9 "C4'" "C3'" SING N N 7 A1MA9 "O4'" "C1'" SING N N 8 A1MA9 "C3'" "O3'" SING N N 9 A1MA9 "C3'" "C2'" SING N N 10 A1MA9 F11 C SING N N 11 A1MA9 "C1'" N9 SING N N 12 A1MA9 "C1'" "C2'" SING N N 13 A1MA9 N2 C2 SING N N 14 A1MA9 N3 C2 DOUB N N 15 A1MA9 N3 C4 SING N N 16 A1MA9 C2 N1 SING N N 17 A1MA9 N9 C4 SING Y N 18 A1MA9 N9 C8 SING Y N 19 A1MA9 C4 C5 DOUB Y N 20 A1MA9 N1 C6 SING N N 21 A1MA9 "C2'" "F2'" SING N N 22 A1MA9 C5 C6 SING N N 23 A1MA9 C5 N7 SING Y N 24 A1MA9 C8 C SING N N 25 A1MA9 C8 N7 DOUB Y N 26 A1MA9 C6 O6 DOUB N N 27 A1MA9 C F12 SING N N 28 A1MA9 C F13 SING N N 29 A1MA9 OP2 HOP2 SING N N 30 A1MA9 "C2'" "H2'" SING N N 31 A1MA9 "C5'" "H5'" SING N N 32 A1MA9 "C5'" "H5''" SING N N 33 A1MA9 "C4'" "H4'" SING N N 34 A1MA9 "C1'" "H1'" SING N N 35 A1MA9 "C3'" "H3'" SING N N 36 A1MA9 "O3'" H3 SING N N 37 A1MA9 N2 H21 SING N N 38 A1MA9 N2 H22 SING N N 39 A1MA9 N1 H1 SING N N 40 A1MA9 P OP3 SING N N 41 A1MA9 OP3 HOP3 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 A1MA9 InChI InChI 1.06 "InChI=1S/C11H12F4N5O7P/c12-3-5(21)2(1-26-28(23,24)25)27-8(3)20-6-4(7(22)19-10(16)18-6)17-9(20)11(13,14)15/h2-3,5,8,21H,1H2,(H2,23,24,25)(H3,16,18,19,22)/t2-,3-,5-,8-/m1/s1" A1MA9 InChIKey InChI 1.06 UZSABTRADQLKAX-YOUMAJLPSA-N A1MA9 SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3F)c(nc2C(=O)N1)C(F)(F)F" A1MA9 SMILES CACTVS 3.385 "NC1=Nc2n([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3F)c(nc2C(=O)N1)C(F)(F)F" A1MA9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]1[C@H]([C@H]([C@@H](O1)n2c3c(nc2C(F)(F)F)C(=O)NC(=N3)N)F)O)OP(=O)(O)O" A1MA9 SMILES "OpenEye OEToolkits" 2.0.7 "C(C1C(C(C(O1)n2c3c(nc2C(F)(F)F)C(=O)NC(=N3)N)F)O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id A1MA9 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-8-(trifluoromethyl)-1~{H}-purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1MA9 _pdbx_chem_comp_synonyms.name "[(2~{R},3~{R},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-8-(trifluoromethyl)-1~{H}-purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1MA9 "Create component" 2025-07-25 PDBJ A1MA9 "Initial release" 2025-08-06 RCSB A1MA9 "Modify atom id" 2026-02-13 PDBJ #