data_CGY # _chem_comp.id CGY _chem_comp.name "(1R)-1,4-anhydro-2-deoxy-1-(2,6-diamino-5-nitropyridin-3-yl)-5-O-phosphono-D-erythro-pentitol" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-22 _chem_comp.pdbx_modified_date 2026-04-04 _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 350.222 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CGY _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 6B1S _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 CGY C1 C1 C 0 1 Y N N N N N -18.556 9.356 181.806 1.945 0.923 0.348 C1 CGY 1 CGY "C1'" C2 C 0 1 N N R N N N -17.466 9.146 180.800 0.650 1.693 0.377 "C1'" CGY 2 CGY C2 C3 C 0 1 Y N N N N N -19.102 8.355 182.592 3.118 1.504 0.815 C2 CGY 3 CGY "C2'" C4 C 0 1 N N N N N N -17.965 9.244 179.383 0.481 2.509 -0.924 "C2'" CGY 4 CGY "C3'" C5 C 0 1 N N S N N N -17.111 10.307 178.699 -1.032 2.423 -1.227 "C3'" CGY 5 CGY C4 C6 C 0 1 Y N N N N N -20.568 9.813 183.596 4.324 -0.410 0.340 C4 CGY 6 CGY "C4'" C7 C 0 1 N N R N N N -15.868 10.284 179.583 -1.598 1.564 -0.075 "C4'" CGY 7 CGY C5 C8 C 0 1 Y N N N N N -20.094 10.881 182.853 3.188 -1.049 -0.142 C5 CGY 8 CGY "C5'" C9 C 0 1 N N N N N N -15.014 11.522 179.484 -2.706 0.644 -0.591 "C5'" CGY 9 CGY C6 C10 C 0 1 Y N N N N N -19.070 10.645 181.939 1.978 -0.373 -0.138 C6 CGY 10 CGY N1 N1 N 0 1 N N N N N N -18.653 7.177 182.483 3.094 2.804 1.306 N1 CGY 11 CGY N3 N2 N 0 1 Y N N N N N -20.090 8.559 183.483 4.259 0.831 0.798 N3 CGY 12 CGY N4 N3 N 0 1 N N N N N N -21.497 10.027 184.430 5.542 -1.080 0.340 N4 CGY 13 CGY N5 N4 N 1 1 N N N N N N -20.578 12.020 183.011 3.269 -2.436 -0.653 N5 CGY 14 CGY "O3'" O1 O 0 1 N N N N N N -16.893 10.157 177.258 -1.620 3.725 -1.217 "O3'" CGY 15 CGY "O4'" O2 O 0 1 N N N N N N -16.404 10.093 180.919 -0.474 0.786 0.391 "O4'" CGY 16 CGY "O5'" O3 O 0 1 N N N N N N -15.843 12.708 179.496 -3.294 -0.055 0.508 "O5'" CGY 17 CGY ON1 O4 O 0 1 N N N N N N -20.034 13.052 182.419 4.001 -3.243 -0.108 ON1 CGY 18 CGY ON2 O5 O -1 1 N N N N N N -21.625 12.187 183.781 2.604 -2.769 -1.617 ON2 CGY 19 CGY OP1 O6 O 0 1 N N N N N N -14.169 14.389 178.825 -5.620 -0.467 -0.382 OP1 CGY 20 CGY OP2 O7 O 0 1 N N N N N N -16.352 15.173 179.879 -3.977 -2.378 -0.516 OP2 CGY 21 CGY P P1 P 0 1 N N N N N N -15.258 14.163 179.800 -4.496 -1.112 0.332 P CGY 22 CGY "H1'1" H1 H 0 0 N N N N N N -17.059 8.134 180.946 0.618 2.350 1.246 "H1'1" CGY 23 CGY "H2'1" H2 H 0 0 N N N N N N -19.024 9.542 179.372 0.780 3.546 -0.765 "H2'1" CGY 24 CGY "H2'2" H3 H 0 0 N N N N N N -17.851 8.277 178.872 1.061 2.065 -1.732 "H2'2" CGY 25 CGY "H3'1" H4 H 0 0 N N N N N N -17.607 11.275 178.865 -1.201 1.934 -2.187 "H3'1" CGY 26 CGY "H4'1" H5 H 0 0 N N N N N N -15.258 9.412 179.305 -1.975 2.203 0.724 "H4'1" CGY 27 CGY "H5'2" H6 H 0 0 N N N N N N -14.438 11.491 178.547 -3.469 1.240 -1.092 "H5'2" CGY 28 CGY "H5'1" H7 H 0 0 N N N N N N -14.322 11.555 180.339 -2.284 -0.074 -1.294 "H5'1" CGY 29 CGY H61 H8 H 0 1 N N N N N N -18.678 11.453 181.339 1.081 -0.848 -0.506 H61 CGY 30 CGY H12 H9 H 0 1 N N N N N N -19.141 6.574 183.115 2.261 3.302 1.321 H12 CGY 31 CGY H11 H10 H 0 1 N N N N N N -18.786 6.855 181.546 3.910 3.215 1.633 H11 CGY 32 CGY H41 H11 H 0 1 N N N N N N -21.733 9.173 184.893 5.621 -1.943 -0.096 H41 CGY 33 CGY H42 H12 H 0 1 N N N N N N -21.191 10.698 185.105 6.313 -0.685 0.775 H42 CGY 34 CGY "H3'2" H13 H 0 0 N N N N N N -16.351 10.871 176.943 -1.257 4.326 -1.883 "H3'2" CGY 35 CGY H1 H16 H 0 1 N N N N N N -16.188 15.867 179.252 -3.240 -2.851 -0.106 H1 CGY 36 CGY OP3 O8 O 0 1 N Y N N N N -14.729 14.047 181.294 -4.994 -1.605 1.782 OP3 CGY 37 CGY "HO3'" H17 H 0 0 N Y N N N N -13.784 14.145 181.304 -5.718 -2.244 1.753 "HO3'" CGY 38 # 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 CGY "O3'" "C3'" SING N N 1 CGY "C3'" "C2'" SING N N 2 CGY "C3'" "C4'" SING N N 3 CGY OP1 P DOUB N N 4 CGY "C2'" "C1'" SING N N 5 CGY "C5'" "O5'" SING N N 6 CGY "C5'" "C4'" SING N N 7 CGY "O5'" P SING N N 8 CGY "C4'" "O4'" SING N N 9 CGY P OP2 SING N N 10 CGY "C1'" "O4'" SING N N 11 CGY "C1'" C1 SING N N 12 CGY C1 C6 DOUB Y N 13 CGY C1 C2 SING Y N 14 CGY C6 C5 SING Y N 15 CGY ON1 N5 DOUB N N 16 CGY N1 C2 SING N N 17 CGY C2 N3 DOUB Y N 18 CGY C5 N5 SING N N 19 CGY C5 C4 DOUB Y N 20 CGY N5 ON2 SING N N 21 CGY N3 C4 SING Y N 22 CGY C4 N4 SING N N 23 CGY "C1'" "H1'1" SING N N 24 CGY "C2'" "H2'1" SING N N 25 CGY "C2'" "H2'2" SING N N 26 CGY "C3'" "H3'1" SING N N 27 CGY "C4'" "H4'1" SING N N 28 CGY "C5'" "H5'2" SING N N 29 CGY "C5'" "H5'1" SING N N 30 CGY C6 H61 SING N N 31 CGY N1 H12 SING N N 32 CGY N1 H11 SING N N 33 CGY N4 H41 SING N N 34 CGY N4 H42 SING N N 35 CGY "O3'" "H3'2" SING N N 36 CGY OP2 H1 SING N N 37 CGY P OP3 SING N N 38 CGY OP3 "HO3'" SING N N 39 # 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 CGY SMILES ACDLabs 14.52 "OP(=O)(O)OCC1OC(CC1O)c1cc([N+]([O-])=O)c(N)nc1N" CGY InChI InChI 1.06 "InChI=1S/C10H15N4O8P/c11-9-4(1-5(14(16)17)10(12)13-9)7-2-6(15)8(22-7)3-21-23(18,19)20/h1,6-8,15H,2-3H2,(H4,11,12,13)(H2,18,19,20)/t6-,7+,8+/m0/s1" CGY InChIKey InChI 1.06 XDFYIZOVZDNRDI-XLPZGREQSA-N CGY SMILES_CANONICAL CACTVS 3.385 "Nc1nc(N)c(cc1[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)[N+]([O-])=O" CGY SMILES CACTVS 3.385 "Nc1nc(N)c(cc1[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)[N+]([O-])=O" CGY SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1c(c(nc(c1[N+](=O)[O-])N)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" CGY SMILES "OpenEye OEToolkits" 3.1.0.0 "c1c(c(nc(c1[N+](=O)[O-])N)N)C2CC(C(O2)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 CGY "SYSTEMATIC NAME" ACDLabs 14.52 "(1R)-1,4-anhydro-2-deoxy-1-(2,6-diamino-5-nitropyridin-3-yl)-5-O-phosphono-D-erythro-pentitol" CGY "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{S},5~{R})-5-[2,6-bis(azanyl)-5-nitro-pyridin-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 CGY "Create component" 2017-09-22 RCSB CGY "Initial release" 2018-09-19 RCSB CGY "Other modification" 2026-04-04 RCSB #