data_CGY # _chem_comp.id CGY _chem_comp.name "(1R)-1,4-anhydro-2-deoxy-1-[2,6-diamino-5-(dihydroxyamino)pyridin-3-yl]-5-O-phosphono-D-erythro-pentitol" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 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 2018-09-14 _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 352.238 _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 # 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 CGY C1 C1 C 0 1 Y N N -18.556 9.356 181.806 1.993 0.880 0.390 C1 CGY 1 CGY "C1'" C2 C 0 1 N N R -17.466 9.146 180.800 0.717 1.681 0.380 "C1'" CGY 2 CGY C2 C3 C 0 1 Y N N -19.102 8.355 182.592 3.172 1.443 0.860 C2 CGY 3 CGY "C2'" C4 C 0 1 N N N -17.965 9.244 179.383 0.586 2.470 -0.941 "C2'" CGY 4 CGY "C3'" C5 C 0 1 N N S -17.111 10.307 178.699 -0.923 2.413 -1.266 "C3'" CGY 5 CGY C4 C6 C 0 1 Y N N -20.568 9.813 183.596 4.345 -0.507 0.451 C4 CGY 6 CGY "C4'" C7 C 0 1 N N R -15.868 10.284 179.583 -1.526 1.596 -0.102 "C4'" CGY 7 CGY C5 C8 C 0 1 Y N N -20.094 10.881 182.853 3.198 -1.135 -0.035 C5 CGY 8 CGY "C5'" C9 C 0 1 N N N -15.014 11.522 179.484 -2.649 0.691 -0.612 "C5'" CGY 9 CGY C6 C10 C 0 1 Y N N -19.070 10.645 181.939 2.001 -0.430 -0.066 C6 CGY 10 CGY N1 N1 N 0 1 N N N -18.653 7.177 182.483 3.170 2.758 1.319 N1 CGY 11 CGY N3 N2 N 0 1 Y N N -20.090 8.559 183.483 4.298 0.745 0.877 N3 CGY 12 CGY N4 N3 N 0 1 N N N -21.497 10.027 184.430 5.550 -1.204 0.487 N4 CGY 13 CGY N5 N4 N 0 1 N N N -20.578 12.020 183.011 3.252 -2.463 -0.487 N5 CGY 14 CGY "O3'" O1 O 0 1 N N N -16.893 10.157 177.258 -1.479 3.729 -1.295 "O3'" CGY 15 CGY "O4'" O2 O 0 1 N N N -16.404 10.093 180.919 -0.429 0.802 0.400 "O4'" CGY 16 CGY "O5'" O3 O 0 1 N N N -15.843 12.708 179.496 -3.270 0.032 0.494 "O5'" CGY 17 CGY ON1 O4 O 0 1 N N N -20.034 13.052 182.419 2.058 -3.204 -0.081 ON1 CGY 18 CGY ON2 O5 O 0 1 N N N -21.625 12.187 183.781 3.434 -2.516 -1.938 ON2 CGY 19 CGY OP1 O6 O 0 1 N N N -14.169 14.389 178.825 -5.592 -0.345 -0.421 OP1 CGY 20 CGY OP2 O7 O 0 1 N N N -16.352 15.173 179.879 -3.995 -2.298 -0.485 OP2 CGY 21 CGY P P1 P 0 1 N N N -15.258 14.163 179.800 -4.495 -1.000 0.325 P CGY 22 CGY "H1'1" H1 H 0 0 N N N -17.059 8.134 180.946 0.689 2.359 1.234 "H1'1" CGY 23 CGY "H2'1" H2 H 0 0 N N N -19.024 9.542 179.372 0.909 3.502 -0.803 "H2'1" CGY 24 CGY "H2'2" H3 H 0 0 N N N -17.851 8.277 178.872 1.167 1.992 -1.730 "H2'2" CGY 25 CGY "H3'1" H4 H 0 0 N N N -17.607 11.275 178.865 -1.091 1.905 -2.216 "H3'1" CGY 26 CGY "H4'1" H5 H 0 0 N N N -15.258 9.412 179.305 -1.899 2.262 0.677 "H4'1" CGY 27 CGY "H5'2" H6 H 0 0 N N N -14.438 11.491 178.547 -3.390 1.292 -1.139 "H5'2" CGY 28 CGY "H5'1" H7 H 0 0 N N N -14.322 11.555 180.339 -2.235 -0.054 -1.292 "H5'1" CGY 29 CGY H61 H8 H 0 1 N N N -18.678 11.453 181.339 1.098 -0.891 -0.437 H61 CGY 30 CGY H12 H9 H 0 1 N N N -19.141 6.574 183.115 2.349 3.275 1.309 H12 CGY 31 CGY H11 H10 H 0 1 N N N -18.786 6.855 181.546 3.990 3.158 1.649 H11 CGY 32 CGY H41 H11 H 0 1 N N N -21.733 9.173 184.893 5.574 -2.144 0.251 H41 CGY 33 CGY H42 H12 H 0 1 N N N -21.191 10.698 185.105 6.366 -0.749 0.749 H42 CGY 34 CGY "H3'2" H13 H 0 0 N N N -16.351 10.871 176.943 -1.093 4.304 -1.969 "H3'2" CGY 35 CGY HN11 H14 H 0 0 N N N -20.520 13.838 182.642 2.050 -4.127 -0.371 HN11 CGY 36 CGY HN21 H15 H 0 0 N N N -21.897 11.347 184.133 3.477 -3.413 -2.297 HN21 CGY 37 CGY H1 H16 H 0 1 N N N -16.188 15.867 179.252 -3.275 -2.778 -0.054 H1 CGY 38 CGY OP3 O8 O 0 1 N Y N -14.729 14.047 181.294 -5.025 -1.445 1.778 O1 CGY 39 CGY "HO3'" H17 H 0 0 N Y N -13.784 14.145 181.304 -5.765 -2.068 1.753 H2 CGY 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 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 SING 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 ON1 HN11 SING N N 37 CGY ON2 HN21 SING N N 38 CGY OP2 H1 SING N N 39 CGY P OP3 SING N N 40 CGY OP3 "HO3'" SING N N 41 # 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 12.01 "c1(cc(c(N)nc1N)N(O)O)C2OC(C(C2)O)COP(=O)(O)O" CGY InChI InChI 1.03 "InChI=1S/C10H17N4O8P/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/h1,6-8,15-17H,2-3H2,(H4,11,12,13)(H2,18,19,20)/t6-,7+,8+/m0/s1" CGY InChIKey InChI 1.03 VFFYYNDFZAMVIU-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" 2.0.6 "c1c(c(nc(c1N(O)O)N)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" CGY SMILES "OpenEye OEToolkits" 2.0.6 "c1c(c(nc(c1N(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 12.01 "(1R)-1,4-anhydro-2-deoxy-1-[2,6-diamino-5-(dihydroxyamino)pyridin-3-yl]-5-O-phosphono-D-erythro-pentitol" CGY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2,6-bis(azanyl)-5-[bis(oxidanyl)amino]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 #