data_OBX # _chem_comp.id OBX _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-2-(4-carbamimidamidobutylamino)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H27 N7 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms agmatidine _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2023-01-30 _chem_comp.pdbx_modified_date 2024-03-29 _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 436.381 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OBX _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 8HTZ _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 OBX P P1 P 0 1 N N N N N N 171.752 189.166 265.812 -6.342 1.249 0.919 P OBX 1 OBX N1 N1 N 1 1 Y N N N N N 175.982 186.558 266.503 -0.377 -1.668 -0.170 N1 OBX 2 OBX C2 C1 C 0 1 Y N N N N N 177.197 186.303 266.020 0.911 -1.936 -0.012 C2 OBX 3 OBX N2 N2 N 0 1 N N N N N N 178.340 186.096 266.893 1.817 -0.891 0.027 N2 OBX 4 OBX N3 N3 N 0 1 Y N N N N N 177.417 186.240 264.720 1.353 -3.178 0.109 N3 OBX 5 OBX C4 C2 C 0 1 Y N N N N N 176.447 186.412 263.849 0.507 -4.204 0.076 C4 OBX 6 OBX N4 N4 N 0 1 N N N N N N 176.729 186.336 262.430 0.973 -5.503 0.198 N4 OBX 7 OBX C5 C3 C 0 1 Y N N N N N 175.173 186.675 264.315 -0.856 -3.953 -0.090 C5 OBX 8 OBX C6 C4 C 0 1 Y N N N N N 174.960 186.744 265.682 -1.275 -2.642 -0.208 C6 OBX 9 OBX CA C5 C 0 1 N N N N N N 179.549 185.454 266.397 3.246 -1.166 0.201 CA OBX 10 OBX CB C6 C 0 1 N N N N N N 179.312 183.962 266.156 4.022 0.153 0.211 CB OBX 11 OBX CD C7 C 0 1 N N N N N N 179.081 181.729 267.399 6.289 1.184 0.401 CD OBX 12 OBX NE N5 N 0 1 N N N N N N 178.466 181.376 266.134 7.718 0.909 0.576 NE OBX 13 OBX CG C8 C 0 1 N N N N N N 179.736 183.110 267.349 5.513 -0.135 0.392 CG OBX 14 OBX CZ C9 C 0 1 N N N N N N 177.024 181.232 266.043 8.618 1.947 0.615 CZ OBX 15 OBX "C1'" C10 C 0 1 N N R N N N 175.730 186.613 267.967 -0.815 -0.276 -0.300 "C1'" OBX 16 OBX OP2 O1 O 0 1 N N N N N N 171.212 187.837 265.360 -6.993 -0.160 0.491 OP2 OBX 17 OBX "C2'" C11 C 0 1 N N R N N N 176.298 187.858 268.639 -0.773 0.165 -1.779 "C2'" OBX 18 OBX "O2'" O2 O 0 1 N N N N N N 176.604 187.529 269.985 0.425 0.897 -2.050 "O2'" OBX 19 OBX OP3 O3 O 0 1 N Y N N N N 170.801 190.179 266.387 -6.625 1.518 2.481 OP3 OBX 20 OBX "C3'" C12 C 0 1 N N S N N N 175.105 188.800 268.582 -2.011 1.077 -1.934 "C3'" OBX 21 OBX "O3'" O4 O 0 1 N N N N N N 175.157 189.847 269.538 -1.615 2.399 -2.305 "O3'" OBX 22 OBX "C4'" C13 C 0 1 N N R N N N 173.919 187.865 268.787 -2.654 1.078 -0.530 "C4'" OBX 23 OBX "O4'" O5 O 0 1 N N N N N N 174.339 186.607 268.192 -2.201 -0.148 0.085 "O4'" OBX 24 OBX "C5'" C14 C 0 1 N N N N N N 172.637 188.311 268.139 -4.180 1.088 -0.643 "C5'" OBX 25 OBX "O5'" O6 O 0 1 N N N N N N 172.903 188.902 266.878 -4.753 1.207 0.660 "O5'" OBX 26 OBX NH1 N6 N 0 1 N N N N N N 176.204 181.442 267.220 8.178 3.244 0.491 NH1 OBX 27 OBX NH2 N7 N 0 1 N N N N N N 176.490 180.927 264.951 9.889 1.702 0.770 NH2 OBX 28 OBX H1 H1 H 0 1 N N N N N N 178.296 186.398 267.845 1.507 0.024 -0.060 H1 OBX 29 OBX H2 H2 H 0 1 N N N N N N 177.701 186.148 262.293 0.350 -6.246 0.170 H2 OBX 30 OBX H3 H3 H 0 1 N N N N N N 176.187 185.602 262.021 1.922 -5.669 0.313 H3 OBX 31 OBX H4 H4 H 0 1 N N N N N N 174.356 186.824 263.624 -1.567 -4.765 -0.121 H4 OBX 32 OBX H5 H5 H 0 1 N N N N N N 173.974 186.947 266.073 -2.323 -2.413 -0.336 H5 OBX 33 OBX H6 H6 H 0 1 N N N N N N 180.352 185.576 267.138 3.403 -1.687 1.146 H6 OBX 34 OBX H7 H7 H 0 1 N N N N N N 179.847 185.929 265.451 3.598 -1.789 -0.621 H7 OBX 35 OBX H8 H8 H 0 1 N N N N N N 178.240 183.800 265.968 3.864 0.674 -0.734 H8 OBX 36 OBX H9 H9 H 0 1 N N N N N N 179.891 183.649 265.274 3.669 0.776 1.032 H9 OBX 37 OBX H10 H10 H 0 1 N N N N N N 178.308 181.730 268.182 5.937 1.807 1.223 H10 OBX 38 OBX H11 H11 H 0 1 N N N N N N 179.849 180.980 267.642 6.132 1.705 -0.543 H11 OBX 39 OBX H12 H12 H 0 1 N N N N N N 179.035 181.232 265.324 8.028 -0.006 0.663 H12 OBX 40 OBX H13 H13 H 0 1 N N N N N N 180.827 182.973 267.305 5.671 -0.655 1.337 H13 OBX 41 OBX H14 H14 H 0 1 N N N N N N 179.472 183.650 268.270 5.866 -0.758 -0.430 H14 OBX 42 OBX H15 H15 H 0 1 N N N N N N 176.187 185.730 268.437 -0.190 0.375 0.311 H15 OBX 43 OBX H16 H16 H 0 1 N N N N N N 171.454 187.688 264.453 -6.645 -0.919 0.979 H16 OBX 44 OBX H17 H17 H 0 1 N N N N N N 177.158 188.260 268.084 -0.848 -0.700 -2.438 H17 OBX 45 OBX H18 H18 H 0 1 N N N N N N 176.960 188.292 270.425 0.503 1.199 -2.965 H18 OBX 46 OBX H19 H19 H 0 1 N Y N N N N 170.862 190.988 265.892 -7.563 1.556 2.710 H19 OBX 47 OBX H20 H20 H 0 1 N N N N N N 175.043 189.223 267.568 -2.700 0.663 -2.670 H20 OBX 48 OBX H21 H21 H 0 1 N N N N N N 174.387 190.396 269.449 -1.152 2.448 -3.152 H21 OBX 49 OBX H22 H22 H 0 1 N N N N N N 173.752 187.732 269.866 -2.311 1.939 0.044 H22 OBX 50 OBX H23 H23 H 0 1 N N N N N N 172.140 189.047 268.787 -4.493 1.933 -1.256 H23 OBX 51 OBX H24 H24 H 0 1 N N N N N N 171.979 187.441 268.000 -4.516 0.160 -1.105 H24 OBX 52 OBX H25 H25 H 0 1 N N N N N N 176.632 181.685 268.091 7.232 3.426 0.376 H25 OBX 53 OBX H26 H26 H 0 1 N N N N N N 175.211 181.344 267.161 8.813 3.976 0.518 H26 OBX 54 OBX H27 H27 H 0 1 N N N N N N 175.495 180.860 265.026 10.524 2.435 0.797 H27 OBX 55 OBX OP1 OP1 O 0 1 N N N N N N 172.534 189.814 264.564 -6.944 2.335 0.114 OP1 OBX 56 # 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 OBX N4 C4 SING N N 1 OBX C4 C5 DOUB Y N 2 OBX C4 N3 SING Y N 3 OBX C5 C6 SING Y N 4 OBX N3 C2 DOUB Y N 5 OBX NH2 CZ DOUB N N 6 OBX OP2 P SING N N 7 OBX C6 N1 DOUB Y N 8 OBX P OP3 SING N N 9 OBX P "O5'" SING N N 10 OBX C2 N1 SING Y N 11 OBX C2 N2 SING N N 12 OBX CZ NE SING N N 13 OBX CZ NH1 SING N N 14 OBX NE CD SING N N 15 OBX CB CA SING N N 16 OBX CB CG SING N N 17 OBX CA N2 SING N N 18 OBX N1 "C1'" SING N N 19 OBX "O5'" "C5'" SING N N 20 OBX CG CD SING N N 21 OBX "C1'" "O4'" SING N N 22 OBX "C1'" "C2'" SING N N 23 OBX "C5'" "C4'" SING N N 24 OBX "O4'" "C4'" SING N N 25 OBX "C3'" "C2'" SING N N 26 OBX "C3'" "C4'" SING N N 27 OBX "C3'" "O3'" SING N N 28 OBX "C2'" "O2'" SING N N 29 OBX N2 H1 SING N N 30 OBX N4 H2 SING N N 31 OBX N4 H3 SING N N 32 OBX C5 H4 SING N N 33 OBX C6 H5 SING N N 34 OBX CA H6 SING N N 35 OBX CA H7 SING N N 36 OBX CB H8 SING N N 37 OBX CB H9 SING N N 38 OBX CD H10 SING N N 39 OBX CD H11 SING N N 40 OBX NE H12 SING N N 41 OBX CG H13 SING N N 42 OBX CG H14 SING N N 43 OBX "C1'" H15 SING N N 44 OBX OP2 H16 SING N N 45 OBX "C2'" H17 SING N N 46 OBX "O2'" H18 SING N N 47 OBX OP3 H19 SING N N 48 OBX "C3'" H20 SING N N 49 OBX "O3'" H21 SING N N 50 OBX "C4'" H22 SING N N 51 OBX "C5'" H23 SING N N 52 OBX "C5'" H24 SING N N 53 OBX NH1 H25 SING N N 54 OBX NH1 H26 SING N N 55 OBX NH2 H27 SING N N 56 OBX P OP1 DOUB N N 57 # 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 OBX InChI InChI 1.06 "InChI=1S/C14H26N7O7P/c15-9-3-6-21(14(20-9)19-5-2-1-4-18-13(16)17)12-11(23)10(22)8(28-12)7-27-29(24,25)26/h3,6,8,10-12,22-23H,1-2,4-5,7H2,(H8,15,16,17,18,19,20,24,25,26)/p+1/t8-,10-,11-,12-/m1/s1" OBX InChIKey InChI 1.06 IIGUQJFGJGKMTR-HJQYOEGKSA-O OBX SMILES_CANONICAL CACTVS 3.385 "NC(=N)NCCCCNc1nc(N)cc[n+]1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" OBX SMILES CACTVS 3.385 "NC(=N)NCCCCNc1nc(N)cc[n+]1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" OBX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\N)/NCCCCNc1nc(cc[n+]1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N" OBX SMILES "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1N)NCCCCNC(=N)N)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id OBX _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~{S},4~{R},5~{R})-5-[4-azanyl-2-(4-carbamimidamidobutylamino)pyrimidin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id OBX _pdbx_chem_comp_synonyms.name agmatidine _pdbx_chem_comp_synonyms.provenance AUTHOR _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 OBX "Create component" 2023-01-30 PDBJ OBX "Initial release" 2024-04-03 RCSB #