data_AG9 # _chem_comp.id AG9 _chem_comp.name AGMATIDINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H30 N7 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-02-14 _chem_comp.pdbx_modified_date 2013-03-29 _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 439.404 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AG9 _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 3ZN7 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 AG9 P P P 0 1 N N N -124.131 29.092 -23.237 -6.010 -1.599 -1.248 P AG9 1 AG9 N1 N1 N 0 1 N N N -120.081 27.891 -26.134 -0.412 1.747 0.401 N1 AG9 2 AG9 C2 C2 C 0 1 N N N -118.730 27.671 -26.522 0.856 1.894 -0.113 C2 AG9 3 AG9 N2 N2 N 0 1 N N N -118.418 27.551 -27.842 1.783 0.895 0.073 N2 AG9 4 AG9 N3 N3 N 0 1 N N N -117.778 27.600 -25.559 1.189 2.961 -0.771 N3 AG9 5 AG9 C4 C4 C 0 1 N N R -118.112 27.736 -24.272 0.257 4.053 -1.019 C4 AG9 6 AG9 N4 N4 N 0 1 N N N -117.133 27.667 -23.367 0.945 5.332 -0.795 N4 AG9 7 AG9 C5 C5 C 0 1 N N N -119.464 27.948 -23.857 -0.937 3.972 -0.112 C5 AG9 8 AG9 C6 C6 C 0 1 N N N -120.405 28.011 -24.808 -1.227 2.866 0.541 C6 AG9 9 AG9 CA CA C 0 1 N N N -117.847 26.333 -28.402 3.135 1.041 -0.470 CA AG9 10 AG9 CB CB C 0 1 N N N -116.361 26.185 -28.036 3.960 -0.201 -0.126 CB AG9 11 AG9 CD CD C 0 1 N N N -115.793 28.334 -29.335 6.197 -1.291 -0.349 CD AG9 12 AG9 NE NE N 0 1 N N N -114.651 29.193 -29.655 7.554 -1.144 -0.893 NE AG9 13 AG9 CG CG C 0 1 N N N -115.515 27.465 -28.107 5.373 -0.049 -0.693 CG AG9 14 AG9 CZ CZ C 0 1 N N N -114.731 30.347 -30.317 8.376 -2.321 -0.581 CZ AG9 15 AG9 "C1'" "C1'" C 0 1 N N R -121.131 28.032 -27.176 -0.901 0.422 0.793 "C1'" AG9 16 AG9 OP1 OP1 O 0 1 N N N -125.547 28.804 -22.858 -6.816 -2.453 -0.347 OP1 AG9 17 AG9 "C2'" "C2'" C 0 1 N N R -121.602 26.816 -27.967 -1.226 0.394 2.303 "C2'" AG9 18 AG9 "O2'" "O2'" O 0 1 N N N -121.766 27.216 -29.316 -0.147 -0.188 3.036 "O2'" AG9 19 AG9 OP2 OP2 O 0 1 N N N -123.483 30.368 -22.789 -5.917 -2.287 -2.700 OP2 AG9 20 AG9 "C3'" "C3'" C 0 1 N N S -122.910 26.499 -27.250 -2.487 -0.495 2.399 "C3'" AG9 21 AG9 "O3'" "O3'" O 0 1 N N N -123.863 25.827 -28.040 -2.224 -1.652 3.195 "O3'" AG9 22 AG9 OP3 OP3 O 0 1 N Y N -123.207 27.853 -22.763 -6.708 -0.154 -1.383 OP3 AG9 23 AG9 "C4'" "C4'" C 0 1 N N R -123.428 27.856 -26.819 -2.774 -0.898 0.936 "C4'" AG9 24 AG9 "O4'" "O4'" O 0 1 N N N -122.255 28.656 -26.589 -2.158 0.138 0.140 "O4'" AG9 25 AG9 "C5'" "C5'" C 0 1 N N N -124.226 27.809 -25.546 -4.282 -0.939 0.681 "C5'" AG9 26 AG9 "O5'" "O5'" O 0 1 N N N -124.075 29.049 -24.830 -4.529 -1.425 -0.640 "O5'" AG9 27 AG9 NH1 NH1 N 0 1 N N N -113.630 31.052 -30.562 9.580 -2.314 -1.423 NH1 AG9 28 AG9 NH2 NH2 N 0 1 N N N -115.909 30.812 -30.716 8.768 -2.283 0.834 NH2 AG9 29 AG9 HN2 HN2 H 0 1 N N N -118.587 28.327 -28.449 1.541 0.094 0.563 HN2 AG9 30 AG9 H1N4 H1N4 H 0 0 N N N -117.517 27.784 -22.451 1.736 5.430 -1.414 H1N4 AG9 31 AG9 H2N4 H2N4 H 0 0 N N N -116.684 26.776 -23.429 0.308 6.108 -0.897 H2N4 AG9 32 AG9 H5 H5 H 0 1 N N N -119.718 28.054 -22.813 -1.571 4.838 0.005 H5 AG9 33 AG9 H6 H6 H 0 1 N N N -121.437 28.159 -24.525 -2.094 2.828 1.184 H6 AG9 34 AG9 H1A H1A H 0 1 N N N -117.944 26.364 -29.497 3.082 1.153 -1.553 H1A AG9 35 AG9 H2A H2A H 0 1 N N N -118.399 25.466 -28.010 3.608 1.922 -0.037 H2A AG9 36 AG9 H1B H1B H 0 1 N N N -116.305 25.803 -27.006 4.013 -0.313 0.957 H1B AG9 37 AG9 H2B H2B H 0 1 N N N -115.917 25.451 -28.724 3.487 -1.082 -0.559 H2B AG9 38 AG9 H1D H1D H 0 1 N N N -116.670 28.966 -29.134 5.725 -2.172 -0.782 H1D AG9 39 AG9 H2D H2D H 0 1 N N N -116.001 27.681 -30.195 6.251 -1.402 0.734 H2D AG9 40 AG9 HNE HNE H 0 1 N N N -114.027 28.621 -30.188 7.989 -0.299 -0.556 HNE AG9 41 AG9 H1G H1G H 0 1 N N N -114.454 27.176 -28.122 5.319 0.063 -1.776 H1G AG9 42 AG9 H2G H2G H 0 1 N N N -115.720 28.064 -27.207 5.845 0.833 -0.260 H2G AG9 43 AG9 "H1'" "H1'" H 0 1 N N N -120.728 28.733 -27.922 -0.164 -0.342 0.547 "H1'" AG9 44 AG9 "H2'" "H2'" H 0 1 N N N -120.890 25.984 -27.861 -1.439 1.399 2.667 "H2'" AG9 45 AG9 "HO2'" "HO2'" H 0 0 N N N -120.916 27.397 -29.699 -0.321 -0.286 3.982 "HO2'" AG9 46 AG9 "H3'" "H3'" H 0 1 N N N -122.681 25.909 -26.351 -3.322 0.071 2.810 "H3'" AG9 47 AG9 "HO3'" "HO3'" H 0 0 N N N -124.645 25.666 -27.525 -1.978 -1.454 4.109 "HO3'" AG9 48 AG9 "H4'" "H4'" H 0 1 N N N -124.040 28.289 -27.624 -2.325 -1.866 0.713 "H4'" AG9 49 AG9 "H15'" "H15'" H 0 0 N N N -125.288 27.653 -25.786 -4.756 -1.601 1.406 "H15'" AG9 50 AG9 "H25'" "H25'" H 0 0 N N N -123.866 26.979 -24.920 -4.695 0.065 0.782 "H25'" AG9 51 AG9 H1H1 H1H1 H 0 0 N N N -112.835 30.566 -30.199 10.163 -3.114 -1.227 H1H1 AG9 52 AG9 H2H1 H2H1 H 0 0 N N N -113.525 31.173 -31.549 9.337 -2.275 -2.401 H2H1 AG9 53 AG9 H1H2 H1H2 H 0 0 N N N -116.628 30.167 -30.456 9.301 -1.452 1.040 H1H2 AG9 54 AG9 H2H2 H2H2 H 0 0 N N N -116.082 31.697 -30.283 7.960 -2.352 1.435 H2H2 AG9 55 AG9 HOP2 HOP2 H 0 0 N N N -124.103 30.876 -22.279 -6.774 -2.423 -3.127 HOP2 AG9 56 AG9 HOP3 HOP3 H 0 0 N N N -123.749 27.196 -22.342 -6.233 0.460 -1.960 HOP3 AG9 57 AG9 HZ HZ H 0 1 N N N -114.610 29.815 -31.272 7.802 -3.227 -0.775 HZ AG9 58 AG9 H4 H4 H 0 1 N N N -117.965 28.823 -24.349 -0.078 4.007 -2.055 H4 AG9 59 # 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 AG9 NH2 CZ SING N N 1 AG9 NH1 CZ SING N N 2 AG9 CZ NE SING N N 3 AG9 NE CD SING N N 4 AG9 CD CG SING N N 5 AG9 "O2'" "C2'" SING N N 6 AG9 CA CB SING N N 7 AG9 CA N2 SING N N 8 AG9 CG CB SING N N 9 AG9 "O3'" "C3'" SING N N 10 AG9 "C2'" "C3'" SING N N 11 AG9 "C2'" "C1'" SING N N 12 AG9 N2 C2 SING N N 13 AG9 "C3'" "C4'" SING N N 14 AG9 "C1'" "O4'" SING N N 15 AG9 "C1'" N1 SING N N 16 AG9 "C4'" "O4'" SING N N 17 AG9 "C4'" "C5'" SING N N 18 AG9 C2 N1 SING N N 19 AG9 C2 N3 DOUB N N 20 AG9 N1 C6 SING N N 21 AG9 N3 C4 SING N N 22 AG9 "C5'" "O5'" SING N N 23 AG9 "O5'" P SING N N 24 AG9 C6 C5 DOUB N N 25 AG9 C4 C5 SING N N 26 AG9 C4 N4 SING N N 27 AG9 P OP1 DOUB N N 28 AG9 P OP2 SING N N 29 AG9 P OP3 SING N N 30 AG9 N2 HN2 SING N N 31 AG9 N4 H1N4 SING N N 32 AG9 N4 H2N4 SING N N 33 AG9 C5 H5 SING N N 34 AG9 C6 H6 SING N N 35 AG9 CA H1A SING N N 36 AG9 CA H2A SING N N 37 AG9 CB H1B SING N N 38 AG9 CB H2B SING N N 39 AG9 CD H1D SING N N 40 AG9 CD H2D SING N N 41 AG9 NE HNE SING N N 42 AG9 CG H1G SING N N 43 AG9 CG H2G SING N N 44 AG9 "C1'" "H1'" SING N N 45 AG9 "C2'" "H2'" SING N N 46 AG9 "O2'" "HO2'" SING N N 47 AG9 "C3'" "H3'" SING N N 48 AG9 "O3'" "HO3'" SING N N 49 AG9 "C4'" "H4'" SING N N 50 AG9 "C5'" "H15'" SING N N 51 AG9 "C5'" "H25'" SING N N 52 AG9 NH1 H1H1 SING N N 53 AG9 NH1 H2H1 SING N N 54 AG9 NH2 H1H2 SING N N 55 AG9 NH2 H2H2 SING N N 56 AG9 OP2 HOP2 SING N N 57 AG9 OP3 HOP3 SING N N 58 AG9 CZ HZ SING N N 59 AG9 C4 H4 SING N N 60 # 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 AG9 SMILES ACDLabs 12.01 "[O-]P([O-])(=O)OCC2OC([n+]1c(nc(N)cc1)NCCCCNC(=[NH2+])\N)C(O)C2O" AG9 InChI InChI 1.03 "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)/t8-,10-,11-,12-/m1/s1" AG9 InChIKey InChI 1.03 IIGUQJFGJGKMTR-HJQYOEGKSA-N AG9 SMILES_CANONICAL CACTVS 3.370 "NC(N)NCCCCNC1=N[C@@H](N)C=CN1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" AG9 SMILES CACTVS 3.370 "NC(N)NCCCCNC1=N[CH](N)C=CN1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" AG9 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=NC1N)NCCCCNC(N)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" AG9 SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=NC1N)NCCCCNC(N)N)C2C(C(C(O2)COP(=O)(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 AG9 "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-2-[(4-{[amino(iminio)methyl]amino}butyl)amino]-1-(5-O-phosphonato-beta-D-ribofuranosyl)pyrimidin-1-ium" AG9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-[4-azanyl-2-[4-[bis(azanyl)methylamino]butylamino]-4H-pyrimidin-1-yl]-3,4-bis(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 AG9 "Create component" 2013-02-14 EBI AG9 "Initial release" 2013-04-03 RCSB #