data_SY5 # _chem_comp.id SY5 _chem_comp.name "2-[[[(3~{R},5~{R})-3-azanyl-6-(3-azanylpropylamino)-5-oxidanyl-hexanoyl]amino]-methyl-amino]ethanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H27 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "N6-(3-aminopropyl)-negamycin" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-03 _chem_comp.pdbx_modified_date 2021-05-21 _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 305.374 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SY5 _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 7B5K _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 SY5 C09 C1 C 0 1 N N R 191.632 104.451 176.590 -0.314 -0.588 -0.059 C09 SY5 1 SY5 C10 C2 C 0 1 N N N 190.476 103.527 176.151 0.956 -0.505 0.789 C10 SY5 2 SY5 C11 C3 C 0 1 N N R 190.026 103.649 174.672 2.156 -0.219 -0.117 C11 SY5 3 SY5 C12 C4 C 0 1 N N N 192.973 104.042 175.972 -1.529 -0.750 0.858 C12 SY5 4 SY5 C13 C5 C 0 1 N N N 189.757 102.272 174.026 3.442 -0.258 0.712 C13 SY5 5 SY5 C14 C6 C 0 1 N N N 194.070 104.323 177.027 -2.789 -0.709 0.033 C14 SY5 6 SY5 C15 C7 C 0 1 N N N 195.541 103.495 179.835 -6.001 0.314 0.302 C15 SY5 7 SY5 C16 C8 C 0 1 N N N 196.875 104.616 178.151 -5.848 -2.077 -0.049 C16 SY5 8 SY5 C17 C9 C 0 1 N N N 194.169 102.900 179.979 -5.314 1.624 0.013 C17 SY5 9 SY5 C18 C10 C 0 1 N N N 188.585 101.516 172.113 5.848 -0.014 0.605 C18 SY5 10 SY5 C19 C11 C 0 1 N N N 187.264 100.783 171.856 7.022 0.276 -0.332 C19 SY5 11 SY5 C20 C12 C 0 1 N N N 187.530 99.244 171.744 8.329 0.245 0.463 C20 SY5 12 SY5 N05 N1 N 0 1 N N N 191.779 104.306 178.001 -0.225 -1.743 -0.962 N05 SY5 13 SY5 N06 N2 N 0 1 N N N 194.997 103.248 177.460 -3.991 -0.833 0.631 N06 SY5 14 SY5 N07 N3 N 0 1 N N N 196.027 103.465 178.453 -5.133 -0.796 -0.117 N07 SY5 15 SY5 N08 N4 N 0 1 N N N 188.461 102.201 173.398 4.593 0.016 -0.158 N08 SY5 16 SY5 N21 N5 N 0 1 N N N 186.253 98.545 171.726 9.456 0.523 -0.438 N21 SY5 17 SY5 O01 O1 O 0 1 N N N 190.976 104.269 173.903 2.009 1.074 -0.707 O01 SY5 18 SY5 O02 O2 O 0 1 N N N 194.107 105.403 177.478 -2.723 -0.565 -1.170 O02 SY5 19 SY5 O03 O3 O 0 1 N N N 193.171 103.566 179.619 -4.216 1.633 -0.489 O03 SY5 20 SY5 O04 O4 O 0 1 N N N 194.024 101.749 180.469 -5.924 2.781 0.315 O04 SY5 21 SY5 H091 H1 H 0 0 N N N 191.398 105.491 176.317 -0.421 0.324 -0.645 H091 SY5 22 SY5 H102 H2 H 0 0 N N N 189.607 103.752 176.786 0.854 0.298 1.520 H102 SY5 23 SY5 H101 H3 H 0 0 N N N 190.794 102.488 176.320 1.110 -1.451 1.308 H101 SY5 24 SY5 H111 H4 H 0 0 N N N 189.087 104.221 174.652 2.206 -0.973 -0.902 H111 SY5 25 SY5 H122 H5 H 0 0 N N N 192.960 102.972 175.718 -1.467 -1.705 1.379 H122 SY5 26 SY5 H121 H6 H 0 0 N N N 193.164 104.632 175.063 -1.545 0.061 1.586 H121 SY5 27 SY5 H132 H7 H 0 0 N N N 189.814 101.499 174.807 3.391 0.496 1.497 H132 SY5 28 SY5 H131 H8 H 0 0 N N N 190.529 102.082 173.265 3.553 -1.245 1.162 H131 SY5 29 SY5 H152 H9 H 0 0 N N N 196.240 102.926 180.466 -6.200 0.235 1.370 H152 SY5 30 SY5 H151 H10 H 0 0 N N N 195.509 104.541 180.174 -6.941 0.267 -0.248 H151 SY5 31 SY5 H162 H11 H 0 0 N N N 197.635 104.729 178.938 -6.115 -2.291 0.986 H162 SY5 32 SY5 H163 H12 H 0 0 N N N 197.371 104.461 177.182 -6.754 -2.020 -0.653 H163 SY5 33 SY5 H161 H13 H 0 0 N N N 196.257 105.525 178.105 -5.207 -2.872 -0.431 H161 SY5 34 SY5 H1 H14 H 0 1 N N N 189.415 100.794 172.150 5.977 -0.998 1.055 H1 SY5 35 SY5 H2 H15 H 0 1 N N N 188.771 102.248 171.313 5.814 0.742 1.390 H2 SY5 36 SY5 H3 H16 H 0 1 N N N 186.820 101.147 170.918 7.056 -0.480 -1.117 H3 SY5 37 SY5 H4 H17 H 0 1 N N N 186.571 100.975 172.688 6.894 1.261 -0.782 H4 SY5 38 SY5 H5 H18 H 0 1 N N N 188.123 98.908 172.607 8.295 1.001 1.247 H5 SY5 39 SY5 H6 H19 H 0 1 N N N 188.081 99.031 170.816 8.458 -0.740 0.912 H6 SY5 40 SY5 H7 H20 H 0 1 N N N 190.925 104.562 178.454 0.531 -1.630 -1.620 H7 SY5 41 SY5 H051 H21 H 0 0 N N N 191.998 103.355 178.217 -0.126 -2.602 -0.442 H051 SY5 42 SY5 H061 H23 H 0 0 N N N 194.907 102.340 177.050 -4.044 -0.948 1.593 H061 SY5 43 SY5 H081 H24 H 0 0 N N N 188.110 103.126 173.251 4.482 0.897 -0.637 H081 SY5 44 SY5 H9 H26 H 0 1 N N N 186.412 97.560 171.655 9.329 1.402 -0.916 H9 SY5 45 SY5 H10 H27 H 0 1 N N N 185.754 98.741 172.570 10.332 0.508 0.064 H10 SY5 46 SY5 H011 H29 H 0 0 N N N 191.171 105.124 174.268 1.958 1.796 -0.065 H011 SY5 47 SY5 H12 H30 H 0 1 N N N 193.100 101.531 180.498 -5.445 3.596 0.111 H12 SY5 48 # # 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 SY5 N21 C20 SING N N 1 SY5 C20 C19 SING N N 2 SY5 C19 C18 SING N N 3 SY5 C18 N08 SING N N 4 SY5 N08 C13 SING N N 5 SY5 O01 C11 SING N N 6 SY5 C13 C11 SING N N 7 SY5 C11 C10 SING N N 8 SY5 C12 C09 SING N N 9 SY5 C12 C14 SING N N 10 SY5 C10 C09 SING N N 11 SY5 C09 N05 SING N N 12 SY5 C14 N06 SING N N 13 SY5 C14 O02 DOUB N N 14 SY5 N06 N07 SING N N 15 SY5 C16 N07 SING N N 16 SY5 N07 C15 SING N N 17 SY5 O03 C17 DOUB N N 18 SY5 C15 C17 SING N N 19 SY5 C17 O04 SING N N 20 SY5 C09 H091 SING N N 21 SY5 C10 H102 SING N N 22 SY5 C10 H101 SING N N 23 SY5 C11 H111 SING N N 24 SY5 C12 H122 SING N N 25 SY5 C12 H121 SING N N 26 SY5 C13 H132 SING N N 27 SY5 C13 H131 SING N N 28 SY5 C15 H152 SING N N 29 SY5 C15 H151 SING N N 30 SY5 C16 H162 SING N N 31 SY5 C16 H163 SING N N 32 SY5 C16 H161 SING N N 33 SY5 C18 H1 SING N N 34 SY5 C18 H2 SING N N 35 SY5 C19 H3 SING N N 36 SY5 C19 H4 SING N N 37 SY5 C20 H5 SING N N 38 SY5 C20 H6 SING N N 39 SY5 N05 H7 SING N N 40 SY5 N05 H051 SING N N 41 SY5 N06 H061 SING N N 42 SY5 N08 H081 SING N N 43 SY5 N21 H9 SING N N 44 SY5 N21 H10 SING N N 45 SY5 O01 H011 SING N N 46 SY5 O04 H12 SING N N 47 # # 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 SY5 InChI InChI 1.03 "InChI=1S/C12H27N5O4/c1-17(8-12(20)21)16-11(19)6-9(14)5-10(18)7-15-4-2-3-13/h9-10,15,18H,2-8,13-14H2,1H3,(H,16,19)(H,20,21)/t9-,10-/m1/s1" SY5 InChIKey InChI 1.03 VBFFWDLIKBQABV-NXEZZACHSA-N SY5 SMILES_CANONICAL CACTVS 3.385 "CN(CC(O)=O)NC(=O)C[C@H](N)C[C@@H](O)CNCCCN" SY5 SMILES CACTVS 3.385 "CN(CC(O)=O)NC(=O)C[CH](N)C[CH](O)CNCCCN" SY5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(CC(=O)O)NC(=O)C[C@@H](C[C@H](CNCCCN)O)N" SY5 SMILES "OpenEye OEToolkits" 2.0.7 "CN(CC(=O)O)NC(=O)CC(CC(CNCCCN)O)N" # _pdbx_chem_comp_identifier.comp_id SY5 _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-[[[(3~{R},5~{R})-3-azanyl-6-(3-azanylpropylamino)-5-oxidanyl-hexanoyl]amino]-methyl-amino]ethanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SY5 _pdbx_chem_comp_synonyms.name "N6-(3-aminopropyl)-negamycin" _pdbx_chem_comp_synonyms.provenance ? _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 SY5 "Create component" 2020-12-03 PDBE SY5 "Initial release" 2021-05-26 RCSB ##