data_SPD # _chem_comp.id SPD _chem_comp.name SPERMIDINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAI _chem_comp.formula "C7 H19 N3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2024-09-27 _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 145.246 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SPD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 293D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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 SPD N1 N1 N 0 1 N N N Y Y N 24.100 26.055 3.515 -0.355 -0.007 5.520 N1 SPD 1 SPD C2 C2 C 0 1 N N N N N N 23.470 25.626 2.142 0.495 -0.030 4.323 C2 SPD 2 SPD C3 C3 C 0 1 N N N N N N 22.619 24.333 1.964 -0.383 -0.007 3.071 C3 SPD 3 SPD C4 C4 C 0 1 N N N N N N 21.198 24.248 2.590 0.502 -0.031 1.824 C4 SPD 4 SPD C5 C5 C 0 1 N N N N N N 21.189 24.826 4.077 -0.377 -0.008 0.573 C5 SPD 5 SPD N6 N6 N 0 1 N N N N N N 21.241 23.936 5.294 0.474 -0.031 -0.623 N6 SPD 6 SPD C7 C7 C 0 1 N N N N N N 21.396 22.394 5.196 -0.427 -0.007 -1.783 C7 SPD 7 SPD C8 C8 C 0 1 N N N N N N 20.673 21.474 6.235 0.397 -0.030 -3.071 C8 SPD 8 SPD C9 C9 C 0 1 N N N N N N 19.140 21.193 6.000 -0.541 -0.005 -4.279 C9 SPD 9 SPD N10 N10 N 0 1 N N N N N N 18.744 20.137 4.896 0.250 -0.027 -5.516 N10 SPD 10 SPD HN11 1HN1 H 0 0 N N N Y Y N 24.657 26.901 3.631 -0.816 0.890 5.530 HN11 SPD 11 SPD HN12 2HN1 H 0 0 N N N Y Y N 24.661 25.272 3.850 0.263 -0.023 6.316 HN12 SPD 12 SPD H21 1H2 H 0 1 N N N N N N 22.856 26.481 1.775 1.148 0.842 4.324 H21 SPD 13 SPD H22 2H2 H 0 1 N N N N N N 24.296 25.586 1.394 1.100 -0.937 4.325 H22 SPD 14 SPD H31 1H3 H 0 1 N N N N N N 22.538 24.110 0.874 -1.037 -0.879 3.070 H31 SPD 15 SPD H32 2H3 H 0 1 N N N N N N 23.216 23.464 2.325 -0.988 0.899 3.069 H32 SPD 16 SPD H41 1H4 H 0 1 N N N N N N 20.436 24.751 1.949 1.155 0.841 1.826 H41 SPD 17 SPD H42 2H4 H 0 1 N N N N N N 20.793 23.209 2.550 1.107 -0.938 1.826 H42 SPD 18 SPD H51 1H5 H 0 1 N N N N N N 22.026 25.557 4.158 -1.030 -0.880 0.571 H51 SPD 19 SPD H52 2H5 H 0 1 N N N N N N 20.292 25.481 4.177 -0.982 0.898 0.571 H52 SPD 20 SPD HN6 HN6 H 0 1 N N N N N N 20.407 24.126 5.850 0.983 0.839 -0.634 HN6 SPD 21 SPD H71 1H7 H 0 1 N N N N N N 21.098 22.072 4.170 -1.080 -0.879 -1.754 H71 SPD 22 SPD H72 2H7 H 0 1 N N N N N N 22.483 22.146 5.199 -1.031 0.899 -1.754 H72 SPD 23 SPD H81 1H8 H 0 1 N N N N N N 21.219 20.505 6.317 1.050 0.842 -3.100 H81 SPD 24 SPD H82 2H8 H 0 1 N N N N N N 20.822 21.883 7.261 1.001 -0.936 -3.100 H82 SPD 25 SPD H91 1H9 H 0 1 N N N N N N 18.667 20.905 6.968 -1.194 -0.877 -4.250 H91 SPD 26 SPD H92 2H9 H 0 1 N N N N N N 18.619 22.156 5.789 -1.145 0.901 -4.250 H92 SPD 27 SPD H101 1H10 H 0 0 N N N N N N 17.751 19.955 4.743 -0.406 -0.009 -6.281 H101 SPD 28 SPD H102 2H10 H 0 0 N N N N N N 19.220 19.255 5.089 0.759 0.843 -5.550 H102 SPD 29 # 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 SPD N1 C2 SING N N 1 SPD N1 HN11 SING N N 2 SPD N1 HN12 SING N N 3 SPD C2 C3 SING N N 4 SPD C2 H21 SING N N 5 SPD C2 H22 SING N N 6 SPD C3 C4 SING N N 7 SPD C3 H31 SING N N 8 SPD C3 H32 SING N N 9 SPD C4 C5 SING N N 10 SPD C4 H41 SING N N 11 SPD C4 H42 SING N N 12 SPD C5 N6 SING N N 13 SPD C5 H51 SING N N 14 SPD C5 H52 SING N N 15 SPD N6 C7 SING N N 16 SPD N6 HN6 SING N N 17 SPD C7 C8 SING N N 18 SPD C7 H71 SING N N 19 SPD C7 H72 SING N N 20 SPD C8 C9 SING N N 21 SPD C8 H81 SING N N 22 SPD C8 H82 SING N N 23 SPD C9 N10 SING N N 24 SPD C9 H91 SING N N 25 SPD C9 H92 SING N N 26 SPD N10 H101 SING N N 27 SPD N10 H102 SING N N 28 # 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 SPD SMILES ACDLabs 10.04 NCCCNCCCCN SPD SMILES_CANONICAL CACTVS 3.341 NCCCCNCCCN SPD SMILES CACTVS 3.341 NCCCCNCCCN SPD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(CCNCCCN)CN" SPD SMILES "OpenEye OEToolkits" 1.5.0 "C(CCNCCCN)CN" SPD InChI InChI 1.03 InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2 SPD InChIKey InChI 1.03 ATHGHQPFGPMSJY-UHFFFAOYSA-N # 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 SPD "SYSTEMATIC NAME" ACDLabs 10.04 "N-(3-aminopropyl)butane-1,4-diamine" SPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-(3-aminopropyl)butane-1,4-diamine" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SPD "Create component" 1999-07-08 RCSB SPD "Modify descriptor" 2011-06-04 RCSB SPD "Modify synonyms" 2020-06-05 PDBE SPD "Modify backbone" 2024-01-23 PDBE SPD "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 SPD "N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE" ? ? 2 SPD "PA(34)" ? ? # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 SPD ? None "Non-standard residue" "Amino-acid side chain and backbone" C-terminal ? ? ? ? 2 SPD GLN None Crosslinker "Amino-acid side chain" "Any position" CD N1 ? ? 3 SPD GLN None Crosslinker "Amino-acid side chain" "Any position" CD N10 ? ? 4 SPD GLN None Crosslinker "Amino-acid side chain" "Any position" N1 CD ? ? 5 SPD GLN None Crosslinker "Amino-acid side chain" "Any position" N10 CD ? ? #