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 ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id SPD
_pdbe_chem_comp_drugbank_details.drugbank_id DB03566
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Spermidine
_pdbe_chem_comp_drugbank_details.description
'Spermidine is a polyamine formed from putrescine. It is found in almost all tissues in association with nucleic acids. It is found as a cation at all pH values, and is thought to help stabilize some membranes and nucleic acid structures. It is a precursor of spermine.'
_pdbe_chem_comp_drugbank_details.cas_number 124-20-9
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE wwPDB ?
SPD PA(34) wwPDB ?
SPD 1,5,10-triazadecane DrugBank ?
SPD 4-azaoctamethylenediamine DrugBank ?
SPD 4-azaoctane-1,8-diamine DrugBank ?
SPD N-(3-Aminopropyl)-1,4-butane-diamine DrugBank ?
SPD N-(3-aminopropyl)butane-1,4-diamine DrugBank ?
SPD Spermidin DrugBank ?
SPD Spermidine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SPD
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03566
_pdbe_chem_comp_drugbank_classification.parent Dialkylamines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organonitrogen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic nitrogen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
SPD DB03566 'Thioredoxin reductase 1, cytoplasmic' Humans Q16881 yes 1
SPD DB03566 'Beta-1 adrenergic receptor' Humans P08588 unknown 2
SPD DB03566 'Beta-2 adrenergic receptor' Humans P07550 unknown 3
SPD DB03566 'Gentamicin 3-N-acetyltransferase' 'Pseudomonas aeruginosa' P23181 unknown 4
SPD DB03566 'Spermidine/putrescine-binding periplasmic protein' 'Escherichia coli (strain K12)' P0AFK9 unknown 5
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
SPD N1 N 3.805 -0.375 1
SPD C2 C 5.104 0.375 2
SPD C3 C 6.404 -0.375 3
SPD C4 C 7.702 0.375 4
SPD C5 C 9.002 -0.375 5
SPD N6 N 10.301 0.375 6
SPD C7 C 11.600 -0.375 7
SPD C8 C 12.899 0.375 8
SPD C9 C 14.198 -0.375 9
SPD N10 N 15.497 0.375 10
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
SPD N1 C2 SINGLE NONE 1
SPD C2 C3 SINGLE NONE 2
SPD C3 C4 SINGLE NONE 3
SPD C4 C5 SINGLE NONE 4
SPD C5 N6 SINGLE NONE 5
SPD N6 C7 SINGLE NONE 6
SPD C7 C8 SINGLE NONE 7
SPD C8 C9 SINGLE NONE 8
SPD C9 N10 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id SPD
_pdbe_chem_comp_rdkit_properties.exactmw 145.158
_pdbe_chem_comp_rdkit_properties.amw 145.250
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 90.143
_pdbe_chem_comp_rdkit_properties.tpsa 64.070
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.336
_pdbe_chem_comp_rdkit_properties.CrippenMR 44.830
_pdbe_chem_comp_rdkit_properties.chi0v 4.842
_pdbe_chem_comp_rdkit_properties.chi1v 2.144
_pdbe_chem_comp_rdkit_properties.chi2v 0.398
_pdbe_chem_comp_rdkit_properties.chi3v 0.398
_pdbe_chem_comp_rdkit_properties.chi4v 0.165
_pdbe_chem_comp_rdkit_properties.chi0n 23.842
_pdbe_chem_comp_rdkit_properties.chi1n 11.380
_pdbe_chem_comp_rdkit_properties.chi2n 0.398
_pdbe_chem_comp_rdkit_properties.chi3n 0.398
_pdbe_chem_comp_rdkit_properties.chi4n 0.165
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.120
_pdbe_chem_comp_rdkit_properties.kappa1 1.002
_pdbe_chem_comp_rdkit_properties.kappa2 8.880
_pdbe_chem_comp_rdkit_properties.kappa3 7.880
_pdbe_chem_comp_rdkit_properties.Phi 0.890
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
SPD UniChem DrugBank DB03566
SPD UniChem 'Guide to Pharmacology' 2390
SPD UniChem 'KEGG LIGAND' C00315
SPD UniChem ChEBI 16610
SPD UniChem ZINC ZINC000001532612
SPD UniChem eMolecules 476108
SPD UniChem fdasrs U87FK77H25
SPD UniChem HMDB HMDB0001257
SPD UniChem NMRShiftDB 60018657
SPD UniChem LINCS LSM-37075
SPD UniChem BindingDb 50009353
SPD UniChem 'EPA CompTox Dashboard' DTXSID4036645
SPD UniChem MetaboLights MTBLC16610
SPD UniChem BRENDA 11155
SPD UniChem BRENDA 13223
SPD UniChem BRENDA 148
SPD UniChem BRENDA 161307
SPD UniChem BRENDA 234573
SPD UniChem BRENDA 55168
SPD UniChem ChemicalBook CB2165662
SPD UniChem ClinicalTrials SPERMIDINE
SPD UniChem rxnorm SPERMIDINE
SPD UniChem MedChemExpress HY-B1776
SPD UniChem 'Probes And Drugs' PD006808
SPD UniChem Nikkaji J10.054D
SPD UniChem SureChEMBL SCHEMBL15618
SPD UniChem 'PubChem TPHARMA' 15146776
SPD UniChem PubChem 1102
SPD UniChem Mcule MCULE-8096530192
SPD UniChem ACTor 124-20-9
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
SPD N1 -4.654 -0.564 -0.001 ETKDGv3 1
SPD C2 -3.829 0.577 0.388 ETKDGv3 2
SPD C3 -2.459 0.523 -0.297 ETKDGv3 3
SPD C4 -1.581 -0.618 0.242 ETKDGv3 4
SPD C5 -0.189 -0.616 -0.397 ETKDGv3 5
SPD N6 0.558 0.582 0.009 ETKDGv3 6
SPD C7 1.724 0.845 -0.851 ETKDGv3 7
SPD C8 2.801 -0.261 -0.816 ETKDGv3 8
SPD C9 3.400 -0.515 0.575 ETKDGv3 9
SPD N10 3.956 0.712 1.139 ETKDGv3 10
SPD HN11 -4.358 -1.393 0.564 ETKDGv3 11
SPD HN12 -5.639 -0.357 0.285 ETKDGv3 12
SPD H21 -3.711 0.611 1.495 ETKDGv3 13
SPD H22 -4.337 1.515 0.073 ETKDGv3 14
SPD H31 -1.947 1.494 -0.121 ETKDGv3 15
SPD H32 -2.599 0.405 -1.394 ETKDGv3 16
SPD H41 -1.479 -0.530 1.346 ETKDGv3 17
SPD H42 -2.062 -1.594 0.017 ETKDGv3 18
SPD H51 0.350 -1.530 -0.063 ETKDGv3 19
SPD H52 -0.299 -0.660 -1.504 ETKDGv3 20
SPD HN6 0.858 0.491 1.006 ETKDGv3 21
SPD H71 2.182 1.810 -0.542 ETKDGv3 22
SPD H72 1.386 0.986 -1.901 ETKDGv3 23
SPD H81 2.385 -1.211 -1.214 ETKDGv3 24
SPD H82 3.623 0.035 -1.503 ETKDGv3 25
SPD H91 2.625 -0.925 1.257 ETKDGv3 26
SPD H92 4.201 -1.282 0.488 ETKDGv3 27
SPD H101 4.300 0.492 2.102 ETKDGv3 28
SPD H102 4.796 0.979 0.577 ETKDGv3 29
#