data_SIN
#
_chem_comp.id SIN
_chem_comp.name "SUCCINIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C4 H6 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2026-02-23
_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 118.088
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SIN
_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 3BIF
_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
SIN C1 C1 C 0 1 N N N N N N -28.983 -83.437 58.414 1.903 -0.044 0.002 C1 SIN 1
SIN O1 O1 O 0 1 N N N N N N -30.100 -83.363 58.885 2.038 -1.245 0.001 O1 SIN 2
SIN O2 O2 O 0 1 N Y N N N N -28.833 -83.518 57.206 2.984 0.753 -0.002 O2 SIN 3
SIN C2 C2 C 0 1 N N N N N N -27.760 -83.413 59.351 0.522 0.559 0.002 C2 SIN 4
SIN C3 C3 C 0 1 N N N N N N -26.685 -84.391 58.850 -0.522 -0.559 0.000 C3 SIN 5
SIN C4 C4 C 0 1 N N N N N N -25.455 -84.308 59.773 -1.903 0.044 -0.000 C4 SIN 6
SIN O3 O3 O 0 1 N N N N N N -24.380 -84.789 59.414 -2.038 1.245 0.001 O3 SIN 7
SIN O4 O4 O 0 1 N Y N N N N -25.550 -83.764 60.861 -2.984 -0.753 -0.002 O4 SIN 8
SIN HO2 HO2 H 0 1 N Y N N N N -29.682 -83.510 56.780 3.848 0.320 -0.006 HO2 SIN 9
SIN H21 H21 H 0 1 N N N N N N -27.341 -82.396 59.373 0.394 1.174 0.892 H21 SIN 10
SIN H22 H22 H 0 1 N N N N N N -28.074 -83.708 60.363 0.396 1.176 -0.888 H22 SIN 11
SIN H31 H31 H 0 1 N N N N N N -27.085 -85.416 58.861 -0.394 -1.174 -0.890 H31 SIN 12
SIN H32 H32 H 0 1 N N N N N N -26.394 -84.124 57.823 -0.396 -1.176 0.890 H32 SIN 13
SIN HO4 HO4 H 0 1 N Y N N N N -24.711 -83.795 61.306 -3.848 -0.320 -0.002 HO4 SIN 14
#
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
SIN C1 O1 DOUB N N 1
SIN C1 O2 SING N N 2
SIN C1 C2 SING N N 3
SIN O2 HO2 SING N N 4
SIN C2 C3 SING N N 5
SIN C2 H21 SING N N 6
SIN C2 H22 SING N N 7
SIN C3 C4 SING N N 8
SIN C3 H31 SING N N 9
SIN C3 H32 SING N N 10
SIN C4 O3 DOUB N N 11
SIN C4 O4 SING N N 12
SIN O4 HO4 SING N N 13
#
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
SIN SMILES ACDLabs 12.01 "O=C(O)CCC(=O)O"
SIN SMILES_CANONICAL CACTVS 3.370 "OC(=O)CCC(O)=O"
SIN SMILES CACTVS 3.370 "OC(=O)CCC(O)=O"
SIN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C(CC(=O)O)C(=O)O"
SIN SMILES "OpenEye OEToolkits" 1.7.0 "C(CC(=O)O)C(=O)O"
SIN InChI InChI 1.03 "InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)"
SIN InChIKey InChI 1.03 KDYFGRWQOYBRFD-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
SIN "SYSTEMATIC NAME" ACDLabs 12.01 "butanedioic acid"
SIN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "butanedioic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SIN 'Create component' 1999-07-08 RCSB
SIN 'Modify descriptor' 2011-06-04 RCSB
SIN 'Modify PCM' 2024-09-27 PDBE
SIN 'Modify PCM' 2026-02-23 RCSB
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SIN
_pdbx_chem_comp_pcm.modified_residue_id ALA
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_pdbx_chem_comp_pcm.position 'Amino-acid backbone'
_pdbx_chem_comp_pcm.polypeptide_position N-terminal
_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 ?
#
_pdbe_chem_comp_drugbank_details.comp_id SIN
_pdbe_chem_comp_drugbank_details.drugbank_id DB00139
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Succinic acid'
_pdbe_chem_comp_drugbank_details.description
"A water-soluble, colorless crystal with an acid taste that is used as a chemical intermediate, in medicine, the manufacture of lacquers, and to make perfume esters. It is also used in foods as a sequestrant, buffer, and a neutralizing agent. (Hawley's Condensed Chemical Dictionary, 12th ed, p1099; McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1851)"
_pdbe_chem_comp_drugbank_details.cas_number 110-15-6
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Succinate is an essential component of the Krebs or citric acid cycle and serves an electron donor in the production of fumaric acid and FADH2. It also has been shown to be a good "natural" antibiotic because of its relative acidic or caustic nature (high concentrations can even cause burns). Succinate supplements have been shown to help reduce the effects of hangovers by activating the degradation of acetaldehyde - a toxic byproduct of alcohol metabolism - into CO2 and H2O through aerobic metabolism. Succinic acid has been shown to stimulate neural system recovery and bolster the immune system. Claims have also been made that it boosts awareness, concentration and reflexes.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
SIN 'Amber acid' ChEMBL 'Other name'
SIN 'Dihydrofumaric acid' ChEMBL 'Other name'
SIN E363 ChEMBL 'Excipient E-Numbers'
SIN 'FEMA NO. 4719' ChEMBL 'Research Code'
SIN NSC-106449 ChEMBL 'Research Code'
SIN 'Succinic acid' ChEMBL 'Merck Index'
SIN 'Succinic acid' ChEMBL 'United States Pharmacopeial Convention'
SIN 'Succinic acid' ChEMBL 'Other name'
SIN 'Succinicum acidum' ChEMBL 'Other name'
SIN '1,2-ethanedicarboxylic acid' DrugBank ?
SIN 'Acidum succinicum' DrugBank ?
SIN 'Amber acid' DrugBank ?
SIN Asuccin DrugBank ?
SIN 'Butanedioic acid' DrugBank ?
SIN 'Butanedionic acid' DrugBank ?
SIN 'Dihydrofumaric acid' DrugBank ?
SIN 'Ethylenesuccinic acid' DrugBank ?
SIN 'Spirit of amber' DrugBank ?
SIN 'Succinic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SIN
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00139
_pdbe_chem_comp_drugbank_classification.parent 'Dicarboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.'
#
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
SIN DB00139 'Succinate-semialdehyde dehydrogenase, mitochondrial' Humans P51649 yes 1
SIN DB00139 'Succinate receptor 1' Humans Q9BXA5 yes 2
#
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
SIN C1 C 9.002 0.375 1
SIN O1 O 10.301 -0.375 2
SIN O2 O 9.002 1.875 3
SIN C2 C 7.702 -0.375 4
SIN C3 C 6.404 0.375 5
SIN C4 C 5.104 -0.375 6
SIN O3 O 3.805 0.375 7
SIN O4 O 5.104 -1.875 8
#
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
SIN C1 O1 DOUBLE NONE 1
SIN C1 O2 SINGLE NONE 2
SIN C1 C2 SINGLE NONE 3
SIN C2 C3 SINGLE NONE 4
SIN C3 C4 SINGLE NONE 5
SIN C4 O3 DOUBLE NONE 6
SIN C4 O4 SINGLE NONE 7
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id SIN
_pdbe_chem_comp_rdkit_properties.exactmw 118.027
_pdbe_chem_comp_rdkit_properties.amw 118.088
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_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 54.349
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.064
_pdbe_chem_comp_rdkit_properties.CrippenMR 24.506
_pdbe_chem_comp_rdkit_properties.chi0v 3.633
_pdbe_chem_comp_rdkit_properties.chi1v 1.566
_pdbe_chem_comp_rdkit_properties.chi2v 0.267
_pdbe_chem_comp_rdkit_properties.chi3v 0.267
_pdbe_chem_comp_rdkit_properties.chi4v 0.102
_pdbe_chem_comp_rdkit_properties.chi0n 9.633
_pdbe_chem_comp_rdkit_properties.chi1n 4.383
_pdbe_chem_comp_rdkit_properties.chi2n 0.267
_pdbe_chem_comp_rdkit_properties.chi3n 0.267
_pdbe_chem_comp_rdkit_properties.chi4n 0.102
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.060
_pdbe_chem_comp_rdkit_properties.kappa1 1.718
_pdbe_chem_comp_rdkit_properties.kappa2 3.010
_pdbe_chem_comp_rdkit_properties.kappa3 4.940
_pdbe_chem_comp_rdkit_properties.Phi 0.646
#
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
SIN UniChem ChEMBL CHEMBL576
SIN UniChem ChEBI CHEBI:15741
SIN UniChem BRENDA 97700
SIN UniChem BRENDA 93193
SIN UniChem BRENDA 58
SIN UniChem BRENDA 2759
SIN UniChem BRENDA 137838
SIN UniChem BRENDA 105625
SIN UniChem BRENDA 103665
SIN UniChem MolPort Molport-000-871-623
SIN UniChem ClinicalTrials NCT05935787
SIN UniChem ClinicalTrials NCT04649203
SIN UniChem ClinicalTrials NCT04631484
SIN UniChem DrugCentral 2487
SIN UniChem SureChEMBL 126337
SIN UniChem SureChEMBL 7116400
SIN UniChem SureChEMBL 829
SIN UniChem 'EPA CompTox Dashboard' DTXSID6023602
SIN UniChem fdasrs AB6MNQ6J6L
SIN UniChem HMDB HMDB0000254
SIN UniChem LipidMaps LMFA01170043
SIN UniChem BindingDb 26121
SIN UniChem PubChem 1110
SIN UniChem PubChem 173239856
SIN UniChem PubChem 21952380
SIN UniChem 'Probes And Drugs' PD010208
SIN UniChem CCDC SUCACB
SIN UniChem 'Guide to Pharmacology' 3637
SIN UniChem DrugBank DB00139
#
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
SIN C1 -1.877 0.129 0.324 ETKDGv3 1
SIN O1 -2.496 -0.646 1.102 ETKDGv3 2
SIN O2 -2.541 0.711 -0.751 ETKDGv3 3
SIN C2 -0.418 0.388 0.527 ETKDGv3 4
SIN C3 0.419 -0.626 -0.254 ETKDGv3 5
SIN C4 1.878 -0.361 -0.059 ETKDGv3 6
SIN O3 2.499 -0.912 0.889 ETKDGv3 7
SIN O4 2.539 0.529 -0.899 ETKDGv3 8
SIN HO2 -3.525 0.532 -0.912 ETKDGv3 9
SIN H21 -0.178 0.322 1.611 ETKDGv3 10
SIN H22 -0.182 1.418 0.181 ETKDGv3 11
SIN H31 0.181 -1.658 0.090 ETKDGv3 12
SIN H32 0.180 -0.558 -1.337 ETKDGv3 13
SIN HO4 3.523 0.732 -0.770 ETKDGv3 14
#