data_MLA
#
_chem_comp.id MLA
_chem_comp.name "MALONIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C3 H4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-08-17
_chem_comp.pdbx_modified_date 2020-06-17
_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 104.061
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MLA
_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 1E7P
_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.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
MLA C1 C1 C 0 1 N N N N N N 41.330 13.970 83.054 -0.067 0.000 1.230 C1 MLA 1
MLA O1A O1A O 0 1 N N N N N N 40.151 13.614 83.317 -0.629 0.000 2.449 O1A MLA 2
MLA O1B O1B O 0 1 N N N N N N 42.146 14.277 83.961 1.135 0.000 1.119 O1B MLA 3
MLA C2 C2 C 0 1 N N N N N N 41.746 14.034 81.560 -0.937 0.000 0.000 C2 MLA 4
MLA C3 C3 C 0 1 N N N N N N 43.275 13.889 81.384 -0.067 0.000 -1.230 C3 MLA 5
MLA O3A O3A O 0 1 N N N N N N 44.055 14.355 82.242 1.135 0.000 -1.119 O3A MLA 6
MLA O3B O3B O 0 1 N N N N N N 43.699 13.316 80.356 -0.629 0.000 -2.449 O3B MLA 7
MLA H1A H1A H 0 1 N N N N N N 39.534 13.382 82.632 -0.071 0.000 3.239 H1A MLA 8
MLA HC21 1HC2 H 0 0 N N N N N N 41.367 14.962 81.072 -1.567 -0.890 -0.000 HC21 MLA 9
MLA HC22 2HC2 H 0 0 N N N N N N 41.194 13.280 80.952 -1.567 0.890 -0.000 HC22 MLA 10
MLA H3B H3B H 0 1 N N N N N N 44.638 13.226 80.247 -0.071 0.000 -3.239 H3B MLA 11
#
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
MLA C1 O1A SING N N 1
MLA C1 O1B DOUB N N 2
MLA C1 C2 SING N N 3
MLA O1A H1A SING N N 4
MLA C2 C3 SING N N 5
MLA C2 HC21 SING N N 6
MLA C2 HC22 SING N N 7
MLA C3 O3A DOUB N N 8
MLA C3 O3B SING N N 9
MLA O3B H3B SING N N 10
#
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
MLA SMILES ACDLabs 10.04 O=C(O)CC(=O)O
MLA SMILES_CANONICAL CACTVS 3.341 OC(=O)CC(O)=O
MLA SMILES CACTVS 3.341 OC(=O)CC(O)=O
MLA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C(=O)O)C(=O)O
MLA SMILES "OpenEye OEToolkits" 1.5.0 C(C(=O)O)C(=O)O
MLA InChI InChI 1.03 InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
MLA InChIKey InChI 1.03 OFOBLEOULBTSOW-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
MLA "SYSTEMATIC NAME" ACDLabs 10.04 "propanedioic acid"
MLA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "propanedioic 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
MLA 'Create component' 2001-08-17 EBI
MLA 'Modify descriptor' 2011-06-04 RCSB
MLA 'Modify synonyms' 2015-04-13 EBI
MLA 'Modify synonyms' 2020-06-05 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 MLA "DICARBOXYLIC ACID C3" ? ?
2 MLA "PROPANEDIOLIC ACID" ? ?
3 MLA "METHANEDICARBOXYLIC ACID" ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id MLA
_pdbe_chem_comp_drugbank_details.drugbank_id DB02175
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Malonic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 141-82-2
_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
MLA 'DICARBOXYLIC ACID C3' wwPDB ?
MLA 'PROPANEDIOLIC ACID' wwPDB ?
MLA 'METHANEDICARBOXYLIC ACID' wwPDB ?
MLA 'Propanedioic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id MLA
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02175
_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
MLA DB02175 'Aspartate 1-decarboxylase' 'Shigella flexneri' P0A793 unknown 1
MLA DB02175 'Proto-oncogene tyrosine-protein kinase Src' Humans P12931 unknown 2
MLA DB02175 'Sigma factor SigB regulation protein RsbQ' 'Bacillus subtilis (strain 168)' O07015 unknown 3
MLA DB02175 'Biflaviolin synthase CYP158A2' 'Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)' Q9FCA6 unknown 4
MLA DB02175 'U1 small nuclear ribonucleoprotein A' Humans P09012 unknown 5
MLA DB02175 'Malonamidase E2' 'Bradyrhizobium japonicum' Q9ZIV5 unknown 6
MLA DB02175 'Acetyl transferase' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' Q8ZPC0 unknown 7
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
MLA C1 C 5.104 0.375 1
MLA O1A O 3.805 1.125 2
MLA O1B O 5.104 -1.125 3
MLA C2 C 6.404 1.125 4
MLA C3 C 7.702 0.375 5
MLA O3A O 9.002 1.125 6
MLA O3B O 7.702 -1.125 7
#
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
MLA C1 O1A SINGLE NONE 1
MLA C1 O1B DOUBLE NONE 2
MLA C1 C2 SINGLE NONE 3
MLA C2 C3 SINGLE NONE 4
MLA C3 O3A DOUBLE NONE 5
MLA C3 O3B SINGLE NONE 6
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id MLA
_pdbe_chem_comp_rdkit_properties.exactmw 104.011
_pdbe_chem_comp_rdkit_properties.amw 104.061
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 11
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_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 45.174
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.454
_pdbe_chem_comp_rdkit_properties.CrippenMR 19.889
_pdbe_chem_comp_rdkit_properties.chi0v 3.133
_pdbe_chem_comp_rdkit_properties.chi1v 1.316
_pdbe_chem_comp_rdkit_properties.chi2v 0.204
_pdbe_chem_comp_rdkit_properties.chi3v 0.204
_pdbe_chem_comp_rdkit_properties.chi4v 0.083
_pdbe_chem_comp_rdkit_properties.chi0n 7.133
_pdbe_chem_comp_rdkit_properties.chi1n 3.133
_pdbe_chem_comp_rdkit_properties.chi2n 0.204
_pdbe_chem_comp_rdkit_properties.chi3n 0.204
_pdbe_chem_comp_rdkit_properties.chi4n 0.083
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.060
_pdbe_chem_comp_rdkit_properties.kappa1 1.814
_pdbe_chem_comp_rdkit_properties.kappa2 2.173
_pdbe_chem_comp_rdkit_properties.kappa3 4.940
_pdbe_chem_comp_rdkit_properties.Phi 0.563
#
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
MLA UniChem ChEMBL CHEMBL7942
MLA UniChem DrugBank DB02175
MLA UniChem PDBe MLA
MLA UniChem 'KEGG LIGAND' C00383
MLA UniChem 'KEGG LIGAND' C02028
MLA UniChem 'KEGG LIGAND' C04025
MLA UniChem ChEBI 30794
MLA UniChem ZINC ZINC000000895212
MLA UniChem eMolecules 494228
MLA UniChem fdasrs 9KX7ZMG0MK
MLA UniChem SureChEMBL SCHEMBL336
MLA UniChem HMDB HMDB0000691
MLA UniChem PubChem 23511544
MLA UniChem NMRShiftDB 10005915
MLA UniChem ACTor 141-82-2
MLA UniChem ACTor 183133-72-4
MLA UniChem BindingDb 14673
MLA UniChem LipidMaps LMFA01170041
MLA UniChem MetaboLights MTBLC30794
MLA UniChem BRENDA 101788
MLA UniChem BRENDA 10708
MLA UniChem BRENDA 107128
MLA UniChem BRENDA 392
MLA UniChem ChemicalBook CB9709256
MLA UniChem 'Probes And Drugs' PD008159
MLA UniChem 'PubChem TPHARMA' 15170483
MLA UniChem PubChem 867
MLA UniChem Mcule MCULE-5893043131
MLA UniChem Nikkaji J2.541K
MLA UniChem 'EPA CompTox Dashboard' DTXSID7021659
#
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
MLA C1 1.107 0.507 -0.115 ETKDGv3 1
MLA O1A 2.028 0.036 0.816 ETKDGv3 2
MLA O1B 1.094 1.729 -0.426 ETKDGv3 3
MLA C2 0.106 -0.428 -0.711 ETKDGv3 4
MLA C3 -1.113 -0.486 0.151 ETKDGv3 5
MLA O3A -1.191 -1.336 1.078 ETKDGv3 6
MLA O3B -2.143 0.429 -0.044 ETKDGv3 7
MLA H1A 2.703 0.661 1.240 ETKDGv3 8
MLA HC21 0.553 -1.441 -0.803 ETKDGv3 9
MLA HC22 -0.174 -0.084 -1.729 ETKDGv3 10
MLA H3B -2.969 0.413 0.542 ETKDGv3 11
#