data_MLT
#
_chem_comp.id MLT
_chem_comp.name D-MALATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAI
_chem_comp.formula "C4 H6 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 DMR
_chem_comp.formula_weight 134.087
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MLT
_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 1AMZ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
MLT C1 C1 C 0 1 N N N N N N 14.432 -5.674 -1.950 1.871 0.184 0.057 C1 MLT 1
MLT O1 O1 O 0 1 N N N N N N 13.237 -5.424 -2.115 2.637 -0.512 -0.565 O1 MLT 2
MLT O2 O2 O 0 1 N N N N N N 15.308 -5.430 -2.798 2.264 1.392 0.491 O2 MLT 3
MLT C2 C2 C 0 1 N N R N N N 14.937 -6.163 -0.619 0.473 -0.300 0.342 C2 MLT 4
MLT O3 O3 O 0 1 N N N N N N 16.152 -6.883 -0.764 0.331 -1.645 -0.121 O3 MLT 5
MLT C3 C3 C 0 1 N N N N N N 13.803 -6.916 0.072 -0.534 0.597 -0.381 C3 MLT 6
MLT C4 C4 C 0 1 N N N N N N 13.363 -8.258 -0.471 -1.934 0.189 0.000 C4 MLT 7
MLT O4 O4 O 0 1 N N N N N N 13.848 -8.696 -1.549 -2.108 -0.725 0.771 O4 MLT 8
MLT O5 O5 O 0 1 N N N N N N 12.584 -8.908 0.281 -2.987 0.841 -0.516 O5 MLT 9
MLT H2 H2 H 0 1 N N N N N N 15.142 -5.272 -0.008 0.287 -0.264 1.415 H2 MLT 10
MLT HO3 HO3 H 0 1 N N N N N N 16.448 -7.180 0.088 0.483 -1.752 -1.070 HO3 MLT 11
MLT H31 H31 H 0 1 N N N N N N 14.115 -7.079 1.114 -0.367 1.635 -0.095 H31 MLT 12
MLT H32 H32 H 0 1 N N N N N N 12.922 -6.258 0.051 -0.406 0.492 -1.459 H32 MLT 13
MLT HO5 HO5 H 0 1 N N N N N N 12.426 -9.767 -0.093 -3.866 0.544 -0.242 HO5 MLT 14
MLT H6 H6 H 0 1 N N N N N N 14.907 -5.033 -3.563 3.169 1.661 0.281 H6 MLT 15
#
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
MLT C1 O1 DOUB N N 1
MLT C1 O2 SING N N 2
MLT C1 C2 SING N N 3
MLT C2 O3 SING N N 4
MLT C2 C3 SING N N 5
MLT C2 H2 SING N N 6
MLT O3 HO3 SING N N 7
MLT C3 C4 SING N N 8
MLT C3 H31 SING N N 9
MLT C3 H32 SING N N 10
MLT C4 O4 DOUB N N 11
MLT C4 O5 SING N N 12
MLT O5 HO5 SING N N 13
MLT O2 H6 SING N N 14
#
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
MLT SMILES ACDLabs 12.01 O=C(O)C(O)CC(=O)O
MLT InChI InChI 1.03 InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
MLT InChIKey InChI 1.03 BJEPYKJPYRNKOW-UWTATZPHSA-N
MLT SMILES_CANONICAL CACTVS 3.370 O[C@H](CC(O)=O)C(O)=O
MLT SMILES CACTVS 3.370 O[CH](CC(O)=O)C(O)=O
MLT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C([C@H](C(=O)O)O)C(=O)O
MLT SMILES "OpenEye OEToolkits" 1.7.6 C(C(C(=O)O)O)C(=O)O
#
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
MLT "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-hydroxybutanedioic acid"
MLT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-2-oxidanylbutanedioic 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
MLT 'Create component' 1999-07-08 RCSB
MLT 'Modify descriptor' 2011-06-04 RCSB
MLT 'Other modification' 2012-02-03 RCSB
MLT 'Other modification' 2013-02-04 RCSB
MLT '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 MLT "(2R)-2-HYDROXYBUTANEDIOIC ACID" ? ?
2 MLT "2-HYDROXY-SUCCINIC ACID" ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id MLT
_pdbe_chem_comp_drugbank_details.drugbank_id DB03499
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'D-Malic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 636-61-3
_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
MLT '(2R)-2-HYDROXYBUTANEDIOIC ACID' wwPDB ?
MLT '2-HYDROXY-SUCCINIC ACID' wwPDB ?
MLT '(+)-D-malic acid' DrugBank ?
MLT '(R)-2-hydroxybutanedioic acid' DrugBank ?
MLT '(R)-malic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id MLT
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03499
_pdbe_chem_comp_drugbank_classification.parent 'Beta hydroxy acids and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Hydroxy 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 beta hydroxy acids and derivatives. These are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.'
#
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
MLT DB03499 'NAD-dependent malic enzyme, mitochondrial' Humans P23368 unknown 1
MLT DB03499 'Citrate synthase, mitochondrial' Humans O75390 unknown 2
MLT DB03499 'Circadian clock protein KaiB' 'Synechocystis sp. (strain PCC 6803 / Kazusa)' P74645 unknown 3
MLT DB03499 'Fumarate hydratase class II' 'Escherichia coli (strain K12)' P05042 unknown 4
MLT DB03499 'Malate synthase G' 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WK17 unknown 5
MLT DB03499 'Capsule biosynthesis protein' 'Neisseria meningitidis' Q57265 unknown 6
#
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
MLT C1 C 9.002 0.608 1
MLT O1 O 10.301 -0.142 2
MLT O2 O 9.002 2.107 3
MLT C2 C 7.702 -0.142 4
MLT O3 O 7.702 -1.643 5
MLT C3 C 6.404 0.608 6
MLT C4 C 5.104 -0.142 7
MLT O4 O 3.805 0.608 8
MLT O5 O 5.104 -1.643 9
#
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
MLT C1 O1 DOUBLE NONE 1
MLT C1 O2 SINGLE NONE 2
MLT C1 C2 SINGLE NONE 3
MLT C2 O3 SINGLE BEGINDASH 4
MLT C2 C3 SINGLE NONE 5
MLT C3 C4 SINGLE NONE 6
MLT C4 O4 DOUBLE NONE 7
MLT C4 O5 SINGLE NONE 8
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id MLT
_pdbe_chem_comp_rdkit_properties.exactmw 134.022
_pdbe_chem_comp_rdkit_properties.amw 134.087
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 59.230
_pdbe_chem_comp_rdkit_properties.tpsa 94.830
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.093
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.895
_pdbe_chem_comp_rdkit_properties.chi0v 4.041
_pdbe_chem_comp_rdkit_properties.chi1v 1.771
_pdbe_chem_comp_rdkit_properties.chi2v 0.401
_pdbe_chem_comp_rdkit_properties.chi3v 0.401
_pdbe_chem_comp_rdkit_properties.chi4v 0.144
_pdbe_chem_comp_rdkit_properties.chi0n 10.041
_pdbe_chem_comp_rdkit_properties.chi1n 4.495
_pdbe_chem_comp_rdkit_properties.chi2n 0.401
_pdbe_chem_comp_rdkit_properties.chi3n 0.401
_pdbe_chem_comp_rdkit_properties.chi4n 0.144
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 2.260
_pdbe_chem_comp_rdkit_properties.kappa2 3.032
_pdbe_chem_comp_rdkit_properties.kappa3 3.480
_pdbe_chem_comp_rdkit_properties.Phi 0.762
#
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
MLT UniChem ChEMBL CHEMBL225986
MLT UniChem DrugBank DB03499
MLT UniChem PDBe MLT
MLT UniChem 'KEGG LIGAND' C00497
MLT UniChem ChEBI 30796
MLT UniChem ZINC ZINC000000895264
MLT UniChem eMolecules 475035
MLT UniChem fdasrs P750Y95K96
MLT UniChem HMDB HMDB0031518
MLT UniChem NMRShiftDB 60021808
MLT UniChem ACTor 617-48-1
MLT UniChem MetaboLights MTBLC30796
MLT UniChem BRENDA 1139
MLT UniChem BRENDA 126338
MLT UniChem BRENDA 29900
MLT UniChem BRENDA 4457
MLT UniChem ChemicalBook CB9373789
MLT UniChem MedChemExpress HY-20558
MLT UniChem 'Probes And Drugs' PD059728
MLT UniChem 'EPA CompTox Dashboard' DTXSID90892496
MLT UniChem SureChEMBL SCHEMBL98496
MLT UniChem 'PubChem TPHARMA' 15321398
MLT UniChem PubChem 92824
MLT UniChem Mcule MCULE-2239273084
MLT UniChem Mcule MCULE-4984266891
MLT UniChem ACTor 636-61-3
MLT UniChem Nikkaji J14.674I
#
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
MLT C1 1.414 -0.211 0.516 ETKDGv3 1
MLT O1 1.152 -0.333 1.743 ETKDGv3 2
MLT O2 2.464 -0.932 -0.043 ETKDGv3 3
MLT C2 0.568 0.673 -0.360 ETKDGv3 4
MLT O3 0.061 1.759 0.374 ETKDGv3 5
MLT C3 -0.587 -0.116 -0.995 ETKDGv3 6
MLT C4 -1.565 -0.621 0.024 ETKDGv3 7
MLT O4 -1.459 -1.792 0.476 ETKDGv3 8
MLT O5 -2.572 0.217 0.493 ETKDGv3 9
MLT H2 1.206 1.057 -1.189 ETKDGv3 10
MLT HO3 0.822 2.377 0.535 ETKDGv3 11
MLT H31 -1.126 0.543 -1.709 ETKDGv3 12
MLT H32 -0.180 -0.971 -1.580 ETKDGv3 13
MLT HO5 -3.233 -0.105 1.190 ETKDGv3 14
MLT H6 3.035 -1.545 0.526 ETKDGv3 15
#