data_PDC
#
_chem_comp.id PDC
_chem_comp.name "PYRIDINE-2,6-DICARBOXYLIC ACID"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H5 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "DIPICOLINIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2025-05-20
_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 167.119
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PDC
_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 1ARZ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
PDC N1 N1 N 0 1 Y N N N N N 76.908 56.312 8.629 0.405 0.004 0.000 N1 PDC 1
PDC C2 C2 C 0 1 Y N N N N N 76.420 55.689 7.482 -0.240 -0.000 1.155 C2 PDC 2
PDC C3 C3 C 0 1 Y N N N N N 76.736 54.359 7.212 -1.636 -0.000 1.191 C3 PDC 3
PDC C4 C4 C 0 1 Y N N N N N 77.536 53.636 8.103 -2.344 -0.000 0.000 C4 PDC 4
PDC C5 C5 C 0 1 Y N N N N N 78.002 54.250 9.281 -1.636 0.000 -1.191 C5 PDC 5
PDC C6 C6 C 0 1 Y N N N N N 77.688 55.599 9.549 -0.240 -0.000 -1.155 C6 PDC 6
PDC C7 C7 C 0 1 N N N Y N Y 75.599 56.419 6.665 0.525 -0.000 2.423 C7 PDC 7
PDC O1 O1 O 0 1 N N N Y N Y 74.992 55.814 5.649 -0.060 -0.000 3.486 O1 PDC 8
PDC O2 O2 O 0 1 N Y N Y N Y 75.320 57.721 6.922 1.871 -0.000 2.396 O2 PDC 9
PDC C8 C8 C 0 1 N N N N N N 78.112 56.269 10.703 0.525 -0.000 -2.423 C8 PDC 10
PDC O3 O3 O 0 1 N N N N N N 78.619 55.586 11.763 -0.060 -0.000 -3.486 O3 PDC 11
PDC O4 O4 O 0 1 N N N N N N 77.906 57.568 10.827 1.871 -0.000 -2.396 O4 PDC 12
PDC H3 H3 H 0 1 N N N N N N 76.353 53.879 6.295 -2.158 -0.001 2.136 H3 PDC 13
PDC H4 H4 H 0 1 N N N N N N 77.797 52.588 7.878 -3.424 -0.000 0.000 H4 PDC 14
PDC H5 H5 H 0 1 N N N N N N 78.613 53.673 9.994 -2.158 -0.000 -2.136 H5 PDC 15
PDC HO2 HO2 H 0 1 N Y N Y N Y 74.750 58.227 6.355 2.371 -0.000 3.224 HO2 PDC 16
PDC HO4 HO4 H 0 1 N N N N N N 78.193 58.022 11.610 2.371 -0.000 -3.224 HO4 PDC 17
#
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
PDC N1 C2 DOUB Y N 1
PDC N1 C6 SING Y N 2
PDC C2 C3 SING Y N 3
PDC C2 C7 SING N N 4
PDC C3 C4 DOUB Y N 5
PDC C3 H3 SING N N 6
PDC C4 C5 SING Y N 7
PDC C4 H4 SING N N 8
PDC C5 C6 DOUB Y N 9
PDC C5 H5 SING N N 10
PDC C6 C8 SING N N 11
PDC C7 O1 DOUB N N 12
PDC C7 O2 SING N N 13
PDC O2 HO2 SING N N 14
PDC C8 O3 DOUB N N 15
PDC C8 O4 SING N N 16
PDC O4 HO4 SING N N 17
#
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
PDC SMILES ACDLabs 10.04 O=C(O)c1nc(C(=O)O)ccc1
PDC SMILES_CANONICAL CACTVS 3.341 OC(=O)c1cccc(n1)C(O)=O
PDC SMILES CACTVS 3.341 OC(=O)c1cccc(n1)C(O)=O
PDC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(nc(c1)C(=O)O)C(=O)O
PDC SMILES "OpenEye OEToolkits" 1.5.0 c1cc(nc(c1)C(=O)O)C(=O)O
PDC InChI InChI 1.03 InChI=1S/C7H5NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-3H,(H,9,10)(H,11,12)
PDC InChIKey InChI 1.03 WJJMNDUMQPNECX-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
PDC "SYSTEMATIC NAME" ACDLabs 10.04 "pyridine-2,6-dicarboxylic acid"
PDC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "pyridine-2,6-dicarboxylic 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
PDC 'Create component' 1999-07-08 EBI
PDC 'Modify descriptor' 2011-06-04 RCSB
PDC 'Modify synonyms' 2021-03-01 PDBE
PDC 'Modify PCM' 2025-05-20 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PDC
_pdbx_chem_comp_synonyms.name "DIPICOLINIC ACID"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PDC
_pdbx_chem_comp_pcm.modified_residue_id ?
_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 PDC
_pdbe_chem_comp_drugbank_details.drugbank_id DB04267
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Dipicolinic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 499-83-2
_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
PDC 'DIPICOLINIC ACID' wwPDB ?
PDC 2,6-dicarboxypyridine DrugBank ?
PDC '2,6-Dipicolinic acid' DrugBank ?
PDC '2,6-pyridinedicarboxylic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PDC
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04267
_pdbe_chem_comp_drugbank_classification.parent 'Pyridinecarboxylic acids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pyridines and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as pyridinecarboxylic acids. These are compounds containing a pyridine ring bearing a carboxylic acid group.'
#
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
PDC DB04267 '4-hydroxy-tetrahydrodipicolinate reductase' 'Escherichia coli (strain K12)' P04036 unknown 1
PDC DB04267 '4-hydroxy-tetrahydrodipicolinate reductase' 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WP23 unknown 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
PDC N1 N 7.702 -0.750 1
PDC C2 C 6.404 0.000 2
PDC C3 C 6.404 1.500 3
PDC C4 C 7.702 2.250 4
PDC C5 C 9.002 1.500 5
PDC C6 C 9.002 0.000 6
PDC C7 C 5.104 -0.750 7
PDC O1 O 3.805 0.000 8
PDC O2 O 5.104 -2.250 9
PDC C8 C 10.301 -0.750 10
PDC O3 O 11.600 0.000 11
PDC O4 O 10.301 -2.250 12
#
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
PDC N1 C2 DOUBLE NONE 1
PDC N1 C6 SINGLE NONE 2
PDC C2 C3 SINGLE NONE 3
PDC C2 C7 SINGLE NONE 4
PDC C3 C4 DOUBLE NONE 5
PDC C4 C5 SINGLE NONE 6
PDC C5 C6 DOUBLE NONE 7
PDC C6 C8 SINGLE NONE 8
PDC C7 O1 DOUBLE NONE 9
PDC C7 O2 SINGLE NONE 10
PDC C8 O3 DOUBLE NONE 11
PDC C8 O4 SINGLE NONE 12
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
PDC MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
PDC pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
PDC N1 S1 1
PDC C2 S1 1
PDC C3 S1 1
PDC C4 S1 1
PDC C5 S1 1
PDC C6 S1 1
PDC C2 F1 1
PDC C3 F1 1
PDC C4 F1 1
PDC C5 F1 1
PDC C6 F1 1
PDC N1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PDC
_pdbe_chem_comp_rdkit_properties.exactmw 167.022
_pdbe_chem_comp_rdkit_properties.amw 167.120
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_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 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 74.491
_pdbe_chem_comp_rdkit_properties.tpsa 87.490
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.369
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.624
_pdbe_chem_comp_rdkit_properties.chi0v 5.580
_pdbe_chem_comp_rdkit_properties.chi1v 2.764
_pdbe_chem_comp_rdkit_properties.chi2v 0.972
_pdbe_chem_comp_rdkit_properties.chi3v 0.972
_pdbe_chem_comp_rdkit_properties.chi4v 0.511
_pdbe_chem_comp_rdkit_properties.chi0n 10.580
_pdbe_chem_comp_rdkit_properties.chi1n 5.080
_pdbe_chem_comp_rdkit_properties.chi2n 0.972
_pdbe_chem_comp_rdkit_properties.chi3n 0.972
_pdbe_chem_comp_rdkit_properties.chi4n 0.511
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.910
_pdbe_chem_comp_rdkit_properties.kappa1 3.661
_pdbe_chem_comp_rdkit_properties.kappa2 2.997
_pdbe_chem_comp_rdkit_properties.kappa3 1.571
_pdbe_chem_comp_rdkit_properties.Phi 0.914
#
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
PDC UniChem DrugBank DB04267
PDC UniChem ChEBI 46837
PDC UniChem ZINC ZINC000000105246
PDC UniChem eMolecules 475045
PDC UniChem fdasrs UE81S5CQ0G
PDC UniChem NMRShiftDB 20031196
PDC UniChem MetaboLights MTBLC46837
PDC UniChem BRENDA 107142
PDC UniChem BRENDA 118533
PDC UniChem BRENDA 12301
PDC UniChem BRENDA 1443
PDC UniChem BRENDA 151183
PDC UniChem BRENDA 153200
PDC UniChem BRENDA 227810
PDC UniChem BRENDA 29346
PDC UniChem BRENDA 4005
PDC UniChem BRENDA 44748
PDC UniChem BRENDA 55903
PDC UniChem BRENDA 7433
PDC UniChem BRENDA 8376
PDC UniChem BRENDA 90869
PDC UniChem ChemicalBook CB1457234
PDC UniChem 'Probes And Drugs' PD006352
PDC UniChem CCDC AFEBUI
PDC UniChem SureChEMBL SCHEMBL34595
PDC UniChem HMDB HMDB0033161
PDC UniChem 'PubChem TPHARMA' 15141025
PDC UniChem PubChem 10367
PDC UniChem Mcule MCULE-1484050836
PDC UniChem ACTor 499-83-2
PDC UniChem Nikkaji J6.184K
PDC UniChem BindingDb 26116
PDC UniChem 'EPA CompTox Dashboard' DTXSID7022043
#
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
PDC N1 -0.253 0.621 0.633 ETKDGv3 1
PDC C2 1.003 0.477 0.316 ETKDGv3 2
PDC C3 1.431 -0.725 -0.438 ETKDGv3 3
PDC C4 0.521 -1.642 -0.780 ETKDGv3 4
PDC C5 -0.894 -1.451 -0.407 ETKDGv3 5
PDC C6 -1.255 -0.351 0.277 ETKDGv3 6
PDC C7 1.980 1.505 0.708 ETKDGv3 7
PDC O1 1.602 2.523 1.350 ETKDGv3 8
PDC O2 3.323 1.362 0.375 ETKDGv3 9
PDC C8 -2.654 -0.113 0.675 ETKDGv3 10
PDC O3 -3.560 -0.940 0.382 ETKDGv3 11
PDC O4 -2.979 1.041 1.382 ETKDGv3 12
PDC H3 2.468 -0.868 -0.713 ETKDGv3 13
PDC H4 0.819 -2.525 -1.331 ETKDGv3 14
PDC H5 -1.619 -2.203 -0.692 ETKDGv3 15
PDC HO2 4.003 2.064 0.640 ETKDGv3 16
PDC HO4 -3.934 1.225 1.665 ETKDGv3 17
#