data_PZA
#
_chem_comp.id PZA
_chem_comp.name PYRAZINE-2-CARBOXAMIDE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H5 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms Pyrazinamide
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-09-06
_chem_comp.pdbx_modified_date 2021-03-01
_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 123.113
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PZA
_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 1X8A
_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
PZA C C C 0 1 N N N N N N -6.946 2.636 5.314 -0.067 -0.000 1.661 C PZA 1
PZA N1 N1 N 0 1 N N N N N N -7.046 3.889 4.447 1.073 -0.001 2.379 N1 PZA 2
PZA O O O 0 1 N N N N N N -7.384 2.947 6.619 -1.142 0.000 2.228 O PZA 3
PZA C1 C1 C 0 1 Y N N N N N -3.282 1.653 4.441 1.210 -0.001 -1.759 C1 PZA 4
PZA C2 C2 C 0 1 Y N N N N N -3.399 0.157 4.752 0.035 -0.000 -2.497 C2 PZA 5
PZA N2 N2 N 0 1 Y N N N N N -4.343 -0.128 5.850 -1.134 0.000 -1.883 N2 PZA 6
PZA C3 C3 C 0 1 Y N N N N N -5.663 0.505 5.668 -1.190 0.000 -0.563 C3 PZA 7
PZA C4 C4 C 0 1 Y N N N N N -5.550 2.006 5.389 -0.011 -0.000 0.180 C4 PZA 8
PZA N3 N3 N 0 1 Y N N N N N -4.667 2.226 4.159 1.164 0.004 -0.442 N3 PZA 9
PZA H1 H1 H 0 1 N N N N N N -7.024 3.611 3.394 1.036 -0.000 3.348 H1 PZA 10
PZA H2 H2 H 0 1 N N N N N N -6.220 4.563 4.669 1.931 -0.005 1.926 H2 PZA 11
PZA H3 H3 H 0 1 N N N N N N -2.633 1.813 3.581 2.164 -0.002 -2.264 H3 PZA 12
PZA H5 H5 H 0 1 N N N N N N -2.418 -0.241 5.012 0.077 -0.001 -3.576 H5 PZA 13
PZA H4 H4 H 0 1 N N N N N N -6.251 0.349 6.571 -2.146 0.000 -0.062 H4 PZA 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
PZA C N1 SING N N 1
PZA C O DOUB N N 2
PZA C C4 SING N N 3
PZA N1 H1 SING N N 4
PZA N1 H2 SING N N 5
PZA C1 C2 DOUB Y N 6
PZA C1 N3 SING Y N 7
PZA C1 H3 SING N N 8
PZA C2 N2 SING Y N 9
PZA C2 H5 SING N N 10
PZA N2 C3 DOUB Y N 11
PZA C3 C4 SING Y N 12
PZA C3 H4 SING N N 13
PZA C4 N3 DOUB Y 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
PZA SMILES ACDLabs 10.04 O=C(N)c1nccnc1
PZA SMILES_CANONICAL CACTVS 3.341 NC(=O)c1cnccn1
PZA SMILES CACTVS 3.341 NC(=O)c1cnccn1
PZA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cnc(cn1)C(=O)N
PZA SMILES "OpenEye OEToolkits" 1.5.0 c1cnc(cn1)C(=O)N
PZA InChI InChI 1.03 InChI=1S/C5H5N3O/c6-5(9)4-3-7-1-2-8-4/h1-3H,(H2,6,9)
PZA InChIKey InChI 1.03 IPEHBUMCGVEMRF-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
PZA "SYSTEMATIC NAME" ACDLabs 10.04 pyrazine-2-carboxamide
PZA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 pyrazine-2-carboxamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PZA 'Create component' 2004-09-06 RCSB
PZA 'Modify descriptor' 2011-06-04 RCSB
PZA 'Modify synonyms' 2016-03-28 RCSB
PZA 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PZA
_pdbx_chem_comp_synonyms.name Pyrazinamide
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id PZA
_pdbe_chem_comp_drugbank_details.drugbank_id DB00339
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Pyrazinamide
_pdbe_chem_comp_drugbank_details.description 'A pyrazine that is used therapeutically as an antitubercular agent.'
_pdbe_chem_comp_drugbank_details.cas_number 98-96-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Pyrazinamide diffuses into active _M. tuberculosis_ that express pyrazinamidase enzyme that converts pyrazinamide to the active form pyrazinoic acid. Pyrazinoic acid can leak out under acidic conditions to be converted to the protonated conjugate acid, which is readily diffused back into the bacilli and accumulate intracellularly. The net effect is that more pyrazinoic acid accumulates inside the bacillus at acid pH than at neutral pH. Pyrazinoic acid was thought to inhibit the enzyme fatty acid synthase (FAS) I, which is required by the bacterium to synthesise fatty acids. However, this theory was thought to have been discounted.[A512] However, further studies reproduced the results of FAS I inhibition as the putative mechanism first in whole cell assay of replicating M. tuberculosis bacilli which have shown that pyrazinoic acid and its ester inhibit the synthesis of fatty acids.[A513] This study was followed by in vitro assay of tuberculous FAS I enzyme that tested the activity with pyrazinamide, pyrazinoic acid and several classes of pyrazinamide analogs. Pyrazinamide and its analogs inhibited the activity of purified FAS I.[A514]   It has also been suggested that the accumulation of pyrazinoic acid disrupts membrane potential and interferes with energy production, necessary for survival of M. tuberculosis at an acidic site of infection. Pyrazinoic acid has also been shown to bind to the ribosomal protein S1 (RpsA) and inhibit trans-translation. This may explain the ability of the drug to kill dormant mycobacteria.[A515]'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
PZA Pyrazinamide ChEMBL Tradename
PZA Pyrazinamide ChEMBL 'United States Accepted Names'
PZA Pyrazinamide wwPDB ?
PZA 2-carbamylpyrazine DrugBank ?
PZA 2-pyrazinecarboxamide DrugBank ?
PZA Aldinamide DrugBank ?
PZA Pirazinamide DrugBank ?
PZA Pyrazinamide DrugBank ?
PZA Pyrazinamidum DrugBank ?
PZA 'Pyrazine carboxamide' DrugBank ?
PZA pyrazine-2-carboxamide DrugBank ?
PZA Pyrazineamide DrugBank ?
PZA Pyrazinecarboxamide DrugBank ?
PZA 'Pyrazinoic acid amide' DrugBank ?
PZA Pyrizinamide DrugBank ?
PZA Piraldina DrugBank 'International brand'
PZA Prazina DrugBank 'International brand'
PZA Pyrafat DrugBank 'International brand'
PZA Pyrazide DrugBank 'International brand'
PZA Tebrazid DrugBank 'International brand'
PZA Tisamid DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id PZA
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00339
_pdbe_chem_comp_drugbank_classification.parent Pyrazines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Diazines
_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 pyrazines. These are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.'
#
_pdbe_chem_comp_drugbank_targets.comp_id PZA
_pdbe_chem_comp_drugbank_targets.drugbank_id DB00339
_pdbe_chem_comp_drugbank_targets.name 'Probable fatty acid synthase Fas (Fatty acid synthetase)'
_pdbe_chem_comp_drugbank_targets.organism 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)'
_pdbe_chem_comp_drugbank_targets.uniprot_id P95029
_pdbe_chem_comp_drugbank_targets.pharmacologically_active yes
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
PZA C C 5.104 -0.750 1
PZA N1 N 5.104 -2.250 2
PZA O O 3.805 0.000 3
PZA C1 C 7.702 2.250 4
PZA C2 C 9.002 1.500 5
PZA N2 N 9.002 0.000 6
PZA C3 C 7.702 -0.750 7
PZA C4 C 6.404 0.000 8
PZA N3 N 6.404 1.500 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
PZA C N1 SINGLE NONE 1
PZA C O DOUBLE NONE 2
PZA C C4 SINGLE NONE 3
PZA C1 C2 DOUBLE NONE 4
PZA C1 N3 SINGLE NONE 5
PZA C2 N2 SINGLE NONE 6
PZA N2 C3 DOUBLE NONE 7
PZA C3 C4 SINGLE NONE 8
PZA C4 N3 DOUBLE NONE 9
#
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
PZA MurckoScaffold S1 scaffold c1cnccn1 InChI=1S/C4H4N2/c1-2-6-4-3-5-1/h1-4H KYQCOXFCLRTKLS-UHFFFAOYSA-N
PZA amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
PZA pyrazine F2 fragment c1cnccn1 InChI=1S/C4H4N2/c1-2-6-4-3-5-1/h1-4H KYQCOXFCLRTKLS-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
PZA C1 S1 1
PZA C2 S1 1
PZA N2 S1 1
PZA C3 S1 1
PZA C4 S1 1
PZA N3 S1 1
PZA N1 F1 1
PZA C F1 1
PZA O F1 1
PZA C4 F1 1
PZA C1 F2 1
PZA C2 F2 1
PZA N2 F2 1
PZA C3 F2 1
PZA C4 F2 1
PZA N3 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PZA
_pdbe_chem_comp_rdkit_properties.exactmw 123.043
_pdbe_chem_comp_rdkit_properties.amw 123.115
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_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 58.878
_pdbe_chem_comp_rdkit_properties.tpsa 68.870
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.479
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.284
_pdbe_chem_comp_rdkit_properties.chi0v 4.250
_pdbe_chem_comp_rdkit_properties.chi1v 2.072
_pdbe_chem_comp_rdkit_properties.chi2v 0.638
_pdbe_chem_comp_rdkit_properties.chi3v 0.638
_pdbe_chem_comp_rdkit_properties.chi4v 0.307
_pdbe_chem_comp_rdkit_properties.chi0n 9.250
_pdbe_chem_comp_rdkit_properties.chi1n 4.467
_pdbe_chem_comp_rdkit_properties.chi2n 0.638
_pdbe_chem_comp_rdkit_properties.chi3n 0.638
_pdbe_chem_comp_rdkit_properties.chi4n 0.307
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.450
_pdbe_chem_comp_rdkit_properties.kappa1 2.057
_pdbe_chem_comp_rdkit_properties.kappa2 2.212
_pdbe_chem_comp_rdkit_properties.kappa3 1.218
_pdbe_chem_comp_rdkit_properties.Phi 0.505
#
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
PZA UniChem ChEMBL CHEMBL614
PZA UniChem DrugBank DB00339
PZA UniChem PDBe PZA
PZA UniChem 'Guide to Pharmacology' 7287
PZA UniChem 'PubChem DOTF' 92309395
PZA UniChem 'KEGG LIGAND' C01956
PZA UniChem ChEBI 45285
PZA UniChem NIH SAM002554927
PZA UniChem ZINC ZINC000000002005
PZA UniChem fdasrs 2KNI5N06TI
PZA UniChem PharmGKB PA451182
PZA UniChem HMDB HMDB0014483
PZA UniChem Selleck Pyrazinamide(Pyrazinoic-acid-amide)
PZA UniChem NMRShiftDB 20050094
PZA UniChem LINCS LSM-5425
PZA UniChem ACTor 98-96-4
PZA UniChem BindingDb 228814
PZA UniChem 'EPA CompTox Dashboard' DTXSID9021215
PZA UniChem DrugCentral 2328
PZA UniChem BRENDA 101385
PZA UniChem BRENDA 3666
PZA UniChem Rhea 45285
PZA UniChem ChemicalBook CB7429387
PZA UniChem DailyMed PYRAZINAMIDE
PZA UniChem ClinicalTrials PYRAZINAMIDE
PZA UniChem rxnorm PYRAZINAMIDE
PZA UniChem MedChemExpress HY-B0271
PZA UniChem 'Probes And Drugs' PD001773
PZA UniChem Nikkaji J3.990J
PZA UniChem eMolecules 27678593
PZA UniChem eMolecules 531199
PZA UniChem SureChEMBL SCHEMBL24102
PZA UniChem 'PubChem TPHARMA' 15119868
PZA UniChem PubChem 1046
PZA UniChem Mcule MCULE-6846697749
#
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
PZA C -1.648 0.483 0.498 ETKDGv3 1
PZA N1 -2.699 -0.180 -0.209 ETKDGv3 2
PZA O -1.942 1.314 1.399 ETKDGv3 3
PZA C1 1.449 -0.943 -1.071 ETKDGv3 4
PZA C2 2.430 -0.322 -0.408 ETKDGv3 5
PZA N2 2.100 0.626 0.620 ETKDGv3 6
PZA C3 0.861 0.892 0.918 ETKDGv3 7
PZA C4 -0.231 0.206 0.186 ETKDGv3 8
PZA N3 0.080 -0.652 -0.744 ETKDGv3 9
PZA H1 -3.696 0.026 0.023 ETKDGv3 10
PZA H2 -2.495 -0.874 -0.962 ETKDGv3 11
PZA H3 1.680 -1.659 -1.848 ETKDGv3 12
PZA H5 3.466 -0.529 -0.641 ETKDGv3 13
PZA H4 0.643 1.611 1.697 ETKDGv3 14
#