data_PZE
#
_chem_comp.id PZE
_chem_comp.name piperazine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H10 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-02-01
_chem_comp.pdbx_modified_date 2011-06-04
_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 86.136
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PZE
_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 3QF1
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
PZE N7 N7 N 0 1 N N N N N N 5.748 3.048 28.132 -0.000 -1.407 0.217 N7 PZE 1
PZE C8 C8 C 0 1 N N N N N N 5.199 1.888 28.930 -1.210 -0.721 -0.257 C8 PZE 2
PZE C9 C9 C 0 1 N N N N N N 4.557 2.401 30.306 -1.210 0.721 0.257 C9 PZE 3
PZE N10 N10 N 0 1 N N N N N N 3.866 3.729 30.071 0.000 1.407 -0.217 N10 PZE 4
PZE C11 C11 C 0 1 N N N N N N 4.477 4.793 29.235 1.210 0.721 0.257 C11 PZE 5
PZE C12 C12 C 0 1 N N N N N N 4.900 4.191 27.827 1.210 -0.721 -0.257 C12 PZE 6
PZE HN7 HN7 H 0 1 N N N N N N 6.518 3.407 28.660 -0.000 -1.487 1.223 HN7 PZE 7
PZE H8 H8 H 0 1 N N N N N N 4.423 1.380 28.339 -1.224 -0.718 -1.347 H8 PZE 8
PZE H8A H8A H 0 1 N N N N N N 6.017 1.187 29.154 -2.093 -1.240 0.117 H8A PZE 9
PZE H9 H9 H 0 1 N N N N N N 3.825 1.664 30.668 -2.092 1.240 -0.117 H9 PZE 10
PZE H9A H9A H 0 1 N N N N N N 5.350 2.527 31.058 -1.224 0.719 1.347 H9A PZE 11
PZE HN10 HN10 H 0 0 N N N N N N 2.998 3.505 29.627 0.000 1.487 -1.223 HN10 PZE 12
PZE H11 H11 H 0 1 N N N N N N 3.747 5.602 29.082 2.093 1.240 -0.117 H11 PZE 13
PZE H11A H11A H 0 0 N N N N N N 5.367 5.192 29.744 1.224 0.718 1.347 H11A PZE 14
PZE H12 H12 H 0 1 N N N N N N 5.448 4.936 27.232 2.092 -1.240 0.117 H12 PZE 15
PZE H12A H12A H 0 0 N N N N N N 4.015 3.879 27.253 1.224 -0.719 -1.347 H12A PZE 16
#
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
PZE N7 C8 SING N N 1
PZE N7 C12 SING N N 2
PZE C8 C9 SING N N 3
PZE C9 N10 SING N N 4
PZE N10 C11 SING N N 5
PZE C11 C12 SING N N 6
PZE N7 HN7 SING N N 7
PZE C8 H8 SING N N 8
PZE C8 H8A SING N N 9
PZE C9 H9 SING N N 10
PZE C9 H9A SING N N 11
PZE N10 HN10 SING N N 12
PZE C11 H11 SING N N 13
PZE C11 H11A SING N N 14
PZE C12 H12 SING N N 15
PZE C12 H12A SING N N 16
#
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
PZE SMILES ACDLabs 12.01 N1CCNCC1
PZE SMILES_CANONICAL CACTVS 3.370 C1CNCCN1
PZE SMILES CACTVS 3.370 C1CNCCN1
PZE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C1CNCCN1
PZE SMILES "OpenEye OEToolkits" 1.7.0 C1CNCCN1
PZE InChI InChI 1.03 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2
PZE InChIKey InChI 1.03 GLUUGHFHXGJENI-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
PZE "SYSTEMATIC NAME" ACDLabs 12.01 piperazine
PZE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 piperazine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PZE 'Create component' 2011-02-01 PDBJ
PZE 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id PZE
_pdbe_chem_comp_drugbank_details.drugbank_id DB00592
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Piperazine
_pdbe_chem_comp_drugbank_details.description
'Piperazine is an organic compound that consists of a six-membered ring containing two opposing nitrogen atoms. First used as a solvent for uric acid, the use of piperazine as an anthelmintic agent was first introduced in 1953. Upon entry into the systemic circulation, the drug is partly oxidized and partly eliminated as an unchanged compound. Outside the body, piperazine has a remarkable power to dissolve uric acid and producing a soluble urate, but in clinical experience it has not proved equally successful. Piperazine was first introduced as an anthelmintic in 1953. Piperazine compounds mediate their anthelmintic action by generally paralyzing parasites, allowing the host body to easily remove or expel the invading organism.'
_pdbe_chem_comp_drugbank_details.cas_number 110-85-0
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Piperazine is a GABA receptor agonist. Piperzine binds directly and selectively to muscle membrane GABA receptors, presumably causing hyperpolarization of nerve endings, resulting in flaccid paralysis of the worm. While the worm is paralyzed, it is dislodged from the intestinal lumen and expelled live from the body by normal intestinal peristalsis.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
PZE Piperazine ChEMBL 'United States Accepted Names'
PZE Diethylenediamine DrugBank ?
PZE Piperazidine DrugBank ?
PZE Piperazine DrugBank ?
PZE Antepar DrugBank 'International brand'
PZE Uvilon DrugBank 'International brand'
PZE Vermidol DrugBank 'International brand'
PZE Vermizine DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id PZE
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00592
_pdbe_chem_comp_drugbank_classification.parent Piperazines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Diazinanes
_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 piperazines. These are compounds containing a piperazine ring, which is a saturated aliphatic six-member heterocyclic with two nitrogen atoms at positions 1 and 4, as well as four carbon atoms.'
#
_pdbe_chem_comp_drugbank_targets.comp_id PZE
_pdbe_chem_comp_drugbank_targets.drugbank_id DB00592
_pdbe_chem_comp_drugbank_targets.name 'Gamma-aminobutyric acid receptor subunit beta-3'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P28472
_pdbe_chem_comp_drugbank_targets.pharmacologically_active yes
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
PZE N7 N 4.299 -1.500 1
PZE C8 C 3.000 -0.750 2
PZE C9 C 3.000 0.750 3
PZE N10 N 4.299 1.500 4
PZE C11 C 5.598 0.750 5
PZE C12 C 5.598 -0.750 6
#
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
PZE N7 C8 SINGLE NONE 1
PZE N7 C12 SINGLE NONE 2
PZE C8 C9 SINGLE NONE 3
PZE C9 N10 SINGLE NONE 4
PZE N10 C11 SINGLE NONE 5
PZE C11 C12 SINGLE NONE 6
#
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
PZE MurckoScaffold S1 scaffold C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-UHFFFAOYSA-N
PZE piperazine F1 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-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
PZE N7 S1 1
PZE C8 S1 1
PZE C9 S1 1
PZE N10 S1 1
PZE C11 S1 1
PZE C12 S1 1
PZE N7 F1 1
PZE C8 F1 1
PZE C9 F1 1
PZE N10 F1 1
PZE C11 F1 1
PZE C12 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PZE
_pdbe_chem_comp_rdkit_properties.exactmw 86.084
_pdbe_chem_comp_rdkit_properties.amw 86.138
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 6
_pdbe_chem_comp_rdkit_properties.NumAtoms 16
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 52.094
_pdbe_chem_comp_rdkit_properties.tpsa 24.060
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.821
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.739
_pdbe_chem_comp_rdkit_properties.chi0v 2.894
_pdbe_chem_comp_rdkit_properties.chi1v 1.394
_pdbe_chem_comp_rdkit_properties.chi2v 0.324
_pdbe_chem_comp_rdkit_properties.chi3v 0.324
_pdbe_chem_comp_rdkit_properties.chi4v 0.156
_pdbe_chem_comp_rdkit_properties.chi0n 12.894
_pdbe_chem_comp_rdkit_properties.chi1n 6.289
_pdbe_chem_comp_rdkit_properties.chi2n 0.324
_pdbe_chem_comp_rdkit_properties.chi3n 0.324
_pdbe_chem_comp_rdkit_properties.chi4n 0.156
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 0.565
_pdbe_chem_comp_rdkit_properties.kappa2 2.157
_pdbe_chem_comp_rdkit_properties.kappa3 0.954
_pdbe_chem_comp_rdkit_properties.Phi 0.203
#
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
PZE UniChem ChEMBL CHEMBL1412
PZE UniChem DrugBank DB00592
PZE UniChem 'KEGG LIGAND' C07973
PZE UniChem ChEBI 28568
PZE UniChem ZINC ZINC000005850277
PZE UniChem eMolecules 531005
PZE UniChem fdasrs 1RTM4PAL0V
PZE UniChem SureChEMBL SCHEMBL238
PZE UniChem PharmGKB PA450977
PZE UniChem HMDB HMDB0014730
PZE UniChem NMRShiftDB 10008641
PZE UniChem ACTor 110-85-0
PZE UniChem 'EPA CompTox Dashboard' DTXSID1021164
PZE UniChem DrugCentral 2188
PZE UniChem BRENDA 135547
PZE UniChem ChemicalBook CB5852824
PZE UniChem ChemicalBook CB7182798
PZE UniChem ClinicalTrials PIPERAZINE
PZE UniChem rxnorm PIPERAZINE
PZE UniChem 'Probes And Drugs' PD001796
PZE UniChem CCDC ITIZOA
PZE UniChem Nikkaji J1.981J
PZE UniChem 'PubChem TPHARMA' 14747360
PZE UniChem PubChem 4837
PZE UniChem Mcule MCULE-5522245554
#
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
PZE N7 0.003 1.335 0.479 ETKDGv3 1
PZE C8 1.197 0.827 -0.218 ETKDGv3 2
PZE C9 1.092 -0.671 -0.583 ETKDGv3 3
PZE N10 0.165 -1.374 0.310 ETKDGv3 4
PZE C11 -1.199 -0.826 0.209 ETKDGv3 5
PZE C12 -1.221 0.701 -0.023 ETKDGv3 6
PZE HN7 0.090 1.129 1.502 ETKDGv3 7
PZE H8 2.089 0.984 0.428 ETKDGv3 8
PZE H8A 1.358 1.420 -1.144 ETKDGv3 9
PZE H9 0.744 -0.779 -1.634 ETKDGv3 10
PZE H9A 2.096 -1.143 -0.519 ETKDGv3 11
PZE HN10 0.505 -1.268 1.295 ETKDGv3 12
PZE H11 -1.733 -1.332 -0.623 ETKDGv3 13
PZE H11A -1.754 -1.062 1.144 ETKDGv3 14
PZE H12 -2.103 1.144 0.487 ETKDGv3 15
PZE H12A -1.328 0.915 -1.110 ETKDGv3 16
#