data_PBG # _chem_comp.id PBG _chem_comp.name "3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N2 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;2-AMINOMETHYLPYRROL-3-ACETIC ACID 4-PROPIONIC ACID; PORPHOBILINOGEN; 5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROLE-3-PROPANOIC ACID ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-07-14 _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 226.229 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PBG _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 1E51 _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 PBG CHA CHA C 0 1 N N N N N N 33.390 74.173 60.780 0.081 -0.107 3.563 CHA PBG 1 PBG C1A C1A C 0 1 Y N N N N N 32.963 73.570 59.415 -0.648 -0.108 2.244 C1A PBG 2 PBG C2A C2A C 0 1 Y N N N N N 32.433 74.373 58.244 -0.153 -0.540 1.067 C2A PBG 3 PBG C3A C3A C 0 1 Y N N N N N 32.242 73.370 57.130 -1.160 -0.367 0.097 C3A PBG 4 PBG C4A C4A C 0 1 Y N N N N N 32.589 71.977 57.662 -2.229 0.172 0.717 C4A PBG 5 PBG NA NA N 0 1 Y N N N N N 33.015 72.144 59.070 -1.921 0.334 2.035 NA PBG 6 PBG C5A C5A C 0 1 N N N N N N 32.005 75.877 58.234 1.220 -1.113 0.833 C5A PBG 7 PBG C6A C6A C 0 1 N N N N N N 33.138 76.795 58.466 2.173 -0.002 0.475 C6A PBG 8 PBG O1A O1A O 0 1 N N N N N N 34.379 76.231 58.657 1.777 1.137 0.415 O1A PBG 9 PBG O2A O2A O 0 1 N N N N N N 33.021 78.153 58.503 3.462 -0.279 0.222 O2A PBG 10 PBG C7A C7A C 0 1 N N N N N N 31.733 73.721 55.696 -1.059 -0.715 -1.365 C7A PBG 11 PBG C8A C8A C 0 1 N N N N N N 30.834 72.616 55.154 -0.520 0.488 -2.140 C8A PBG 12 PBG C9A C9A C 0 1 N N N N N N 29.754 73.154 54.235 -0.419 0.140 -3.602 C9A PBG 13 PBG O3A O3A O 0 1 N N N N N N 29.574 74.495 53.907 -0.745 -0.957 -3.986 O3A PBG 14 PBG O4A O4A O 0 1 N N N N N N 28.821 72.328 53.627 0.032 1.050 -4.479 O4A PBG 15 PBG N1 N1 N 0 1 N N N N N N 33.841 73.096 61.642 -0.791 0.447 4.606 N1 PBG 16 PBG HHA2 2HHA H 0 0 N N N N N N 34.151 74.980 60.670 0.981 0.502 3.480 HHA2 PBG 17 PBG HHA1 1HHA H 0 0 N N N N N N 32.583 74.785 61.247 0.357 -1.128 3.825 HHA1 PBG 18 PBG H4A1 1H4A H 0 0 N N N N N N 32.540 71.016 57.122 -3.168 0.432 0.250 H4A1 PBG 19 PBG HA HA H 0 1 N N N N N N 33.299 71.395 59.702 -2.509 0.703 2.712 HA PBG 20 PBG H5A2 2H5A H 0 0 N N N N N N 31.469 76.133 57.290 1.565 -1.610 1.740 H5A2 PBG 21 PBG H5A1 1H5A H 0 0 N N N N N N 31.183 76.063 58.964 1.179 -1.835 0.017 H5A1 PBG 22 PBG H2AO OH2A H 0 0 N N N N N N 33.750 78.743 58.652 4.073 0.433 -0.007 H2AO PBG 23 PBG H7A2 2H7A H 0 0 N N N N N N 31.227 74.714 55.669 -0.383 -1.561 -1.491 H7A2 PBG 24 PBG H7A1 1H7A H 0 0 N N N N N N 32.576 73.943 55.002 -2.046 -0.979 -1.745 H7A1 PBG 25 PBG H8A2 2H8A H 0 0 N N N N N N 31.431 71.820 54.651 -1.196 1.334 -2.013 H8A2 PBG 26 PBG H8A1 1H8A H 0 0 N N N N N N 30.394 72.011 55.981 0.466 0.752 -1.760 H8A1 PBG 27 PBG H4AO OH4A H 0 0 N N N N N N 28.144 72.665 53.051 0.097 0.827 -5.418 H4AO PBG 28 PBG H12 2H1 H 0 1 N N N N N N 34.121 73.492 62.539 -0.264 0.428 5.466 H12 PBG 29 PBG H11 1H1 H 0 1 N N N N N N 34.578 72.536 61.214 -0.936 1.419 4.376 H11 PBG 30 # 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 PBG CHA C1A SING N N 1 PBG CHA N1 SING N N 2 PBG CHA HHA2 SING N N 3 PBG CHA HHA1 SING N N 4 PBG C1A C2A DOUB Y N 5 PBG C1A NA SING Y N 6 PBG C2A C3A SING Y N 7 PBG C2A C5A SING N N 8 PBG C3A C4A DOUB Y N 9 PBG C3A C7A SING N N 10 PBG C4A NA SING Y N 11 PBG C4A H4A1 SING N N 12 PBG NA HA SING N N 13 PBG C5A C6A SING N N 14 PBG C5A H5A2 SING N N 15 PBG C5A H5A1 SING N N 16 PBG C6A O1A DOUB N N 17 PBG C6A O2A SING N N 18 PBG O2A H2AO SING N N 19 PBG C7A C8A SING N N 20 PBG C7A H7A2 SING N N 21 PBG C7A H7A1 SING N N 22 PBG C8A C9A SING N N 23 PBG C8A H8A2 SING N N 24 PBG C8A H8A1 SING N N 25 PBG C9A O3A DOUB N N 26 PBG C9A O4A SING N N 27 PBG O4A H4AO SING N N 28 PBG N1 H12 SING N N 29 PBG N1 H11 SING N N 30 # 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 PBG SMILES ACDLabs 10.04 O=C(O)CCc1c(c(nc1)CN)CC(=O)O PBG SMILES_CANONICAL CACTVS 3.341 NCc1[nH]cc(CCC(O)=O)c1CC(O)=O PBG SMILES CACTVS 3.341 NCc1[nH]cc(CCC(O)=O)c1CC(O)=O PBG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1c(c(c([nH]1)CN)CC(=O)O)CCC(=O)O PBG SMILES "OpenEye OEToolkits" 1.5.0 c1c(c(c([nH]1)CN)CC(=O)O)CCC(=O)O PBG InChI InChI 1.03 InChI=1S/C10H14N2O4/c11-4-8-7(3-10(15)16)6(5-12-8)1-2-9(13)14/h5,12H,1-4,11H2,(H,13,14)(H,15,16) PBG InChIKey InChI 1.03 QSHWIQZFGQKFMA-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 PBG "SYSTEMATIC NAME" ACDLabs 10.04 "3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid" PBG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic 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 PBG 'Create component' 2000-07-14 EBI PBG 'Modify descriptor' 2011-06-04 RCSB PBG '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 PBG "2-AMINOMETHYLPYRROL-3-ACETIC ACID 4-PROPIONIC ACID" ? ? 2 PBG PORPHOBILINOGEN ? ? 3 PBG "5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROLE-3-PROPANOIC ACID" ? ? # _pdbe_chem_comp_drugbank_details.comp_id PBG _pdbe_chem_comp_drugbank_details.drugbank_id DB02272 _pdbe_chem_comp_drugbank_details.type 'small molecule' _pdbe_chem_comp_drugbank_details.name Porphobilinogen _pdbe_chem_comp_drugbank_details.description 'Porphobilinogen is a pyrrole involved in porphyrin metabolism. It is generated by the enzyme ALA dehydratase, and converted into hydroxymethyl bilane by the enzyme porphobilinogen deaminase.' _pdbe_chem_comp_drugbank_details.cas_number 487-90-1 _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 PBG '2-AMINOMETHYLPYRROL-3-ACETIC ACID 4-PROPIONIC ACID' wwPDB ? PBG PORPHOBILINOGEN wwPDB ? PBG '5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROLE-3-PROPANOIC ACID' wwPDB ? PBG '5-(Aminomethyl)-4-(carboxymethyl)-1H-pyrrole-3-propionic acid' DrugBank ? PBG Porphobilinogen DrugBank ? # _pdbe_chem_comp_drugbank_classification.comp_id PBG _pdbe_chem_comp_drugbank_classification.drugbank_id DB02272 _pdbe_chem_comp_drugbank_classification.parent Aralkylamines _pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds' _pdbe_chem_comp_drugbank_classification.class 'Organonitrogen compounds' _pdbe_chem_comp_drugbank_classification.superclass 'Organic nitrogen compounds' _pdbe_chem_comp_drugbank_classification.description 'This compound belongs to the class of organic compounds known as aralkylamines. These are alkylamines in which the alkyl group is substituted at one carbon atom by an aromatic hydrocarbyl group.' # _pdbe_chem_comp_drugbank_targets.comp_id PBG _pdbe_chem_comp_drugbank_targets.drugbank_id DB02272 _pdbe_chem_comp_drugbank_targets.name 'Delta-aminolevulinic acid dehydratase' _pdbe_chem_comp_drugbank_targets.organism Humans _pdbe_chem_comp_drugbank_targets.uniprot_id P13716 _pdbe_chem_comp_drugbank_targets.pharmacologically_active yes _pdbe_chem_comp_drugbank_targets.ordinal 1 # 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 PBG CHA C 11.684 -2.224 1 PBG C1A C 10.257 -1.760 2 PBG C2A C 9.793 -0.334 3 PBG C3A C 8.293 -0.334 4 PBG C4A C 7.830 -1.760 5 PBG NA N 9.043 -2.642 6 PBG C5A C 10.675 0.880 7 PBG C6A C 10.065 2.250 8 PBG O1A O 10.947 3.464 9 PBG O2A O 8.573 2.407 10 PBG C7A C 7.412 0.880 11 PBG C8A C 5.920 0.723 12 PBG C9A C 5.038 1.937 13 PBG O3A O 3.547 1.780 14 PBG O4A O 5.649 3.307 15 PBG N1 N 11.995 -3.691 16 # 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 PBG CHA C1A SINGLE NONE 1 PBG CHA N1 SINGLE NONE 2 PBG C1A C2A DOUBLE NONE 3 PBG C1A NA SINGLE NONE 4 PBG C2A C3A SINGLE NONE 5 PBG C2A C5A SINGLE NONE 6 PBG C3A C4A DOUBLE NONE 7 PBG C3A C7A SINGLE NONE 8 PBG C4A NA SINGLE NONE 9 PBG C5A C6A SINGLE NONE 10 PBG C6A O1A DOUBLE NONE 11 PBG C6A O2A SINGLE NONE 12 PBG C7A C8A SINGLE NONE 13 PBG C8A C9A SINGLE NONE 14 PBG C9A O3A DOUBLE NONE 15 PBG C9A O4A SINGLE NONE 16 # 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 PBG MurckoScaffold S1 scaffold 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-UHFFFAOYSA-N PBG pyrrole F1 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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 PBG C1A S1 1 PBG C2A S1 1 PBG C3A S1 1 PBG C4A S1 1 PBG NA S1 1 PBG C1A F1 1 PBG C2A F1 1 PBG C3A F1 1 PBG C4A F1 1 PBG NA F1 1 # _pdbe_chem_comp_rdkit_properties.comp_id PBG _pdbe_chem_comp_rdkit_properties.exactmw 226.095 _pdbe_chem_comp_rdkit_properties.amw 226.232 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 6 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 5 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7 _pdbe_chem_comp_rdkit_properties.NumHBD 4 _pdbe_chem_comp_rdkit_properties.NumHBA 5 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16 _pdbe_chem_comp_rdkit_properties.NumAtoms 30 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.400 _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 112.099 _pdbe_chem_comp_rdkit_properties.tpsa 116.410 _pdbe_chem_comp_rdkit_properties.CrippenClogP -0.046 _pdbe_chem_comp_rdkit_properties.CrippenMR 55.183 _pdbe_chem_comp_rdkit_properties.chi0v 7.527 _pdbe_chem_comp_rdkit_properties.chi1v 3.737 _pdbe_chem_comp_rdkit_properties.chi2v 1.389 _pdbe_chem_comp_rdkit_properties.chi3v 1.389 _pdbe_chem_comp_rdkit_properties.chi4v 0.851 _pdbe_chem_comp_rdkit_properties.chi0n 21.527 _pdbe_chem_comp_rdkit_properties.chi1n 10.395 _pdbe_chem_comp_rdkit_properties.chi2n 1.389 _pdbe_chem_comp_rdkit_properties.chi3n 1.389 _pdbe_chem_comp_rdkit_properties.chi4n 0.851 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.820 _pdbe_chem_comp_rdkit_properties.kappa1 3.102 _pdbe_chem_comp_rdkit_properties.kappa2 5.315 _pdbe_chem_comp_rdkit_properties.kappa3 3.095 _pdbe_chem_comp_rdkit_properties.Phi 1.030 # 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 PBG UniChem DrugBank DB02272 PBG UniChem 'KEGG LIGAND' C00931 PBG UniChem ChEBI 17381 PBG UniChem ZINC ZINC000000056609 PBG UniChem eMolecules 531059 PBG UniChem fdasrs 74KHC72QXK PBG UniChem HMDB HMDB0000245 PBG UniChem 'PubChem TPHARMA' 15220559 PBG UniChem NMRShiftDB 60020552 PBG UniChem MetaboLights MTBLC17381 PBG UniChem BRENDA 1763 PBG UniChem ChemicalBook CB5481219 PBG UniChem MedChemExpress HY-W013495 PBG UniChem 'Probes And Drugs' PD039223 PBG UniChem 'EPA CompTox Dashboard' DTXSID4060070 PBG UniChem SureChEMBL SCHEMBL188532 PBG UniChem PubChem 1021 PBG UniChem Nikkaji J6.026G # 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 PBG CHA -2.782 -1.118 0.812 ETKDGv3 1 PBG C1A -1.555 -0.945 -0.040 ETKDGv3 2 PBG C2A -0.572 -0.066 0.163 ETKDGv3 3 PBG C3A 0.444 -0.314 -0.868 ETKDGv3 4 PBG C4A 0.039 -1.352 -1.589 ETKDGv3 5 PBG NA -1.223 -1.808 -1.123 ETKDGv3 6 PBG C5A -0.522 1.008 1.215 ETKDGv3 7 PBG C6A -1.158 2.260 0.704 ETKDGv3 8 PBG O1A -0.483 3.081 0.027 ETKDGv3 9 PBG O2A -2.507 2.502 0.944 ETKDGv3 10 PBG C7A 1.770 0.374 -1.014 ETKDGv3 11 PBG C8A 2.828 -0.306 -0.143 ETKDGv3 12 PBG C9A 4.143 0.394 -0.276 ETKDGv3 13 PBG O3A 4.432 1.347 0.496 ETKDGv3 14 PBG O4A 5.027 0.021 -1.283 ETKDGv3 15 PBG N1 -3.868 -1.701 0.032 ETKDGv3 16 PBG HHA2 -3.112 -0.141 1.227 ETKDGv3 17 PBG HHA1 -2.532 -1.794 1.658 ETKDGv3 18 PBG H4A1 0.593 -1.810 -2.398 ETKDGv3 19 PBG HA -1.763 -2.629 -1.477 ETKDGv3 20 PBG H5A2 -1.039 0.672 2.138 ETKDGv3 21 PBG H5A1 0.533 1.214 1.493 ETKDGv3 22 PBG H2AO -2.956 3.339 0.591 ETKDGv3 23 PBG H7A2 2.086 0.347 -2.080 ETKDGv3 24 PBG H7A1 1.665 1.441 -0.720 ETKDGv3 25 PBG H8A2 2.510 -0.294 0.923 ETKDGv3 26 PBG H8A1 2.948 -1.366 -0.456 ETKDGv3 27 PBG H4AO 5.915 0.496 -1.397 ETKDGv3 28 PBG H12 -4.674 -1.864 0.679 ETKDGv3 29 PBG H11 -4.186 -0.989 -0.666 ETKDGv3 30 #