data_PBE
#
_chem_comp.id PBE
_chem_comp.name 1,1-DIMETHYL-PROLINIUM
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H14 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "PROLINE BETAINE"
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2000-04-20
_chem_comp.pdbx_modified_date 2023-11-03
_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 144.192
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PBE
_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 1R9Q
_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
PBE N N N 1 1 N N N Y Y N 26.536 23.085 73.309 -0.764 0.678 0.037 N PBE 1
PBE CD CD C 0 1 N N N N N N 27.208 21.909 73.873 -1.859 -0.005 -0.685 CD PBE 2
PBE CA CA C 0 1 N N S Y N N 25.199 22.592 73.243 0.136 -0.345 0.599 CA PBE 3
PBE CB CB C 0 1 N N N N N N 25.231 21.235 72.655 -0.447 -1.723 0.227 CB PBE 4
PBE CG CG C 0 1 N N N N N N 26.537 20.698 73.255 -1.943 -1.410 -0.037 CG PBE 5
PBE CE CE C 0 1 N N N N N N 26.734 24.254 74.184 -0.018 1.535 -0.894 CE PBE 6
PBE CF CF C 0 1 N N N N N N 27.153 23.387 72.007 -1.323 1.495 1.122 CF PBE 7
PBE C C C 0 1 N N N Y N Y 24.247 22.742 74.174 1.516 -0.197 0.012 C PBE 8
PBE O O O 0 1 N N N Y N Y 24.492 22.362 75.307 1.666 -0.193 -1.187 O PBE 9
PBE OXT OXT O 0 1 N Y N Y N Y 23.122 23.154 73.943 2.579 -0.071 0.822 OXT PBE 10
PBE HD1 1HD H 0 1 N N N N N N 27.128 21.892 74.970 -2.797 0.532 -0.548 HD1 PBE 11
PBE HD2 2HD H 0 1 N N N N N N 28.280 21.923 73.628 -1.620 -0.090 -1.745 HD2 PBE 12
PBE HA HA H 0 1 N N N Y N N 24.762 23.401 72.639 0.181 -0.242 1.683 HA PBE 13
PBE HB1 1HB H 0 1 N N N N N N 25.195 21.216 71.556 -0.340 -2.424 1.056 HB1 PBE 14
PBE HB2 2HB H 0 1 N N N N N N 24.357 20.631 72.940 0.030 -2.113 -0.672 HB2 PBE 15
PBE HG1 1HG H 0 1 N N N N N N 26.355 19.905 73.995 -2.506 -1.377 0.896 HG1 PBE 16
PBE HG2 2HG H 0 1 N N N N N N 27.173 20.248 72.478 -2.377 -2.133 -0.728 HG2 PBE 17
PBE HE1 1HE H 0 1 N N N N N N 25.893 24.952 74.059 0.891 1.892 -0.410 HE1 PBE 18
PBE HE2 2HE H 0 1 N N N N N N 27.673 24.759 73.914 0.244 0.963 -1.784 HE2 PBE 19
PBE HE3 3HE H 0 1 N N N N N N 26.783 23.924 75.232 -0.636 2.387 -1.179 HE3 PBE 20
PBE HF1 1HF H 0 1 N N N N N N 27.854 22.583 71.738 -1.985 2.253 0.703 HF1 PBE 21
PBE HF2 2HF H 0 1 N N N N N N 27.696 24.341 72.071 -1.885 0.858 1.804 HF2 PBE 22
PBE HF3 3HF H 0 1 N N N N N N 26.370 23.462 71.238 -0.512 1.981 1.665 HF3 PBE 23
PBE HXT HXT H 0 1 N Y N Y N Y 22.598 23.105 74.734 3.465 0.024 0.445 HXT PBE 24
#
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
PBE N CD SING N N 1
PBE N CA SING N N 2
PBE N CE SING N N 3
PBE N CF SING N N 4
PBE CD CG SING N N 5
PBE CD HD1 SING N N 6
PBE CD HD2 SING N N 7
PBE CA CB SING N N 8
PBE CA C SING N N 9
PBE CA HA SING N N 10
PBE CB CG SING N N 11
PBE CB HB1 SING N N 12
PBE CB HB2 SING N N 13
PBE CG HG1 SING N N 14
PBE CG HG2 SING N N 15
PBE CE HE1 SING N N 16
PBE CE HE2 SING N N 17
PBE CE HE3 SING N N 18
PBE CF HF1 SING N N 19
PBE CF HF2 SING N N 20
PBE CF HF3 SING N N 21
PBE C O DOUB N N 22
PBE C OXT SING N N 23
PBE OXT HXT SING N N 24
#
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
PBE SMILES ACDLabs 10.04 O=C(O)C1[N+](C)(C)CCC1
PBE SMILES_CANONICAL CACTVS 3.341 C[N+]1(C)CCC[C@H]1C(O)=O
PBE SMILES CACTVS 3.341 C[N+]1(C)CCC[CH]1C(O)=O
PBE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[N+]1(CCC[C@H]1C(=O)O)C
PBE SMILES "OpenEye OEToolkits" 1.5.0 C[N+]1(CCCC1C(=O)O)C
PBE InChI InChI 1.03 InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/p+1/t6-/m0/s1
PBE InChIKey InChI 1.03 CMUNUTVVOOHQPW-LURJTMIESA-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
PBE "SYSTEMATIC NAME" ACDLabs 10.04 (2S)-2-carboxy-1,1-dimethylpyrrolidinium
PBE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-1,1-dimethylpyrrolidin-1-ium-2-carboxylic 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
PBE 'Create component' 2000-04-20 RCSB
PBE 'Modify descriptor' 2011-06-04 RCSB
PBE 'Modify synonyms' 2020-06-05 PDBE
PBE 'Modify backbone' 2023-11-03 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PBE
_pdbx_chem_comp_synonyms.name "PROLINE BETAINE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id PBE
_pdbe_chem_comp_synonyms.name 'PROLINE BETAINE'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
PBE N N 4.213 -0.547 1
PBE CD C 3.000 0.334 2
PBE CA C 5.427 0.334 3
PBE CB C 4.963 1.761 4
PBE CG C 3.463 1.761 5
PBE CE C 3.332 -1.761 6
PBE CF C 5.095 -1.761 7
PBE C C 6.854 -0.129 8
PBE O O 7.968 0.875 9
PBE OXT O 7.165 -1.596 10
#
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
PBE N CD SINGLE NONE 1
PBE N CA SINGLE NONE 2
PBE N CE SINGLE NONE 3
PBE N CF SINGLE NONE 4
PBE CD CG SINGLE NONE 5
PBE CA CB SINGLE NONE 6
PBE CA C SINGLE BEGINWEDGE 7
PBE CB CG SINGLE NONE 8
PBE C O DOUBLE NONE 9
PBE C OXT SINGLE NONE 10
#
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
PBE MurckoScaffold S1 scaffold 'C1CC[NH2+]C1' InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/p+1 RWRDLPDLKQPQOW-UHFFFAOYSA-O
PBE peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
PBE Z2856434905 F2 fragment 'CN1CCC[C@@H]1CO' InChI=1S/C6H13NO/c1-7-4-2-3-6(7)5-8/h6,8H,2-5H2,1H3/t6-/m1/s1 VCOJPHPOVDIRJK-ZCFIWIBFSA-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
PBE N S1 1
PBE CD S1 1
PBE CA S1 1
PBE CB S1 1
PBE CG S1 1
PBE O F1 1
PBE C F1 1
PBE CA F1 1
PBE N F1 1
PBE CE F2 1
PBE N F2 1
PBE CD F2 1
PBE CG F2 1
PBE CB F2 1
PBE CA F2 1
PBE C F2 1
PBE OXT F2 1
PBE CF F2 2
PBE N F2 2
PBE CD F2 2
PBE CG F2 2
PBE CB F2 2
PBE CA F2 2
PBE C F2 2
PBE OXT F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id PBE
_pdbe_chem_comp_rdkit_properties.exactmw 144.102
_pdbe_chem_comp_rdkit_properties.amw 144.194
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.857
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 80.605
_pdbe_chem_comp_rdkit_properties.tpsa 37.300
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.310
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.633
_pdbe_chem_comp_rdkit_properties.chi0v 4.764
_pdbe_chem_comp_rdkit_properties.chi1v 2.303
_pdbe_chem_comp_rdkit_properties.chi2v 0.933
_pdbe_chem_comp_rdkit_properties.chi3v 0.933
_pdbe_chem_comp_rdkit_properties.chi4v 0.499
_pdbe_chem_comp_rdkit_properties.chi0n 18.764
_pdbe_chem_comp_rdkit_properties.chi1n 9.211
_pdbe_chem_comp_rdkit_properties.chi2n 0.933
_pdbe_chem_comp_rdkit_properties.chi3n 0.933
_pdbe_chem_comp_rdkit_properties.chi4n 0.499
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 1.221
_pdbe_chem_comp_rdkit_properties.kappa2 2.235
_pdbe_chem_comp_rdkit_properties.kappa3 1.138
_pdbe_chem_comp_rdkit_properties.Phi 0.273
#
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
PBE UniChem PDBe PBE
PBE UniChem ChEBI 44813
PBE UniChem ZINC ZINC000002528042
PBE UniChem fdasrs 8DQ7SQ4VA9
PBE UniChem SureChEMBL SCHEMBL578113
PBE UniChem Nikkaji J5.947A
PBE UniChem MetaboLights MTBLC44813
PBE UniChem BRENDA 208058
PBE UniChem BRENDA 208059
PBE UniChem BRENDA 88134
PBE UniChem Nikkaji J342.906G
PBE UniChem PubChem 448301
#
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
PBE N -0.560 -0.354 0.176 ETKDGv3 1
PBE CD -1.425 0.778 -0.230 ETKDGv3 2
PBE CA 0.800 0.088 -0.235 ETKDGv3 3
PBE CB 0.855 1.602 -0.022 ETKDGv3 4
PBE CG -0.595 2.057 -0.112 ETKDGv3 5
PBE CE -0.960 -1.594 -0.528 ETKDGv3 6
PBE CF -0.679 -0.566 1.644 ETKDGv3 7
PBE C 1.936 -0.664 0.427 ETKDGv3 8
PBE O 2.392 -0.299 1.545 ETKDGv3 9
PBE OXT 2.456 -1.797 -0.190 ETKDGv3 10
PBE HD1 -1.744 0.677 -1.294 ETKDGv3 11
PBE HD2 -2.354 0.851 0.380 ETKDGv3 12
PBE HA 0.923 -0.066 -1.334 ETKDGv3 13
PBE HB1 1.481 2.093 -0.799 ETKDGv3 14
PBE HB2 1.258 1.863 0.981 ETKDGv3 15
PBE HG1 -0.751 2.711 -0.998 ETKDGv3 16
PBE HG2 -0.880 2.616 0.806 ETKDGv3 17
PBE HE1 -0.303 -2.443 -0.236 ETKDGv3 18
PBE HE2 -0.891 -1.477 -1.632 ETKDGv3 19
PBE HE3 -2.010 -1.866 -0.280 ETKDGv3 20
PBE HF1 -0.347 0.331 2.211 ETKDGv3 21
PBE HF2 -0.073 -1.436 1.978 ETKDGv3 22
PBE HF3 -1.733 -0.779 1.930 ETKDGv3 23
PBE HXT 3.204 -2.326 0.241 ETKDGv3 24
#