data_LPB
#
_chem_comp.id LPB
_chem_comp.name "5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H14 O2 S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-09-08
_chem_comp.pdbx_modified_date 2011-09-08
_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 206.326
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LPB
_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 1HPC
_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
LPB O1 O1 O 0 1 N N N N N N 23.007 -8.115 9.812 4.654 0.943 -0.780 O1 LPB 1
LPB O2 O2 O 0 1 N N N N N N 21.485 -9.563 8.998 5.703 -0.801 0.082 O2 LPB 2
LPB C1 C1 C 0 1 N N N N N N 22.673 -9.251 9.569 4.592 -0.083 -0.144 C1 LPB 3
LPB C2 C2 C 0 1 N N N N N N 23.538 -10.439 9.884 3.267 -0.555 0.397 C2 LPB 4
LPB C3 C3 C 0 1 N N N N N N 23.813 -10.759 11.372 2.172 0.438 0.001 C3 LPB 5
LPB C4 C4 C 0 1 N N N N N N 25.273 -11.223 11.550 0.826 -0.041 0.550 C4 LPB 6
LPB C5 C5 C 0 1 N N N N N N 25.352 -12.743 11.325 -0.269 0.951 0.155 C5 LPB 7
LPB C6 C6 C 0 1 N N S N N N 26.040 -13.195 10.002 -1.614 0.472 0.704 C6 LPB 8
LPB C7 C7 C 0 1 N N N N N N 26.967 -14.432 10.070 -2.682 1.519 0.418 C7 LPB 9
LPB C8 C8 C 0 1 N N N N N N 26.447 -15.539 9.169 -3.851 1.134 -0.491 C8 LPB 10
LPB S8 S8 S 0 1 N N N N N N 24.668 -15.396 9.010 -4.109 -0.674 -0.243 S8 LPB 11
LPB S6 S6 S 0 1 N N N N N N 24.887 -13.394 8.574 -2.080 -1.107 -0.109 S6 LPB 12
LPB HO2 HO2 H 0 1 N N N N N N 20.993 -8.767 8.834 6.530 -0.458 -0.285 HO2 LPB 13
LPB H21 H21 H 0 1 N N N N N N 23.035 -11.320 9.458 3.034 -1.536 -0.017 H21 LPB 14
LPB H22 H22 H 0 1 N N N N N N 24.515 -10.254 9.414 3.321 -0.622 1.484 H22 LPB 15
LPB H31 H31 H 0 1 N N N N N N 23.642 -9.855 11.976 2.404 1.419 0.415 H31 LPB 16
LPB H32 H32 H 0 1 N N N N N N 23.134 -11.559 11.703 2.118 0.505 -1.085 H32 LPB 17
LPB H41 H41 H 0 1 N N N N N N 25.915 -10.709 10.819 0.594 -1.023 0.137 H41 LPB 18
LPB H42 H42 H 0 1 N N N N N N 25.614 -10.983 12.568 0.881 -0.109 1.637 H42 LPB 19
LPB H51 H51 H 0 1 N N N N N N 25.928 -13.170 12.159 -0.036 1.933 0.569 H51 LPB 20
LPB H52 H52 H 0 1 N N N N N N 24.322 -13.128 11.309 -0.323 1.019 -0.932 H52 LPB 21
LPB H6 H6 H 0 1 N N N N N N 26.696 -12.328 9.834 -1.534 0.317 1.780 H6 LPB 22
LPB H71 H71 H 0 1 N N N N N N 27.976 -14.144 9.741 -3.097 1.837 1.374 H71 LPB 23
LPB H72 H72 H 0 1 N N N N N N 27.003 -14.798 11.107 -2.188 2.383 -0.026 H72 LPB 24
LPB H81 H81 H 0 1 N N N N N N 26.912 -15.452 8.176 -4.747 1.684 -0.204 H81 LPB 25
LPB H82 H82 H 0 1 N N N N N N 26.698 -16.516 9.607 -3.601 1.338 -1.532 H82 LPB 26
#
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
LPB O1 C1 DOUB N N 1
LPB O2 C1 SING N N 2
LPB O2 HO2 SING N N 3
LPB C1 C2 SING N N 4
LPB C2 C3 SING N N 5
LPB C2 H21 SING N N 6
LPB C2 H22 SING N N 7
LPB C3 C4 SING N N 8
LPB C3 H31 SING N N 9
LPB C3 H32 SING N N 10
LPB C4 C5 SING N N 11
LPB C4 H41 SING N N 12
LPB C4 H42 SING N N 13
LPB C5 C6 SING N N 14
LPB C5 H51 SING N N 15
LPB C5 H52 SING N N 16
LPB C6 C7 SING N N 17
LPB C6 S6 SING N N 18
LPB C6 H6 SING N N 19
LPB C7 C8 SING N N 20
LPB C7 H71 SING N N 21
LPB C7 H72 SING N N 22
LPB C8 S8 SING N N 23
LPB C8 H81 SING N N 24
LPB C8 H82 SING N N 25
LPB S8 S6 SING N N 26
#
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
LPB SMILES ACDLabs 12.01 O=C(O)CCCCC1SSCC1
LPB InChI InChI 1.03 InChI=1S/C8H14O2S2/c9-8(10)4-2-1-3-7-5-6-11-12-7/h7H,1-6H2,(H,9,10)/t7-/m0/s1
LPB InChIKey InChI 1.03 AGBQKNBQESQNJD-ZETCQYMHSA-N
LPB SMILES_CANONICAL CACTVS 3.370 OC(=O)CCCC[C@H]1CCSS1
LPB SMILES CACTVS 3.370 OC(=O)CCCC[CH]1CCSS1
LPB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 C1CSS[C@H]1CCCCC(=O)O
LPB SMILES "OpenEye OEToolkits" 1.7.2 C1CSSC1CCCCC(=O)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
LPB "SYSTEMATIC NAME" ACDLabs 12.01 "5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid"
LPB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid"
#
_pdbx_chem_comp_audit.comp_id LPB
_pdbx_chem_comp_audit.action_type 'Create component'
_pdbx_chem_comp_audit.date 2011-09-08
_pdbx_chem_comp_audit.processing_site RCSB
#
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
LPB O1 O 3.884 1.251 1
LPB O2 O 4.687 -1.220 2
LPB C1 C 4.999 0.247 3
LPB C2 C 6.426 0.711 4
LPB C3 C 7.540 -0.293 5
LPB C4 C 8.967 0.171 6
LPB C5 C 10.082 -0.833 7
LPB C6 C 11.508 -0.369 8
LPB C7 C 12.722 -1.251 9
LPB C8 C 13.935 -0.369 10
LPB S8 S 13.472 1.057 11
LPB S6 S 11.972 1.057 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
LPB O1 C1 DOUBLE NONE 1
LPB O2 C1 SINGLE NONE 2
LPB C1 C2 SINGLE NONE 3
LPB C2 C3 SINGLE NONE 4
LPB C3 C4 SINGLE NONE 5
LPB C4 C5 SINGLE NONE 6
LPB C6 C5 SINGLE BEGINDASH 7
LPB C6 C7 SINGLE NONE 8
LPB C6 S6 SINGLE NONE 9
LPB C7 C8 SINGLE NONE 10
LPB C8 S8 SINGLE NONE 11
LPB S8 S6 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
LPB MurckoScaffold S1 scaffold C1CSSC1 InChI=1S/C3H6S2/c1-2-4-5-3-1/h1-3H2 MUZIZEZCKKMZRT-UHFFFAOYSA-N
LPB dithiolane F1 fragment C1CSSC1 InChI=1S/C3H6S2/c1-2-4-5-3-1/h1-3H2 MUZIZEZCKKMZRT-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
LPB C6 S1 1
LPB C7 S1 1
LPB C8 S1 1
LPB S8 S1 1
LPB S6 S1 1
LPB S8 F1 1
LPB C8 F1 1
LPB C7 F1 1
LPB C6 F1 1
LPB S6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LPB
_pdbe_chem_comp_rdkit_properties.exactmw 206.044
_pdbe_chem_comp_rdkit_properties.amw 206.332
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_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 100.646
_pdbe_chem_comp_rdkit_properties.tpsa 37.300
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.785
_pdbe_chem_comp_rdkit_properties.CrippenMR 54.558
_pdbe_chem_comp_rdkit_properties.chi0v 7.266
_pdbe_chem_comp_rdkit_properties.chi1v 4.883
_pdbe_chem_comp_rdkit_properties.chi2v 2.374
_pdbe_chem_comp_rdkit_properties.chi3v 2.374
_pdbe_chem_comp_rdkit_properties.chi4v 1.642
_pdbe_chem_comp_rdkit_properties.chi0n 19.633
_pdbe_chem_comp_rdkit_properties.chi1n 9.641
_pdbe_chem_comp_rdkit_properties.chi2n 0.734
_pdbe_chem_comp_rdkit_properties.chi3n 0.734
_pdbe_chem_comp_rdkit_properties.chi4n 0.373
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.170
_pdbe_chem_comp_rdkit_properties.kappa1 2.217
_pdbe_chem_comp_rdkit_properties.kappa2 5.754
_pdbe_chem_comp_rdkit_properties.kappa3 4.259
_pdbe_chem_comp_rdkit_properties.Phi 1.063
#
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
LPB UniChem ChEMBL CHEMBL1234071
LPB UniChem PDBe LPB
LPB UniChem ChEBI 43796
LPB UniChem ZINC ZINC000001532729
LPB UniChem eMolecules 10678602
LPB UniChem fdasrs J2Y905FQ57
LPB UniChem HMDB HMDB0014312
LPB UniChem 'PubChem TPHARMA' 15171831
LPB UniChem ACTor 1077-27-6
LPB UniChem Nikkaji J231.967E
LPB UniChem MetaboLights MTBLC43796
LPB UniChem BRENDA 130842
LPB UniChem BRENDA 132268
LPB UniChem BRENDA 32966
LPB UniChem BRENDA 57776
LPB UniChem ChemicalBook CB7855122
LPB UniChem 'Probes And Drugs' PD132143
LPB UniChem SureChEMBL SCHEMBL2128472
LPB UniChem PubChem 445125
LPB UniChem Mcule MCULE-4196115946
#
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
LPB O1 4.262 -0.836 1.115 ETKDGv3 1
LPB O2 3.535 1.292 0.644 ETKDGv3 2
LPB C1 3.631 -0.063 0.345 ETKDGv3 3
LPB C2 2.953 -0.609 -0.875 ETKDGv3 4
LPB C3 1.619 -1.284 -0.530 ETKDGv3 5
LPB C4 0.562 -0.276 -0.057 ETKDGv3 6
LPB C5 -0.780 -0.973 0.212 ETKDGv3 7
LPB C6 -1.844 0.001 0.751 ETKDGv3 8
LPB C7 -2.236 1.079 -0.275 ETKDGv3 9
LPB C8 -3.709 1.407 -0.133 ETKDGv3 10
LPB S8 -4.594 -0.162 -0.202 ETKDGv3 11
LPB S6 -3.314 -0.940 1.308 ETKDGv3 12
LPB HO2 3.976 1.674 1.472 ETKDGv3 13
LPB H21 3.623 -1.356 -1.352 ETKDGv3 14
LPB H22 2.788 0.208 -1.610 ETKDGv3 15
LPB H31 1.245 -1.798 -1.443 ETKDGv3 16
LPB H32 1.783 -2.058 0.252 ETKDGv3 17
LPB H41 0.429 0.504 -0.838 ETKDGv3 18
LPB H42 0.910 0.216 0.877 ETKDGv3 19
LPB H51 -1.151 -1.454 -0.720 ETKDGv3 20
LPB H52 -0.618 -1.774 0.967 ETKDGv3 21
LPB H6 -1.439 0.506 1.656 ETKDGv3 22
LPB H71 -2.057 0.721 -1.314 ETKDGv3 23
LPB H72 -1.629 1.997 -0.120 ETKDGv3 24
LPB H81 -4.040 2.063 -0.966 ETKDGv3 25
LPB H82 -3.907 1.915 0.835 ETKDGv3 26
#