data_L5A
#
_chem_comp.id L5A
_chem_comp.name "(4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H20 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-02-06
_chem_comp.pdbx_modified_date 2020-02-07
_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 276.328
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L5A
_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 6NVF
_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
L5A C10 C1 C 0 1 N N S N N N 53.815 138.253 22.327 1.474 0.237 -0.092 C10 L5A 1
L5A C11 C2 C 0 1 N N S N N N 55.002 139.056 21.598 3.000 0.218 -0.284 C11 L5A 2
L5A C12 C3 C 0 1 N N N N N N 52.709 139.063 22.206 1.102 1.671 0.339 C12 L5A 3
L5A C01 C4 C 0 1 Y N N N N N 50.877 134.065 22.051 -2.656 -1.472 -0.610 C01 L5A 4
L5A C02 C5 C 0 1 Y N N N N N 50.571 134.098 23.518 -3.441 -0.345 -0.762 C02 L5A 5
L5A C03 C6 C 0 1 Y N N N N N 51.263 135.093 24.428 -2.862 0.858 -1.123 C03 L5A 6
L5A C04 C7 C 0 1 Y N N N N N 52.279 136.055 23.803 -1.497 0.932 -1.331 C04 L5A 7
L5A C05 C8 C 0 1 Y N N N N N 52.566 136.006 22.311 -0.712 -0.195 -1.179 C05 L5A 8
L5A C06 C9 C 0 1 Y N N N N N 51.870 135.014 21.433 -1.291 -1.396 -0.813 C06 L5A 9
L5A C07 C10 C 0 1 N N N N N N 53.540 136.920 21.598 0.775 -0.114 -1.407 C07 L5A 10
L5A C08 C11 C 0 1 N N N N N N 56.317 138.691 22.039 3.637 -0.791 0.674 C08 L5A 11
L5A C09 C12 C 0 1 N N N N N N 56.733 137.278 21.615 5.119 -0.865 0.413 C09 L5A 12
L5A C13 C13 C 0 1 N N N N N N 53.284 140.620 22.069 2.407 2.232 0.957 C13 L5A 13
L5A C14 C14 C 0 1 N N N N N N 54.661 140.546 22.050 3.503 1.640 0.036 C14 L5A 14
L5A C17 C15 C 0 1 N N N N N N 49.564 133.117 24.059 -4.929 -0.426 -0.535 C17 L5A 15
L5A C18 C16 C 0 1 N N N N N N 50.162 132.592 25.346 -5.232 -0.135 0.913 C18 L5A 16
L5A O15 O1 O 0 1 N N N N N N 56.875 136.369 22.475 5.888 -1.691 1.140 O15 L5A 17
L5A O16 O2 O 0 1 N N N N N N 56.942 137.009 20.402 5.616 -0.180 -0.450 O16 L5A 18
L5A O19 O3 O 0 1 N N N N N N 51.112 131.760 25.289 -4.333 0.113 1.681 O19 L5A 19
L5A O20 O4 O 0 1 N N N N N N 49.718 133.028 26.428 -6.502 -0.151 1.349 O20 L5A 20
L5A H1 H1 H 0 1 N N N N N N 54.092 138.063 23.374 1.186 -0.473 0.684 H1 L5A 21
L5A H2 H2 H 0 1 N N N N N N 54.892 138.965 20.507 3.243 -0.042 -1.315 H2 L5A 22
L5A H3 H3 H 0 1 N N N N N N 52.069 138.970 23.096 0.803 2.263 -0.525 H3 L5A 23
L5A H4 H4 H 0 1 N N N N N N 52.133 138.789 21.310 0.304 1.651 1.081 H4 L5A 24
L5A H5 H5 H 0 1 N N N N N N 50.374 133.345 21.423 -3.109 -2.411 -0.329 H5 L5A 25
L5A H6 H6 H 0 1 N N N N N N 51.046 135.123 25.486 -3.476 1.738 -1.242 H6 L5A 26
L5A H7 H7 H 0 1 N N N N N N 52.794 136.772 24.426 -1.045 1.871 -1.613 H7 L5A 27
L5A H8 H8 H 0 1 N N N N N N 52.076 134.979 20.373 -0.678 -2.277 -0.695 H8 L5A 28
L5A H9 H9 H 0 1 N N N N N N 54.495 136.385 21.487 0.988 0.656 -2.148 H9 L5A 29
L5A H10 H10 H 0 1 N N N N N N 53.131 137.150 20.603 1.141 -1.076 -1.767 H10 L5A 30
L5A H11 H11 H 0 1 N N N N N N 57.037 139.407 21.617 3.464 -0.475 1.702 H11 L5A 31
L5A H12 H12 H 0 1 N N N N N N 56.344 138.747 23.137 3.191 -1.773 0.516 H12 L5A 32
L5A H13 H13 H 0 1 N N N N N N 52.951 141.222 22.927 2.415 3.321 0.918 H13 L5A 33
L5A H14 H14 H 0 1 N N N N N N 52.918 141.076 21.137 2.530 1.883 1.982 H14 L5A 34
L5A H15 H15 H 0 1 N N N N N N 55.071 140.747 23.051 4.458 1.599 0.559 H15 L5A 35
L5A H16 H16 H 0 1 N N N N N N 55.075 141.270 21.332 3.592 2.228 -0.877 H16 L5A 36
L5A H17 H17 H 0 1 N N N N N N 48.606 133.620 24.257 -5.433 0.305 -1.166 H17 L5A 37
L5A H18 H18 H 0 1 N N N N N N 49.406 132.295 23.345 -5.280 -1.427 -0.785 H18 L5A 38
L5A H19 H19 H 0 1 N N N N N N 57.137 135.563 22.045 6.834 -1.703 0.937 H19 L5A 39
L5A H20 H20 H 0 1 N N N N N N 50.200 132.639 27.148 -6.647 0.042 2.285 H20 L5A 40
#
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
L5A O16 C09 DOUB N N 1
L5A C06 C01 DOUB Y N 2
L5A C06 C05 SING Y N 3
L5A C11 C08 SING N N 4
L5A C11 C14 SING N N 5
L5A C11 C10 SING N N 6
L5A C07 C05 SING N N 7
L5A C07 C10 SING N N 8
L5A C09 C08 SING N N 9
L5A C09 O15 SING N N 10
L5A C14 C13 SING N N 11
L5A C01 C02 SING Y N 12
L5A C13 C12 SING N N 13
L5A C12 C10 SING N N 14
L5A C05 C04 DOUB Y N 15
L5A C02 C17 SING N N 16
L5A C02 C03 DOUB Y N 17
L5A C04 C03 SING Y N 18
L5A C17 C18 SING N N 19
L5A O19 C18 DOUB N N 20
L5A C18 O20 SING N N 21
L5A C10 H1 SING N N 22
L5A C11 H2 SING N N 23
L5A C12 H3 SING N N 24
L5A C12 H4 SING N N 25
L5A C01 H5 SING N N 26
L5A C03 H6 SING N N 27
L5A C04 H7 SING N N 28
L5A C06 H8 SING N N 29
L5A C07 H9 SING N N 30
L5A C07 H10 SING N N 31
L5A C08 H11 SING N N 32
L5A C08 H12 SING N N 33
L5A C13 H13 SING N N 34
L5A C13 H14 SING N N 35
L5A C14 H15 SING N N 36
L5A C14 H16 SING N N 37
L5A C17 H17 SING N N 38
L5A C17 H18 SING N N 39
L5A O15 H19 SING N N 40
L5A O20 H20 SING N N 41
#
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
L5A SMILES ACDLabs 12.01 C1(C(CC(O)=O)CCC1)Cc2ccc(cc2)CC(O)=O
L5A InChI InChI 1.03 InChI=1S/C16H20O4/c17-15(18)9-12-6-4-11(5-7-12)8-13-2-1-3-14(13)10-16(19)20/h4-7,13-14H,1-3,8-10H2,(H,17,18)(H,19,20)/t13-,14-/m0/s1
L5A InChIKey InChI 1.03 QKXFMUHRVZWRPO-KBPBESRZSA-N
L5A SMILES_CANONICAL CACTVS 3.385 OC(=O)C[C@@H]1CCC[C@H]1Cc2ccc(CC(O)=O)cc2
L5A SMILES CACTVS 3.385 OC(=O)C[CH]1CCC[CH]1Cc2ccc(CC(O)=O)cc2
L5A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(ccc1C[C@@H]2CCC[C@H]2CC(=O)O)CC(=O)O
L5A SMILES "OpenEye OEToolkits" 2.0.7 c1cc(ccc1CC2CCCC2CC(=O)O)CC(=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
L5A "SYSTEMATIC NAME" ACDLabs 12.01 "(4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid"
L5A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[4-[[(1~{S},2~{S})-2-(2-hydroxy-2-oxoethyl)cyclopentyl]methyl]phenyl]ethanoic 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
L5A 'Create component' 2019-02-06 RCSB
L5A 'Initial release' 2020-02-12 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
L5A C10 C 6.897 3.831 1
L5A C11 C 8.267 3.220 2
L5A C12 C 7.054 5.322 3
L5A C01 C 6.897 -0.669 4
L5A C02 C 5.598 -1.419 5
L5A C03 C 4.299 -0.669 6
L5A C04 C 4.299 0.831 7
L5A C05 C 5.598 1.581 8
L5A C06 C 6.897 0.831 9
L5A C07 C 5.598 3.081 10
L5A C08 C 8.579 1.753 11
L5A C09 C 10.006 1.290 12
L5A C13 C 8.521 5.634 13
L5A C14 C 9.271 4.335 14
L5A C17 C 5.598 -2.919 15
L5A C18 C 4.299 -3.669 16
L5A O15 O 10.318 -0.177 17
L5A O16 O 11.121 2.293 18
L5A O19 O 4.299 -5.169 19
L5A O20 O 3.000 -2.919 20
#
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
L5A O16 C09 DOUBLE NONE 1
L5A C06 C01 DOUBLE NONE 2
L5A C06 C05 SINGLE NONE 3
L5A C11 C08 SINGLE BEGINWEDGE 4
L5A C11 C14 SINGLE NONE 5
L5A C11 C10 SINGLE NONE 6
L5A C07 C05 SINGLE NONE 7
L5A C10 C07 SINGLE BEGINDASH 8
L5A C09 C08 SINGLE NONE 9
L5A C09 O15 SINGLE NONE 10
L5A C14 C13 SINGLE NONE 11
L5A C01 C02 SINGLE NONE 12
L5A C13 C12 SINGLE NONE 13
L5A C12 C10 SINGLE NONE 14
L5A C05 C04 DOUBLE NONE 15
L5A C02 C17 SINGLE NONE 16
L5A C02 C03 DOUBLE NONE 17
L5A C04 C03 SINGLE NONE 18
L5A C17 C18 SINGLE NONE 19
L5A O19 C18 DOUBLE NONE 20
L5A C18 O20 SINGLE NONE 21
#
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
L5A MurckoScaffold S1 scaffold c1ccc(CC2CCCC2)cc1 InChI=1S/C12H16/c1-2-6-11(7-3-1)10-12-8-4-5-9-12/h1-3,6-7,12H,4-5,8-10H2 WAAUXNSLVPBVRA-UHFFFAOYSA-N
L5A cyclopentane F1 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
L5A phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
L5A C10 S1 1
L5A C11 S1 1
L5A C12 S1 1
L5A C01 S1 1
L5A C02 S1 1
L5A C03 S1 1
L5A C04 S1 1
L5A C05 S1 1
L5A C06 S1 1
L5A C07 S1 1
L5A C13 S1 1
L5A C14 S1 1
L5A C10 F1 1
L5A C11 F1 1
L5A C14 F1 1
L5A C13 F1 1
L5A C12 F1 1
L5A C01 F2 1
L5A C06 F2 1
L5A C05 F2 1
L5A C04 F2 1
L5A C03 F2 1
L5A C02 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id L5A
_pdbe_chem_comp_rdkit_properties.exactmw 276.136
_pdbe_chem_comp_rdkit_properties.amw 276.332
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 40
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 146.259
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.638
_pdbe_chem_comp_rdkit_properties.CrippenMR 74.038
_pdbe_chem_comp_rdkit_properties.chi0v 9.633
_pdbe_chem_comp_rdkit_properties.chi1v 5.066
_pdbe_chem_comp_rdkit_properties.chi2v 1.954
_pdbe_chem_comp_rdkit_properties.chi3v 1.954
_pdbe_chem_comp_rdkit_properties.chi4v 1.235
_pdbe_chem_comp_rdkit_properties.chi0n 29.633
_pdbe_chem_comp_rdkit_properties.chi1n 14.883
_pdbe_chem_comp_rdkit_properties.chi2n 1.954
_pdbe_chem_comp_rdkit_properties.chi3n 1.954
_pdbe_chem_comp_rdkit_properties.chi4n 1.235
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 3.487
_pdbe_chem_comp_rdkit_properties.kappa2 6.548
_pdbe_chem_comp_rdkit_properties.kappa3 4.083
_pdbe_chem_comp_rdkit_properties.Phi 1.142
#
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
L5A UniChem PDBe L5A
L5A UniChem PubChem 145915895
#
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
L5A C10 -1.695 -1.344 -0.103 ETKDGv3 1
L5A C11 -1.943 0.181 -0.192 ETKDGv3 2
L5A C12 -3.058 -1.993 -0.324 ETKDGv3 3
L5A C01 2.709 -1.362 0.583 ETKDGv3 4
L5A C02 3.258 -0.232 -0.205 ETKDGv3 5
L5A C03 2.535 0.278 -1.218 ETKDGv3 6
L5A C04 1.215 -0.293 -1.553 ETKDGv3 7
L5A C05 0.719 -1.322 -0.843 ETKDGv3 8
L5A C06 1.512 -1.879 0.280 ETKDGv3 9
L5A C07 -0.658 -1.864 -1.123 ETKDGv3 10
L5A C08 -1.176 0.949 0.906 ETKDGv3 11
L5A C09 -1.217 2.427 0.670 ETKDGv3 12
L5A C13 -4.062 -0.994 0.212 ETKDGv3 13
L5A C14 -3.467 0.374 -0.079 ETKDGv3 14
L5A C17 4.576 0.378 0.181 ETKDGv3 15
L5A C18 4.362 1.467 1.181 ETKDGv3 16
L5A O15 -2.117 3.220 1.375 ETKDGv3 17
L5A O16 -0.454 2.950 -0.187 ETKDGv3 18
L5A O19 4.398 1.209 2.414 ETKDGv3 19
L5A O20 4.074 2.758 0.749 ETKDGv3 20
L5A H1 -1.361 -1.619 0.924 ETKDGv3 21
L5A H2 -1.618 0.556 -1.190 ETKDGv3 22
L5A H3 -3.252 -2.152 -1.409 ETKDGv3 23
L5A H4 -3.137 -2.967 0.206 ETKDGv3 24
L5A H5 3.274 -1.771 1.412 ETKDGv3 25
L5A H6 2.903 1.120 -1.790 ETKDGv3 26
L5A H7 0.645 0.147 -2.362 ETKDGv3 27
L5A H8 1.119 -2.700 0.866 ETKDGv3 28
L5A H9 -0.617 -2.973 -1.066 ETKDGv3 29
L5A H10 -0.977 -1.608 -2.159 ETKDGv3 30
L5A H11 -1.604 0.718 1.906 ETKDGv3 31
L5A H12 -0.112 0.632 0.924 ETKDGv3 32
L5A H13 -5.056 -1.119 -0.271 ETKDGv3 33
L5A H14 -4.169 -1.129 1.311 ETKDGv3 34
L5A H15 -3.867 0.749 -1.048 ETKDGv3 35
L5A H16 -3.760 1.094 0.716 ETKDGv3 36
L5A H17 5.243 -0.401 0.610 ETKDGv3 37
L5A H18 5.091 0.793 -0.713 ETKDGv3 38
L5A H19 -2.164 4.219 1.216 ETKDGv3 39
L5A H20 3.907 3.504 1.414 ETKDGv3 40
#