data_4Z9
#
_chem_comp.id 4Z9
_chem_comp.name "(2R)-2-hydroxy-3-(1H-indol-3-yl)propanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H11 N O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-06-30
_chem_comp.pdbx_modified_date 2016-08-05
_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 205.210
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 4Z9
_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 5CAK
_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
4Z9 C8 C1 C 0 1 Y N N N N N 32.400 75.237 62.250 2.474 0.687 -0.008 C8 4Z9 1
4Z9 C5 C2 C 0 1 Y N N N N N 32.039 77.176 60.296 2.780 -2.064 0.205 C5 4Z9 2
4Z9 C9 C3 C 0 1 Y N N N N N 33.153 76.473 62.307 1.385 -0.175 -0.235 C9 4Z9 3
4Z9 O12 O1 O 0 1 N N N N N N 38.462 78.218 64.746 -4.293 0.126 0.313 O12 4Z9 4
4Z9 C10 C4 C 0 1 N N N N N N 37.256 78.010 64.831 -3.300 -0.525 0.087 C10 4Z9 5
4Z9 O11 O2 O 0 1 N N N N N N 36.785 78.402 66.050 -3.408 -1.751 -0.447 O11 4Z9 6
4Z9 C13 C5 C 0 1 N N R N N N 36.420 77.071 63.956 -1.941 0.041 0.406 C13 4Z9 7
4Z9 O14 O3 O 0 1 N N N N N N 36.879 77.171 62.624 -2.091 1.299 1.068 O14 4Z9 8
4Z9 C15 C6 C 0 1 N N N N N N 34.928 77.444 63.969 -1.153 0.238 -0.891 C15 4Z9 9
4Z9 C3 C7 C 0 1 Y N N N N N 34.005 76.396 63.485 0.248 0.688 -0.565 C3 4Z9 10
4Z9 C2 C8 C 0 1 Y N N N N N 33.736 75.158 64.075 0.690 1.954 -0.522 C2 4Z9 11
4Z9 N1 N1 N 0 1 Y N N N N N 32.780 74.451 63.340 2.018 1.974 -0.191 N1 4Z9 12
4Z9 C7 C9 C 0 1 Y N N N N N 31.485 74.991 61.210 3.711 0.148 0.325 C7 4Z9 13
4Z9 C6 C10 C 0 1 Y N N N N N 31.315 75.972 60.243 3.857 -1.218 0.429 C6 4Z9 14
4Z9 C4 C11 C 0 1 Y N N N N N 32.950 77.432 61.309 1.554 -1.556 -0.119 C4 4Z9 15
4Z9 H1 H1 H 0 1 N N N N N N 31.882 77.920 59.529 2.910 -3.132 0.295 H1 4Z9 16
4Z9 H2 H2 H 0 1 N N N N N N 37.500 78.752 66.568 -4.301 -2.071 -0.634 H2 4Z9 17
4Z9 H3 H3 H 0 1 N N N N N N 36.532 76.042 64.328 -1.403 -0.649 1.056 H3 4Z9 18
4Z9 H4 H4 H 0 1 N N N N N N 37.722 77.609 62.611 -2.562 1.964 0.547 H4 4Z9 19
4Z9 H5 H5 H 0 1 N N N N N N 34.795 78.332 63.334 -1.115 -0.703 -1.439 H5 4Z9 20
4Z9 H6 H6 H 0 1 N N N N N N 34.649 77.689 65.004 -1.645 0.995 -1.503 H6 4Z9 21
4Z9 H7 H7 H 0 1 N N N N N N 34.204 74.796 64.978 0.088 2.829 -0.720 H7 4Z9 22
4Z9 H8 H8 H 0 1 N N N N N N 32.429 73.540 63.557 2.558 2.774 -0.099 H8 4Z9 23
4Z9 H9 H9 H 0 1 N N N N N N 30.931 74.065 61.165 4.556 0.798 0.501 H9 4Z9 24
4Z9 H10 H10 H 0 1 N N N N N N 30.615 75.808 59.437 4.820 -1.635 0.684 H10 4Z9 25
4Z9 H11 H11 H 0 1 N N N N N N 33.498 78.363 61.328 0.720 -2.220 -0.292 H11 4Z9 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
4Z9 C6 C5 DOUB Y N 1
4Z9 C6 C7 SING Y N 2
4Z9 C5 C4 SING Y N 3
4Z9 C7 C8 DOUB Y N 4
4Z9 C4 C9 DOUB Y N 5
4Z9 C8 C9 SING Y N 6
4Z9 C8 N1 SING Y N 7
4Z9 C9 C3 SING Y N 8
4Z9 O14 C13 SING N N 9
4Z9 N1 C2 SING Y N 10
4Z9 C3 C15 SING N N 11
4Z9 C3 C2 DOUB Y N 12
4Z9 C13 C15 SING N N 13
4Z9 C13 C10 SING N N 14
4Z9 O12 C10 DOUB N N 15
4Z9 C10 O11 SING N N 16
4Z9 C5 H1 SING N N 17
4Z9 O11 H2 SING N N 18
4Z9 C13 H3 SING N N 19
4Z9 O14 H4 SING N N 20
4Z9 C15 H5 SING N N 21
4Z9 C15 H6 SING N N 22
4Z9 C2 H7 SING N N 23
4Z9 N1 H8 SING N N 24
4Z9 C7 H9 SING N N 25
4Z9 C6 H10 SING N N 26
4Z9 C4 H11 SING N N 27
#
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
4Z9 SMILES ACDLabs 12.01 c12c(c(CC(C(=O)O)O)cn1)cccc2
4Z9 InChI InChI 1.03 InChI=1S/C11H11NO3/c13-10(11(14)15)5-7-6-12-9-4-2-1-3-8(7)9/h1-4,6,10,12-13H,5H2,(H,14,15)/t10-/m1/s1
4Z9 InChIKey InChI 1.03 XGILAAMKEQUXLS-SNVBAGLBSA-N
4Z9 SMILES_CANONICAL CACTVS 3.385 O[C@H](Cc1c[nH]c2ccccc12)C(O)=O
4Z9 SMILES CACTVS 3.385 O[CH](Cc1c[nH]c2ccccc12)C(O)=O
4Z9 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1ccc2c(c1)c(c[nH]2)C[C@H](C(=O)O)O
4Z9 SMILES "OpenEye OEToolkits" 1.9.2 c1ccc2c(c1)c(c[nH]2)CC(C(=O)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
4Z9 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-hydroxy-3-(1H-indol-3-yl)propanoic acid"
4Z9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2R)-3-(1H-indol-3-yl)-2-oxidanyl-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
4Z9 'Create component' 2015-06-30 RCSB
4Z9 'Initial release' 2016-08-10 RCSB
#
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
4Z9 C8 C 5.598 -2.485 1
4Z9 C5 C 3.000 -0.985 2
4Z9 C9 C 5.598 -0.985 3
4Z9 O12 O 10.885 2.942 4
4Z9 C10 C 9.417 2.633 5
4Z9 O11 O 8.415 3.749 6
4Z9 C13 C 8.951 1.207 7
4Z9 O14 O 9.953 0.091 8
4Z9 C15 C 7.483 0.898 9
4Z9 C3 C 7.018 -0.528 10
4Z9 C2 C 7.893 -1.735 11
4Z9 N1 N 7.018 -2.942 12
4Z9 C7 C 4.299 -3.235 13
4Z9 C6 C 3.000 -2.485 14
4Z9 C4 C 4.299 -0.235 15
#
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
4Z9 C6 C5 DOUBLE NONE 1
4Z9 C6 C7 SINGLE NONE 2
4Z9 C5 C4 SINGLE NONE 3
4Z9 C7 C8 DOUBLE NONE 4
4Z9 C4 C9 DOUBLE NONE 5
4Z9 C8 C9 SINGLE NONE 6
4Z9 C8 N1 SINGLE NONE 7
4Z9 C9 C3 SINGLE NONE 8
4Z9 C13 O14 SINGLE BEGINDASH 9
4Z9 N1 C2 SINGLE NONE 10
4Z9 C3 C15 SINGLE NONE 11
4Z9 C3 C2 DOUBLE NONE 12
4Z9 C13 C15 SINGLE NONE 13
4Z9 C13 C10 SINGLE NONE 14
4Z9 O12 C10 DOUBLE NONE 15
4Z9 C10 O11 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
4Z9 MurckoScaffold S1 scaffold 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
4Z9 indole F1 fragment 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
4Z9 phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
4Z9 pyrrole F3 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
4Z9 C8 S1 1
4Z9 C5 S1 1
4Z9 C9 S1 1
4Z9 C3 S1 1
4Z9 C2 S1 1
4Z9 N1 S1 1
4Z9 C7 S1 1
4Z9 C6 S1 1
4Z9 C4 S1 1
4Z9 C8 F1 1
4Z9 C9 F1 1
4Z9 C3 F1 1
4Z9 C2 F1 1
4Z9 N1 F1 1
4Z9 C4 F1 1
4Z9 C5 F1 1
4Z9 C6 F1 1
4Z9 C7 F1 1
4Z9 C8 F2 1
4Z9 C7 F2 1
4Z9 C6 F2 1
4Z9 C5 F2 1
4Z9 C4 F2 1
4Z9 C9 F2 1
4Z9 C8 F3 1
4Z9 C9 F3 1
4Z9 C3 F3 1
4Z9 C2 F3 1
4Z9 N1 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 4Z9
_pdbe_chem_comp_rdkit_properties.exactmw 205.074
_pdbe_chem_comp_rdkit_properties.amw 205.213
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_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 0.182
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 101.853
_pdbe_chem_comp_rdkit_properties.tpsa 73.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.673
_pdbe_chem_comp_rdkit_properties.CrippenMR 53.173
_pdbe_chem_comp_rdkit_properties.chi0v 7.172
_pdbe_chem_comp_rdkit_properties.chi1v 3.810
_pdbe_chem_comp_rdkit_properties.chi2v 1.621
_pdbe_chem_comp_rdkit_properties.chi3v 1.621
_pdbe_chem_comp_rdkit_properties.chi4v 0.993
_pdbe_chem_comp_rdkit_properties.chi0n 18.172
_pdbe_chem_comp_rdkit_properties.chi1n 9.073
_pdbe_chem_comp_rdkit_properties.chi2n 1.621
_pdbe_chem_comp_rdkit_properties.chi3n 1.621
_pdbe_chem_comp_rdkit_properties.chi4n 0.993
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.810
_pdbe_chem_comp_rdkit_properties.kappa1 3.089
_pdbe_chem_comp_rdkit_properties.kappa2 3.744
_pdbe_chem_comp_rdkit_properties.kappa3 1.845
_pdbe_chem_comp_rdkit_properties.Phi 0.771
#
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
4Z9 UniChem ChEBI 55528
4Z9 UniChem ZINC ZINC000000039099
4Z9 UniChem fdasrs ET6F387NGD
4Z9 UniChem SureChEMBL SCHEMBL891879
4Z9 UniChem NMRShiftDB 80003437
4Z9 UniChem BRENDA 228363
4Z9 UniChem BRENDA 237210
4Z9 UniChem Nikkaji J931.598E
4Z9 UniChem PubChem 676158
#
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
4Z9 C8 -2.136 -0.945 -0.075 ETKDGv3 1
4Z9 C5 -2.424 1.282 -1.728 ETKDGv3 2
4Z9 C9 -1.123 0.077 -0.087 ETKDGv3 3
4Z9 O12 4.574 -0.356 1.079 ETKDGv3 4
4Z9 C10 3.648 0.365 0.619 ETKDGv3 5
4Z9 O11 3.851 1.733 0.456 ETKDGv3 6
4Z9 C13 2.325 -0.250 0.255 ETKDGv3 7
4Z9 O14 2.045 -0.032 -1.105 ETKDGv3 8
4Z9 C15 1.205 0.301 1.155 ETKDGv3 9
4Z9 C3 -0.106 -0.371 0.860 ETKDGv3 10
4Z9 C2 -0.499 -1.554 1.356 ETKDGv3 11
4Z9 N1 -1.764 -1.972 0.827 ETKDGv3 12
4Z9 C7 -3.229 -0.873 -0.837 ETKDGv3 13
4Z9 C6 -3.375 0.320 -1.716 ETKDGv3 14
4Z9 C4 -1.218 1.160 -0.863 ETKDGv3 15
4Z9 H1 -2.536 2.146 -2.369 ETKDGv3 16
4Z9 H2 4.736 2.159 0.701 ETKDGv3 17
4Z9 H3 2.393 -1.349 0.417 ETKDGv3 18
4Z9 H4 1.947 0.947 -1.242 ETKDGv3 19
4Z9 H5 1.467 0.128 2.222 ETKDGv3 20
4Z9 H6 1.099 1.398 1.012 ETKDGv3 21
4Z9 H7 0.076 -2.143 2.059 ETKDGv3 22
4Z9 H8 -2.279 -2.856 1.038 ETKDGv3 23
4Z9 H9 -3.979 -1.653 -0.820 ETKDGv3 24
4Z9 H10 -4.248 0.416 -2.348 ETKDGv3 25
4Z9 H11 -0.450 1.922 -0.867 ETKDGv3 26
#