data_L5X
#
_chem_comp.id L5X
_chem_comp.name 3-{[(5S)-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino}phenol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H12 N2 O S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-02-28
_chem_comp.pdbx_modified_date 2022-09-30
_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 208.280
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L5X
_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 7U3I
_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
L5X C01 C1 C 0 1 N N N N N N -2.628 4.326 -20.286 4.421 -0.559 1.019 C01 L5X 1
L5X C02 C2 C 0 1 N N S N N N -1.623 3.559 -21.113 3.419 -0.697 -0.129 C02 L5X 2
L5X C03 C3 C 0 1 N N N N N N -0.605 2.723 -20.321 2.190 -1.505 0.319 C03 L5X 3
L5X C05 C4 C 0 1 N N N N N N -1.466 0.969 -21.501 1.043 0.500 -0.183 C05 L5X 4
L5X C07 C5 C 0 1 Y N N N N N -2.729 -0.618 -23.055 -1.331 0.866 -0.086 C07 L5X 5
L5X C08 C6 C 0 1 Y N N N N N -3.806 -1.455 -22.761 -2.312 1.717 0.408 C08 L5X 6
L5X C09 C7 C 0 1 Y N N N N N -4.716 -1.792 -23.756 -3.591 1.243 0.629 C09 L5X 7
L5X C10 C8 C 0 1 Y N N N N N -4.577 -1.313 -25.049 -3.897 -0.077 0.360 C10 L5X 8
L5X C11 C9 C 0 1 Y N N N N N -3.493 -0.479 -25.329 -2.921 -0.932 -0.133 C11 L5X 9
L5X C13 C10 C 0 1 Y N N N N N -2.560 -0.127 -24.363 -1.638 -0.458 -0.362 C13 L5X 10
L5X N04 N1 N 0 1 N N N N N N -0.656 1.281 -20.635 0.983 -0.715 0.230 N04 L5X 11
L5X N06 N2 N 0 1 N N N N N N -1.787 -0.284 -22.047 -0.036 1.346 -0.309 N06 L5X 12
L5X O12 O1 O 0 1 N N N N N N -3.377 -0.019 -26.614 -3.224 -2.230 -0.396 O12 L5X 13
L5X S14 S1 S 0 1 N N N N N N -2.437 2.356 -22.224 2.715 0.925 -0.568 S14 L5X 14
L5X H1 H1 H 0 1 N N N N N N -2.100 5.037 -19.633 4.747 -1.548 1.339 H1 L5X 15
L5X H2 H2 H 0 1 N N N N N N -3.308 4.876 -20.953 5.283 0.016 0.681 H2 L5X 16
L5X H3 H3 H 0 1 N N N N N N -3.208 3.623 -19.670 3.947 -0.045 1.855 H3 L5X 17
L5X H4 H4 H 0 1 N N N N N N -1.082 4.257 -21.769 3.890 -1.162 -0.995 H4 L5X 18
L5X H5 H5 H 0 1 N N N N N N 0.405 3.094 -20.551 2.089 -2.384 -0.318 H5 L5X 19
L5X H6 H6 H 0 1 N N N N N N -0.807 2.853 -19.248 2.331 -1.826 1.351 H6 L5X 20
L5X H7 H7 H 0 1 N N N N N N -3.932 -1.841 -21.760 -2.075 2.749 0.619 H7 L5X 21
L5X H8 H8 H 0 1 N N N N N N -5.547 -2.439 -23.517 -4.352 1.906 1.013 H8 L5X 22
L5X H9 H9 H 0 1 N N N N N N -5.287 -1.577 -25.818 -4.898 -0.445 0.534 H9 L5X 23
L5X H10 H10 H 0 1 N N N N N N -1.723 0.509 -24.610 -0.877 -1.122 -0.745 H10 L5X 24
L5X H11 H11 H 0 1 N N N N N N -1.276 -1.056 -21.670 0.101 2.275 -0.553 H11 L5X 25
L5X H12 H12 H 0 1 N N N N N N -2.608 0.535 -26.684 -3.535 -2.386 -1.298 H12 L5X 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
L5X O12 C11 SING N N 1
L5X C11 C10 DOUB Y N 2
L5X C11 C13 SING Y N 3
L5X C10 C09 SING Y N 4
L5X C13 C07 DOUB Y N 5
L5X C09 C08 DOUB Y N 6
L5X C07 C08 SING Y N 7
L5X C07 N06 SING N N 8
L5X S14 C05 SING N N 9
L5X S14 C02 SING N N 10
L5X N06 C05 SING N N 11
L5X C05 N04 DOUB N N 12
L5X C02 C03 SING N N 13
L5X C02 C01 SING N N 14
L5X N04 C03 SING N N 15
L5X C01 H1 SING N N 16
L5X C01 H2 SING N N 17
L5X C01 H3 SING N N 18
L5X C02 H4 SING N N 19
L5X C03 H5 SING N N 20
L5X C03 H6 SING N N 21
L5X C08 H7 SING N N 22
L5X C09 H8 SING N N 23
L5X C10 H9 SING N N 24
L5X C13 H10 SING N N 25
L5X N06 H11 SING N N 26
L5X O12 H12 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
L5X SMILES ACDLabs 12.01 CC1CN=C(Nc2cc(O)ccc2)S1
L5X InChI InChI 1.03 InChI=1S/C10H12N2OS/c1-7-6-11-10(14-7)12-8-3-2-4-9(13)5-8/h2-5,7,13H,6H2,1H3,(H,11,12)/t7-/m0/s1
L5X InChIKey InChI 1.03 WAICHRCMCQSSEP-ZETCQYMHSA-N
L5X SMILES_CANONICAL CACTVS 3.385 C[C@H]1CN=C(Nc2cccc(O)c2)S1
L5X SMILES CACTVS 3.385 C[CH]1CN=C(Nc2cccc(O)c2)S1
L5X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@H]1CN=C(S1)Nc2cccc(c2)O
L5X SMILES "OpenEye OEToolkits" 2.0.7 CC1CN=C(S1)Nc2cccc(c2)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
L5X "SYSTEMATIC NAME" ACDLabs 12.01 3-{[(5S)-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino}phenol
L5X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 3-[[(5~{S})-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino]phenol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L5X 'Create component' 2022-02-28 RCSB
L5X 'Initial release' 2022-10-05 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
L5X C01 C 9.131 4.677 1
L5X C02 C 8.521 3.307 2
L5X C03 C 9.271 2.008 3
L5X C05 C 6.897 1.503 4
L5X C07 C 5.598 -0.747 5
L5X C08 C 6.897 -1.497 6
L5X C09 C 6.897 -2.997 7
L5X C10 C 5.598 -3.747 8
L5X C11 C 4.299 -2.997 9
L5X C13 C 4.299 -1.497 10
L5X N04 N 8.267 0.893 11
L5X N06 N 5.598 0.753 12
L5X O12 O 3.000 -3.747 13
L5X S14 S 7.054 2.995 14
#
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
L5X O12 C11 SINGLE NONE 1
L5X C11 C10 DOUBLE NONE 2
L5X C11 C13 SINGLE NONE 3
L5X C10 C09 SINGLE NONE 4
L5X C13 C07 DOUBLE NONE 5
L5X C09 C08 DOUBLE NONE 6
L5X C07 C08 SINGLE NONE 7
L5X C07 N06 SINGLE NONE 8
L5X S14 C05 SINGLE NONE 9
L5X S14 C02 SINGLE NONE 10
L5X N06 C05 SINGLE NONE 11
L5X C05 N04 DOUBLE NONE 12
L5X C02 C03 SINGLE NONE 13
L5X C02 C01 SINGLE BEGINWEDGE 14
L5X N04 C03 SINGLE NONE 15
#
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
L5X MurckoScaffold S1 scaffold c1ccc(NC2=NCCS2)cc1 InChI=1S/C9H10N2S/c1-2-4-8(5-3-1)11-9-10-6-7-12-9/h1-5H,6-7H2,(H,10,11) NNRDYOXKIWFNPP-UHFFFAOYSA-N
L5X phenyl F1 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
L5X C02 S1 1
L5X C03 S1 1
L5X C05 S1 1
L5X C07 S1 1
L5X C08 S1 1
L5X C09 S1 1
L5X C10 S1 1
L5X C11 S1 1
L5X C13 S1 1
L5X N04 S1 1
L5X N06 S1 1
L5X S14 S1 1
L5X C07 F1 1
L5X C13 F1 1
L5X C11 F1 1
L5X C10 F1 1
L5X C09 F1 1
L5X C08 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id L5X
_pdbe_chem_comp_rdkit_properties.exactmw 208.067
_pdbe_chem_comp_rdkit_properties.amw 208.286
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_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 0.300
_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 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 104.252
_pdbe_chem_comp_rdkit_properties.tpsa 44.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.452
_pdbe_chem_comp_rdkit_properties.CrippenMR 59.651
_pdbe_chem_comp_rdkit_properties.chi0v 7.527
_pdbe_chem_comp_rdkit_properties.chi1v 4.323
_pdbe_chem_comp_rdkit_properties.chi2v 1.903
_pdbe_chem_comp_rdkit_properties.chi3v 1.903
_pdbe_chem_comp_rdkit_properties.chi4v 1.254
_pdbe_chem_comp_rdkit_properties.chi0n 18.711
_pdbe_chem_comp_rdkit_properties.chi1n 9.362
_pdbe_chem_comp_rdkit_properties.chi2n 1.243
_pdbe_chem_comp_rdkit_properties.chi3n 1.243
_pdbe_chem_comp_rdkit_properties.chi4n 0.752
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.160
_pdbe_chem_comp_rdkit_properties.kappa1 2.696
_pdbe_chem_comp_rdkit_properties.kappa2 3.920
_pdbe_chem_comp_rdkit_properties.kappa3 2.200
_pdbe_chem_comp_rdkit_properties.Phi 0.755
#
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
L5X UniChem PDBe L5X
L5X UniChem ZINC ZINC000000333213
L5X UniChem PubChem 818363
L5X UniChem Mcule MCULE-8135878321
#
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
L5X C01 -4.759 -0.139 -0.449 ETKDGv3 1
L5X C02 -3.365 -0.120 0.174 ETKDGv3 2
L5X C03 -2.426 -1.148 -0.468 ETKDGv3 3
L5X C05 -1.023 0.656 -0.148 ETKDGv3 4
L5X C07 1.497 0.704 0.150 ETKDGv3 5
L5X C08 1.628 -0.560 0.923 ETKDGv3 6
L5X C09 2.827 -1.137 1.075 ETKDGv3 7
L5X C10 4.029 -0.516 0.485 ETKDGv3 8
L5X C11 3.925 0.638 -0.192 ETKDGv3 9
L5X C13 2.602 1.278 -0.355 ETKDGv3 10
L5X N04 -1.082 -0.614 -0.361 ETKDGv3 11
L5X N06 0.223 1.352 -0.009 ETKDGv3 12
L5X O12 5.051 1.245 -0.746 ETKDGv3 13
L5X S14 -2.582 1.512 -0.040 ETKDGv3 14
L5X H1 -5.213 -1.146 -0.331 ETKDGv3 15
L5X H2 -5.409 0.603 0.061 ETKDGv3 16
L5X H3 -4.708 0.112 -1.530 ETKDGv3 17
L5X H4 -3.445 -0.327 1.264 ETKDGv3 18
L5X H5 -2.490 -2.127 0.053 ETKDGv3 19
L5X H6 -2.666 -1.290 -1.545 ETKDGv3 20
L5X H7 0.764 -1.010 1.395 ETKDGv3 21
L5X H8 2.920 -2.053 1.643 ETKDGv3 22
L5X H9 4.991 -0.994 0.613 ETKDGv3 23
L5X H10 2.532 2.210 -0.902 ETKDGv3 24
L5X H11 0.202 2.393 -0.102 ETKDGv3 25
L5X H12 5.975 0.838 -0.657 ETKDGv3 26
#