data_LXA
#
_chem_comp.id LXA
_chem_comp.name ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-2-methoxy-ethanamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H13 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-03-15
_chem_comp.pdbx_modified_date 2020-04-24
_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 219.240
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LXA
_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 5QQ3
_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
LXA N1 N1 N 0 1 Y N N N N N -28.535 -9.385 -31.557 -1.546 1.019 0.731 N1 LXA 1
LXA C4 C1 C 0 1 Y N N N N N -28.385 -10.553 -32.210 -0.781 0.664 -0.337 C4 LXA 2
LXA C5 C2 C 0 1 Y N N N N N -27.891 -8.381 -32.278 -2.772 0.401 0.581 C5 LXA 3
LXA C6 C3 C 0 1 Y N N N N N -27.782 -6.981 -32.021 -3.940 0.376 1.331 C6 LXA 4
LXA C7 C4 C 0 1 Y N N N N N -27.060 -6.207 -32.928 -5.018 -0.362 0.891 C7 LXA 5
LXA C8 C5 C 0 1 Y N N N N N -26.463 -6.832 -34.078 -4.942 -1.079 -0.294 C8 LXA 6
LXA C10 C6 C 0 1 Y N N N N N -27.333 -9.001 -33.379 -2.696 -0.325 -0.619 C10 LXA 7
LXA N N2 N 0 1 N N N N N N -28.884 -12.866 -32.725 1.562 0.100 -0.052 N LXA 8
LXA C C7 C 0 1 N N N N N N -29.782 -14.714 -37.095 6.175 -1.248 0.630 C LXA 9
LXA O O1 O 0 1 N N N N N N -29.894 -13.765 -36.080 5.189 -0.326 0.160 O LXA 10
LXA C1 C8 C 0 1 N N N N N N -29.355 -14.110 -34.810 3.843 -0.753 0.380 C1 LXA 11
LXA C2 C9 C 0 1 N N N N N N -29.683 -12.949 -33.869 2.893 0.289 -0.151 C2 LXA 12
LXA C3 C10 C 0 1 N N N N N N -29.009 -11.842 -31.704 0.638 1.113 -0.569 C3 LXA 13
LXA C9 C11 C 0 1 Y N N N N N -26.575 -8.227 -34.323 -3.801 -1.066 -1.045 C9 LXA 14
LXA N2 N3 N 0 1 Y N N N N N -27.652 -10.395 -33.349 -1.453 -0.120 -1.128 N2 LXA 15
LXA O1 O2 O 0 1 N N N N N N -30.567 -12.164 -34.102 3.326 1.297 -0.668 O1 LXA 16
LXA H1 H1 H 0 1 N N N N N N -29.028 -9.259 -30.696 -1.278 1.596 1.463 H1 LXA 17
LXA H2 H2 H 0 1 N N N N N N -28.244 -6.536 -31.152 -4.003 0.932 2.255 H2 LXA 18
LXA H3 H3 H 0 1 N N N N N N -26.949 -5.145 -32.768 -5.927 -0.383 1.474 H3 LXA 19
LXA H4 H4 H 0 1 N N N N N N -25.912 -6.221 -34.778 -5.794 -1.654 -0.627 H4 LXA 20
LXA H5 H5 H 0 1 N N N N N N -28.176 -13.561 -32.601 1.216 -0.706 0.361 H5 LXA 21
LXA H6 H6 H 0 1 N N N N N N -30.236 -14.321 -38.017 7.170 -0.852 0.425 H6 LXA 22
LXA H7 H7 H 0 1 N N N N N N -28.719 -14.934 -37.275 6.055 -1.392 1.703 H7 LXA 23
LXA H8 H8 H 0 1 N N N N N N -30.302 -15.636 -36.794 6.053 -2.203 0.119 H8 LXA 24
LXA H9 H9 H 0 1 N N N N N N -29.815 -15.039 -34.442 3.672 -1.697 -0.136 H9 LXA 25
LXA H10 H10 H 0 1 N N N N N N -28.266 -14.244 -34.883 3.675 -0.887 1.449 H10 LXA 26
LXA H11 H11 H 0 1 N N N N N N -30.073 -11.673 -31.481 0.807 1.247 -1.638 H11 LXA 27
LXA H12 H12 H 0 1 N N N N N N -28.490 -12.168 -30.791 0.810 2.058 -0.053 H12 LXA 28
LXA H13 H13 H 0 1 N N N N N N -26.110 -8.686 -35.183 -3.753 -1.628 -1.967 H13 LXA 29
#
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
LXA C O SING N N 1
LXA O C1 SING N N 2
LXA C1 C2 SING N N 3
LXA C9 C8 DOUB Y N 4
LXA C9 C10 SING Y N 5
LXA O1 C2 DOUB N N 6
LXA C8 C7 SING Y N 7
LXA C2 N SING N N 8
LXA C10 N2 SING Y N 9
LXA C10 C5 DOUB Y N 10
LXA N2 C4 DOUB Y N 11
LXA C7 C6 DOUB Y N 12
LXA N C3 SING N N 13
LXA C5 C6 SING Y N 14
LXA C5 N1 SING Y N 15
LXA C4 C3 SING N N 16
LXA C4 N1 SING Y N 17
LXA N1 H1 SING N N 18
LXA C6 H2 SING N N 19
LXA C7 H3 SING N N 20
LXA C8 H4 SING N N 21
LXA N H5 SING N N 22
LXA C H6 SING N N 23
LXA C H7 SING N N 24
LXA C H8 SING N N 25
LXA C1 H9 SING N N 26
LXA C1 H10 SING N N 27
LXA C3 H11 SING N N 28
LXA C3 H12 SING N N 29
LXA C9 H13 SING N N 30
#
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
LXA InChI InChI 1.03 InChI=1S/C11H13N3O2/c1-16-7-11(15)12-6-10-13-8-4-2-3-5-9(8)14-10/h2-5H,6-7H2,1H3,(H,12,15)(H,13,14)
LXA InChIKey InChI 1.03 LZINBAGZNCYRNQ-UHFFFAOYSA-N
LXA SMILES_CANONICAL CACTVS 3.385 COCC(=O)NCc1[nH]c2ccccc2n1
LXA SMILES CACTVS 3.385 COCC(=O)NCc1[nH]c2ccccc2n1
LXA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 COCC(=O)NCc1[nH]c2ccccc2n1
LXA SMILES "OpenEye OEToolkits" 2.0.6 COCC(=O)NCc1[nH]c2ccccc2n1
#
_pdbx_chem_comp_identifier.comp_id LXA
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-2-methoxy-ethanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LXA 'Create component' 2019-03-15 RCSB
LXA 'Initial release' 2020-04-29 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
LXA N1 N 7.018 -0.304 1
LXA C4 C 7.893 0.903 2
LXA C5 C 5.598 0.153 3
LXA C6 C 4.299 -0.597 4
LXA C7 C 3.000 0.153 5
LXA C8 C 3.000 1.653 6
LXA C10 C 5.598 1.653 7
LXA N N 10.143 -0.396 8
LXA C C 14.643 -2.994 9
LXA O O 13.893 -1.695 10
LXA C1 C 12.393 -1.695 11
LXA C2 C 11.643 -0.396 12
LXA C3 C 9.393 0.903 13
LXA C9 C 4.299 2.403 14
LXA N2 N 7.018 2.110 15
LXA O1 O 12.393 0.903 16
#
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
LXA C O SINGLE NONE 1
LXA O C1 SINGLE NONE 2
LXA C1 C2 SINGLE NONE 3
LXA C9 C8 DOUBLE NONE 4
LXA C9 C10 SINGLE NONE 5
LXA O1 C2 DOUBLE NONE 6
LXA C8 C7 SINGLE NONE 7
LXA C2 N SINGLE NONE 8
LXA C10 N2 SINGLE NONE 9
LXA C10 C5 DOUBLE NONE 10
LXA N2 C4 DOUBLE NONE 11
LXA C7 C6 DOUBLE NONE 12
LXA N C3 SINGLE NONE 13
LXA C5 C6 SINGLE NONE 14
LXA C5 N1 SINGLE NONE 15
LXA C4 C3 SINGLE NONE 16
LXA C4 N1 SINGLE NONE 17
#
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
LXA MurckoScaffold S1 scaffold 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
LXA amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
LXA benzimidazole F2 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
LXA imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
LXA phenyl F4 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
LXA Z1203191681 F5 fragment 'CC(=O)NCc1ncc[nH]1' InChI=1S/C6H9N3O/c1-5(10)9-4-6-7-2-3-8-6/h2-3H,4H2,1H3,(H,7,8)(H,9,10) SXKAQLCLHGQXHB-UHFFFAOYSA-N
LXA Z111529496 F6 fragment 'COCC(=O)NCc1nc2ccccc2[nH]1' InChI=1S/C11H13N3O2/c1-16-7-11(15)12-6-10-13-8-4-2-3-5-9(8)14-10/h2-5H,6-7H2,1H3,(H,12,15)(H,13,14) LZINBAGZNCYRNQ-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
LXA N1 S1 1
LXA C4 S1 1
LXA C5 S1 1
LXA C6 S1 1
LXA C7 S1 1
LXA C8 S1 1
LXA C10 S1 1
LXA C9 S1 1
LXA N2 S1 1
LXA N F1 1
LXA C2 F1 1
LXA O1 F1 1
LXA C1 F1 1
LXA C5 F2 1
LXA N1 F2 1
LXA C4 F2 1
LXA N2 F2 1
LXA C10 F2 1
LXA C9 F2 1
LXA C8 F2 1
LXA C7 F2 1
LXA C6 F2 1
LXA C5 F3 1
LXA C10 F3 1
LXA N2 F3 1
LXA C4 F3 1
LXA N1 F3 1
LXA C5 F4 1
LXA C10 F4 1
LXA C9 F4 1
LXA C8 F4 1
LXA C7 F4 1
LXA C6 F4 1
LXA C1 F5 1
LXA C2 F5 1
LXA O1 F5 1
LXA N F5 1
LXA C3 F5 1
LXA C4 F5 1
LXA N2 F5 1
LXA C10 F5 1
LXA C5 F5 1
LXA N1 F5 1
LXA C F6 1
LXA O F6 1
LXA C1 F6 1
LXA C2 F6 1
LXA O1 F6 1
LXA N F6 1
LXA C3 F6 1
LXA C4 F6 1
LXA N2 F6 1
LXA C10 F6 1
LXA C9 F6 1
LXA C8 F6 1
LXA C7 F6 1
LXA C6 F6 1
LXA C5 F6 1
LXA N1 F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LXA
_pdbe_chem_comp_rdkit_properties.exactmw 219.101
_pdbe_chem_comp_rdkit_properties.amw 219.244
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.273
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 111.207
_pdbe_chem_comp_rdkit_properties.tpsa 67.010
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.342
_pdbe_chem_comp_rdkit_properties.CrippenMR 57.344
_pdbe_chem_comp_rdkit_properties.chi0v 7.658
_pdbe_chem_comp_rdkit_properties.chi1v 3.954
_pdbe_chem_comp_rdkit_properties.chi2v 1.480
_pdbe_chem_comp_rdkit_properties.chi3v 1.480
_pdbe_chem_comp_rdkit_properties.chi4v 0.915
_pdbe_chem_comp_rdkit_properties.chi0n 20.658
_pdbe_chem_comp_rdkit_properties.chi1n 10.348
_pdbe_chem_comp_rdkit_properties.chi2n 1.480
_pdbe_chem_comp_rdkit_properties.chi3n 1.480
_pdbe_chem_comp_rdkit_properties.chi4n 0.915
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.880
_pdbe_chem_comp_rdkit_properties.kappa1 3.074
_pdbe_chem_comp_rdkit_properties.kappa2 4.761
_pdbe_chem_comp_rdkit_properties.kappa3 2.375
_pdbe_chem_comp_rdkit_properties.Phi 0.915
#
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
LXA UniChem ChEMBL CHEMBL1409021
LXA UniChem PDBe LXA
LXA UniChem ZINC ZINC000000200675
LXA UniChem eMolecules 2283087
LXA UniChem PubChem 751092
LXA UniChem Mcule MCULE-4178410755
#
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
LXA N1 1.559 -0.625 0.769 ETKDGv3 1
LXA C4 1.065 -1.258 -0.415 ETKDGv3 2
LXA C5 2.341 0.421 0.228 ETKDGv3 3
LXA C6 3.109 1.452 0.942 ETKDGv3 4
LXA C7 3.772 2.365 0.206 ETKDGv3 5
LXA C8 3.715 2.317 -1.287 ETKDGv3 6
LXA C10 2.289 0.376 -1.083 ETKDGv3 7
LXA N -1.176 -2.005 0.118 ETKDGv3 8
LXA C -4.321 0.749 1.425 ETKDGv3 9
LXA O -3.110 0.328 0.839 ETKDGv3 10
LXA C1 -3.367 -0.738 -0.050 ETKDGv3 11
LXA C2 -2.073 -1.189 -0.648 ETKDGv3 12
LXA C3 0.128 -2.423 -0.388 ETKDGv3 13
LXA C9 3.001 1.362 -1.912 ETKDGv3 14
LXA N2 1.465 -0.698 -1.520 ETKDGv3 15
LXA O1 -1.760 -0.816 -1.811 ETKDGv3 16
LXA H1 1.366 -0.854 1.770 ETKDGv3 17
LXA H2 3.140 1.477 2.023 ETKDGv3 18
LXA H3 4.348 3.139 0.696 ETKDGv3 19
LXA H4 4.251 3.057 -1.866 ETKDGv3 20
LXA H5 -1.462 -2.315 1.074 ETKDGv3 21
LXA H6 -5.033 1.123 0.656 ETKDGv3 22
LXA H7 -4.785 -0.068 2.021 ETKDGv3 23
LXA H8 -4.105 1.588 2.117 ETKDGv3 24
LXA H9 -4.050 -0.414 -0.869 ETKDGv3 25
LXA H10 -3.826 -1.601 0.484 ETKDGv3 26
LXA H11 0.018 -2.866 -1.402 ETKDGv3 27
LXA H12 0.552 -3.202 0.281 ETKDGv3 28
LXA H13 2.951 1.319 -2.992 ETKDGv3 29
#