data_80X
#
_chem_comp.id 80X
_chem_comp.name N-(3-chlorophenyl)-2-[(2R)-1-ethanoyl-3-oxidanylidene-piperazin-2-yl]ethanamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H16 Cl N3 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-11-09
_chem_comp.pdbx_modified_date 2022-02-25
_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 309.748
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 80X
_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 7VVT
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
80X N1 N1 N 0 1 N N N N N N 24.128 -3.639 9.696 -2.747 0.430 0.694 N1 80X 1
80X N3 N2 N 0 1 N N N N N N 25.474 -3.117 14.320 1.025 0.352 -1.514 N3 80X 2
80X C4 C1 C 0 1 N N N N N N 24.701 -5.466 11.279 -3.457 -1.439 -0.670 C4 80X 3
80X C5 C2 C 0 1 N N N N N N 24.808 -3.092 12.010 -1.360 -0.235 -1.215 C5 80X 4
80X C6 C3 C 0 1 N N N N N N 24.436 -3.212 13.463 0.037 -0.040 -0.684 C6 80X 5
80X C7 C4 C 0 1 Y N N N N N 25.465 -2.749 15.687 2.341 0.430 -1.046 C7 80X 6
80X C8 C5 C 0 1 Y N N N N N 26.673 -2.707 16.367 3.191 1.420 -1.523 C8 80X 7
80X C10 C6 C 0 1 Y N N N N N 25.548 -2.018 18.370 4.946 0.587 -0.123 C10 80X 8
80X C13 C7 C 0 1 N N N N N N 23.152 -2.886 9.126 -2.134 1.628 0.622 C13 80X 9
80X C1 C8 C 0 1 N N R N N N 24.096 -4.089 11.100 -2.270 -0.722 -0.086 C1 80X 10
80X C11 C9 C 0 1 Y N N N N N 24.357 -2.053 17.682 4.100 -0.397 0.359 C11 80X 11
80X C12 C10 C 0 1 Y N N N N N 24.291 -2.408 16.348 2.799 -0.477 -0.101 C12 80X 12
80X C14 C11 C 0 1 N N N N N N 21.995 -2.460 9.980 -2.719 2.818 1.337 C14 80X 13
80X C2 C12 C 0 1 N N N N N N 25.397 -3.989 9.028 -3.918 0.219 1.562 C2 80X 14
80X C3 C13 C 0 1 N N N N N N 25.532 -5.485 8.928 -5.102 -0.179 0.679 C3 80X 15
80X C9 C14 C 0 1 Y N N N N N 26.703 -2.349 17.701 4.490 1.495 -1.061 C9 80X 16
80X N2 N3 N 0 1 N N N N N N 25.249 -6.062 10.236 -4.711 -1.209 -0.274 N2 80X 17
80X O1 O1 O 0 1 N N N N N N 24.646 -6.014 12.388 -3.264 -2.271 -1.531 O1 80X 18
80X O2 O2 O 0 1 N N N N N N 23.273 -3.403 13.809 0.273 -0.235 0.490 O2 80X 19
80X O3 O3 O 0 1 N N N N N N 23.197 -2.574 7.941 -1.110 1.747 -0.018 O3 80X 20
80X CL1 CL1 CL 0 0 N N N N N N 22.885 -1.637 18.509 4.674 -1.531 1.541 CL1 80X 21
80X H1 H1 H 0 1 N N N N N N 26.372 -3.336 13.938 0.822 0.579 -2.435 H1 80X 22
80X H2 H2 H 0 1 N N N N N N 25.892 -3.252 11.917 -1.737 0.711 -1.603 H2 80X 23
80X H3 H3 H 0 1 N N N N N N 24.557 -2.076 11.672 -1.344 -0.975 -2.014 H3 80X 24
80X H4 H4 H 0 1 N N N N N N 27.590 -2.954 15.854 2.836 2.130 -2.256 H4 80X 25
80X H5 H5 H 0 1 N N N N N N 25.575 -1.737 19.412 5.962 0.648 0.237 H5 80X 26
80X H6 H6 H 0 1 N N N N N N 23.045 -4.140 11.421 -1.718 -1.400 0.565 H6 80X 27
80X H7 H7 H 0 1 N N N N N N 23.344 -2.420 15.829 2.139 -1.245 0.276 H7 80X 28
80X H8 H8 H 0 1 N N N N N N 21.286 -1.877 9.374 -3.579 2.501 1.927 H8 80X 29
80X H9 H9 H 0 1 N N N N N N 21.488 -3.350 10.381 -1.967 3.253 1.995 H9 80X 30
80X H10 H10 H 0 1 N N N N N N 22.362 -1.841 10.812 -3.035 3.562 0.605 H10 80X 31
80X H11 H11 H 0 1 N N N N N N 26.238 -3.586 9.611 -3.708 -0.576 2.277 H11 80X 32
80X H12 H12 H 0 1 N N N N N N 25.409 -3.554 8.018 -4.150 1.141 2.096 H12 80X 33
80X H13 H13 H 0 1 N N N N N N 24.817 -5.874 8.188 -5.907 -0.560 1.308 H13 80X 34
80X H14 H14 H 0 1 N N N N N N 26.556 -5.746 8.621 -5.455 0.697 0.136 H14 80X 35
80X H15 H15 H 0 1 N N N N N N 27.647 -2.329 18.226 5.151 2.265 -1.432 H15 80X 36
80X H16 H16 H 0 1 N N N N N N 25.499 -7.022 10.358 -5.412 -1.763 -0.652 H16 80X 37
#
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
80X O3 C13 DOUB N N 1
80X C3 C2 SING N N 2
80X C3 N2 SING N N 3
80X C2 N1 SING N N 4
80X C13 N1 SING N N 5
80X C13 C14 SING N N 6
80X N1 C1 SING N N 7
80X N2 C4 SING N N 8
80X C1 C4 SING N N 9
80X C1 C5 SING N N 10
80X C4 O1 DOUB N N 11
80X C5 C6 SING N N 12
80X C6 O2 DOUB N N 13
80X C6 N3 SING N N 14
80X N3 C7 SING N N 15
80X C7 C12 DOUB Y N 16
80X C7 C8 SING Y N 17
80X C12 C11 SING Y N 18
80X C8 C9 DOUB Y N 19
80X C11 C10 DOUB Y N 20
80X C11 CL1 SING N N 21
80X C9 C10 SING Y N 22
80X N3 H1 SING N N 23
80X C5 H2 SING N N 24
80X C5 H3 SING N N 25
80X C8 H4 SING N N 26
80X C10 H5 SING N N 27
80X C1 H6 SING N N 28
80X C12 H7 SING N N 29
80X C14 H8 SING N N 30
80X C14 H9 SING N N 31
80X C14 H10 SING N N 32
80X C2 H11 SING N N 33
80X C2 H12 SING N N 34
80X C3 H13 SING N N 35
80X C3 H14 SING N N 36
80X C9 H15 SING N N 37
80X N2 H16 SING N N 38
#
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
80X InChI InChI 1.03 InChI=1S/C14H16ClN3O3/c1-9(19)18-6-5-16-14(21)12(18)8-13(20)17-11-4-2-3-10(15)7-11/h2-4,7,12H,5-6,8H2,1H3,(H,16,21)(H,17,20)/t12-/m1/s1
80X InChIKey InChI 1.03 VFCHONURCHBPEO-GFCCVEGCSA-N
80X SMILES_CANONICAL CACTVS 3.385 CC(=O)N1CCNC(=O)[C@H]1CC(=O)Nc2cccc(Cl)c2
80X SMILES CACTVS 3.385 CC(=O)N1CCNC(=O)[CH]1CC(=O)Nc2cccc(Cl)c2
80X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(=O)N1CCNC(=O)[C@H]1CC(=O)Nc2cccc(c2)Cl
80X SMILES "OpenEye OEToolkits" 2.0.7 CC(=O)N1CCNC(=O)C1CC(=O)Nc2cccc(c2)Cl
#
_pdbx_chem_comp_identifier.comp_id 80X
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
~{N}-(3-chlorophenyl)-2-[(2~{R})-1-ethanoyl-3-oxidanylidene-piperazin-2-yl]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
80X 'Create component' 2021-11-09 PDBJ
80X 'Initial release' 2022-03-02 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
80X N1 N 13.392 -0.840 1
80X N3 N 8.196 -0.840 2
80X C4 C 12.093 1.410 3
80X C5 C 10.794 -0.840 4
80X C6 C 9.495 -0.090 5
80X C7 C 6.897 -0.090 6
80X C8 C 6.897 1.410 7
80X C10 C 4.299 1.410 8
80X C13 C 13.392 -2.340 9
80X C1 C 12.093 -0.090 10
80X C11 C 4.299 -0.090 11
80X C12 C 5.598 -0.840 12
80X C14 C 14.691 -3.090 13
80X C2 C 14.691 -0.090 14
80X C3 C 14.691 1.410 15
80X C9 C 5.598 2.160 16
80X N2 N 13.392 2.160 17
80X O1 O 10.794 2.160 18
80X O2 O 9.495 1.410 19
80X O3 O 12.093 -3.090 20
80X CL1 Cl 3.000 -0.840 21
#
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
80X O3 C13 DOUBLE NONE 1
80X C3 C2 SINGLE NONE 2
80X C3 N2 SINGLE NONE 3
80X C2 N1 SINGLE NONE 4
80X C13 N1 SINGLE NONE 5
80X C13 C14 SINGLE NONE 6
80X N1 C1 SINGLE NONE 7
80X N2 C4 SINGLE NONE 8
80X C1 C4 SINGLE NONE 9
80X C1 C5 SINGLE BEGINDASH 10
80X C4 O1 DOUBLE NONE 11
80X C5 C6 SINGLE NONE 12
80X C6 O2 DOUBLE NONE 13
80X C6 N3 SINGLE NONE 14
80X N3 C7 SINGLE NONE 15
80X C7 C12 SINGLE NONE 16
80X C7 C8 DOUBLE NONE 17
80X C12 C11 DOUBLE NONE 18
80X C8 C9 SINGLE NONE 19
80X C11 C10 SINGLE NONE 20
80X C11 CL1 SINGLE NONE 21
80X C9 C10 DOUBLE NONE 22
#
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
80X MurckoScaffold S1 scaffold 'O=C(C[C@H]1NCCNC1=O)Nc1ccccc1' InChI=1S/C12H15N3O2/c16-11(15-9-4-2-1-3-5-9)8-10-12(17)14-7-6-13-10/h1-5,10,13H,6-8H2,(H,14,17)(H,15,16)/t10-/m1/s1 YDVYIIPPSVSXQH-SNVBAGLBSA-N
80X amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
80X peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
80X phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
80X piperazine F4 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-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
80X N1 S1 1
80X N3 S1 1
80X C4 S1 1
80X C5 S1 1
80X C6 S1 1
80X C7 S1 1
80X C8 S1 1
80X C10 S1 1
80X C1 S1 1
80X C11 S1 1
80X C12 S1 1
80X C2 S1 1
80X C3 S1 1
80X C9 S1 1
80X N2 S1 1
80X O1 S1 1
80X O2 S1 1
80X N1 F1 1
80X C13 F1 1
80X O3 F1 1
80X C14 F1 1
80X N3 F1 2
80X C6 F1 2
80X O2 F1 2
80X C5 F1 2
80X N2 F1 3
80X C4 F1 3
80X O1 F1 3
80X C1 F1 3
80X O1 F2 1
80X C4 F2 1
80X C1 F2 1
80X N1 F2 1
80X C7 F3 1
80X C12 F3 1
80X C11 F3 1
80X C10 F3 1
80X C9 F3 1
80X C8 F3 1
80X N1 F4 1
80X C2 F4 1
80X C3 F4 1
80X N2 F4 1
80X C4 F4 1
80X C1 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 80X
_pdbe_chem_comp_rdkit_properties.exactmw 309.088
_pdbe_chem_comp_rdkit_properties.amw 309.753
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.357
_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 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 149.588
_pdbe_chem_comp_rdkit_properties.tpsa 78.510
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.635
_pdbe_chem_comp_rdkit_properties.CrippenMR 78.059
_pdbe_chem_comp_rdkit_properties.chi0v 10.700
_pdbe_chem_comp_rdkit_properties.chi1v 5.495
_pdbe_chem_comp_rdkit_properties.chi2v 2.157
_pdbe_chem_comp_rdkit_properties.chi3v 2.157
_pdbe_chem_comp_rdkit_properties.chi4v 1.327
_pdbe_chem_comp_rdkit_properties.chi0n 25.944
_pdbe_chem_comp_rdkit_properties.chi1n 13.011
_pdbe_chem_comp_rdkit_properties.chi2n 1.969
_pdbe_chem_comp_rdkit_properties.chi3n 1.969
_pdbe_chem_comp_rdkit_properties.chi4n 1.190
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.080
_pdbe_chem_comp_rdkit_properties.kappa1 4.709
_pdbe_chem_comp_rdkit_properties.kappa2 6.581
_pdbe_chem_comp_rdkit_properties.kappa3 3.947
_pdbe_chem_comp_rdkit_properties.Phi 1.476
#
_pdbe_chem_comp_external_mappings.comp_id 80X
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id 80X
#
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
80X N1 -2.651 0.516 0.497 ETKDGv3 1
80X N3 2.000 0.566 -0.576 ETKDGv3 2
80X C4 -1.019 -1.070 -0.420 ETKDGv3 3
80X C5 -0.323 1.272 0.191 ETKDGv3 4
80X C6 1.117 0.964 0.484 ETKDGv3 5
80X C7 3.277 -0.058 -0.360 ETKDGv3 6
80X C8 4.267 0.129 -1.250 ETKDGv3 7
80X C10 5.788 -1.311 0.002 ETKDGv3 8
80X C13 -3.274 1.022 1.701 ETKDGv3 9
80X C1 -1.242 0.083 0.532 ETKDGv3 10
80X C11 4.698 -1.553 0.969 ETKDGv3 11
80X C12 3.506 -0.965 0.797 ETKDGv3 12
80X C14 -4.759 1.192 1.811 ETKDGv3 13
80X C2 -3.326 0.580 -0.809 ETKDGv3 14
80X C3 -3.299 -0.796 -1.466 ETKDGv3 15
80X C9 5.581 -0.517 -1.054 ETKDGv3 16
80X N2 -1.942 -1.332 -1.484 ETKDGv3 17
80X O1 0.006 -1.794 -0.297 ETKDGv3 18
80X O2 1.539 1.062 1.668 ETKDGv3 19
80X O3 -2.561 1.337 2.692 ETKDGv3 20
80X CL1 4.963 -2.630 2.328 ETKDGv3 21
80X H1 1.714 0.780 -1.559 ETKDGv3 22
80X H2 -0.622 2.155 0.797 ETKDGv3 23
80X H3 -0.441 1.555 -0.878 ETKDGv3 24
80X H4 4.117 0.767 -2.112 ETKDGv3 25
80X H5 6.752 -1.784 0.143 ETKDGv3 26
80X H6 -0.997 -0.285 1.554 ETKDGv3 27
80X H7 2.703 -1.178 1.490 ETKDGv3 28
80X H8 -5.056 1.320 2.874 ETKDGv3 29
80X H9 -5.275 0.294 1.413 ETKDGv3 30
80X H10 -5.077 2.093 1.245 ETKDGv3 31
80X H11 -4.380 0.914 -0.726 ETKDGv3 32
80X H12 -2.803 1.313 -1.460 ETKDGv3 33
80X H13 -3.956 -1.490 -0.899 ETKDGv3 34
80X H14 -3.682 -0.718 -2.506 ETKDGv3 35
80X H15 6.377 -0.344 -1.768 ETKDGv3 36
80X H16 -1.720 -2.091 -2.167 ETKDGv3 37
#