data_0YI
#
_chem_comp.id 0YI
_chem_comp.name 3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H11 Cl N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-06-09
_chem_comp.pdbx_modified_date 2021-07-23
_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 262.695
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 0YI
_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 7OT0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
0YI C3 C1 C 0 1 Y N N N N N 5.404 35.655 29.494 1.638 -0.628 0.180 C3 0YI 1
0YI C5 C2 C 0 1 Y N N N N N 7.307 34.539 30.037 3.254 -2.227 -0.127 C5 0YI 2
0YI C11 C3 C 0 1 N N N N N N 3.187 34.849 30.213 -0.733 -1.305 0.213 C11 0YI 3
0YI C12 C4 C 0 1 Y N N N N N 2.239 34.042 29.355 -2.085 -0.673 0.422 C12 0YI 4
0YI C13 C5 C 0 1 Y N N N N N 1.500 32.985 29.882 -2.693 0.018 -0.612 C13 0YI 5
0YI C14 C6 C 0 1 Y N N N N N 0.658 32.216 29.097 -3.934 0.599 -0.419 C14 0YI 6
0YI C15 C7 C 0 1 Y N N N N N 0.549 32.494 27.747 -4.566 0.488 0.805 C15 0YI 7
0YI C16 C8 C 0 1 Y N N N N N 1.265 33.535 27.198 -3.958 -0.202 1.837 C16 0YI 8
0YI N9 N1 N 0 1 N N N N N N 6.290 38.637 27.557 3.200 2.745 0.242 N9 0YI 9
0YI C17 C9 C 0 1 Y N N N N N 2.097 34.304 27.995 -2.721 -0.787 1.644 C17 0YI 10
0YI C2 C10 C 0 1 Y N N N N N 6.167 36.732 29.022 2.631 0.365 0.181 C2 0YI 11
0YI C6 C11 C 0 1 Y N N N N N 8.065 35.603 29.582 4.234 -1.245 -0.126 C6 0YI 12
0YI C7 C12 C 0 1 N N N N N N 5.523 37.940 28.390 2.260 1.785 0.353 C7 0YI 13
0YI N1 N2 N 0 1 Y N N N N N 7.509 36.712 29.073 3.907 0.022 0.027 N1 0YI 14
0YI N10 N3 N 0 1 N N N N N N 4.059 35.713 29.433 0.308 -0.282 0.334 N10 0YI 15
0YI N4 N4 N 0 1 Y N N N N N 5.966 34.549 30.005 1.983 -1.902 0.025 N4 0YI 16
0YI O8 O1 O 0 1 N N N N N N 4.349 38.240 28.634 1.108 2.087 0.593 O8 0YI 17
0YI CL1 CL1 CL 0 0 N N N N N N 1.637 32.584 31.562 -1.898 0.157 -2.148 CL1 0YI 18
0YI H1 H1 H 0 1 N N N N N N 7.812 33.670 30.432 3.531 -3.264 -0.253 H1 0YI 19
0YI H2 H2 H 0 1 N N N N N N 2.595 35.474 30.898 -0.573 -2.077 0.966 H2 0YI 20
0YI H3 H3 H 0 1 N N N N N N 3.810 34.155 30.796 -0.691 -1.752 -0.780 H3 0YI 21
0YI H4 H4 H 0 1 N N N N N N 0.092 31.407 29.535 -4.408 1.138 -1.226 H4 0YI 22
0YI H5 H5 H 0 1 N N N N N N -0.098 31.895 27.123 -5.535 0.941 0.955 H5 0YI 23
0YI H6 H6 H 0 1 N N N N N N 1.177 33.752 26.144 -4.453 -0.288 2.793 H6 0YI 24
0YI H7 H7 H 0 1 N N N N N N 5.922 39.444 27.096 2.956 3.677 0.355 H7 0YI 25
0YI H8 H8 H 0 1 N N N N N N 7.235 38.354 27.392 4.119 2.504 0.050 H8 0YI 26
0YI H9 H9 H 0 1 N N N N N N 2.646 35.122 27.553 -2.246 -1.326 2.451 H9 0YI 27
0YI H10 H10 H 0 1 N N N N N N 9.142 35.538 29.639 5.271 -1.521 -0.251 H10 0YI 28
0YI H11 H11 H 0 1 N N N N N N 3.813 36.649 29.684 0.065 0.638 0.521 H11 0YI 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
0YI C16 C15 DOUB Y N 1
0YI C16 C17 SING Y N 2
0YI N9 C7 SING N N 3
0YI C15 C14 SING Y N 4
0YI C17 C12 DOUB Y N 5
0YI C7 O8 DOUB N N 6
0YI C7 C2 SING N N 7
0YI C2 N1 DOUB Y N 8
0YI C2 C3 SING Y N 9
0YI N1 C6 SING Y N 10
0YI C14 C13 DOUB Y N 11
0YI C12 C13 SING Y N 12
0YI C12 C11 SING N N 13
0YI N10 C3 SING N N 14
0YI N10 C11 SING N N 15
0YI C3 N4 DOUB Y N 16
0YI C6 C5 DOUB Y N 17
0YI C13 CL1 SING N N 18
0YI N4 C5 SING Y N 19
0YI C5 H1 SING N N 20
0YI C11 H2 SING N N 21
0YI C11 H3 SING N N 22
0YI C14 H4 SING N N 23
0YI C15 H5 SING N N 24
0YI C16 H6 SING N N 25
0YI N9 H7 SING N N 26
0YI N9 H8 SING N N 27
0YI C17 H9 SING N N 28
0YI C6 H10 SING N N 29
0YI N10 H11 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
0YI InChI InChI 1.03 InChI=1S/C12H11ClN4O/c13-9-4-2-1-3-8(9)7-17-12-10(11(14)18)15-5-6-16-12/h1-6H,7H2,(H2,14,18)(H,16,17)
0YI InChIKey InChI 1.03 SZIKCJPPVPPUMU-UHFFFAOYSA-N
0YI SMILES_CANONICAL CACTVS 3.385 NC(=O)c1nccnc1NCc2ccccc2Cl
0YI SMILES CACTVS 3.385 NC(=O)c1nccnc1NCc2ccccc2Cl
0YI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(c(c1)CNc2c(nccn2)C(=O)N)Cl
0YI SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(c(c1)CNc2c(nccn2)C(=O)N)Cl
#
_pdbx_chem_comp_identifier.comp_id 0YI
_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 3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
0YI 'Create component' 2021-06-09 PDBE
0YI 'Initial release' 2021-07-28 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
0YI C3 C 7.702 -1.875 1
0YI C5 C 9.002 -4.125 2
0YI C11 C 9.002 0.375 3
0YI C12 C 9.002 1.875 4
0YI C13 C 10.301 2.625 5
0YI C14 C 10.301 4.125 6
0YI C15 C 9.002 4.875 7
0YI C16 C 7.702 4.125 8
0YI N9 N 5.104 -0.375 9
0YI C17 C 7.702 2.625 10
0YI C2 C 6.404 -2.625 11
0YI C6 C 7.702 -4.875 12
0YI C7 C 5.104 -1.875 13
0YI N1 N 6.404 -4.125 14
0YI N10 N 7.702 -0.375 15
0YI N4 N 9.002 -2.625 16
0YI O8 O 3.805 -2.625 17
0YI CL1 Cl 11.600 1.875 18
#
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
0YI C16 C15 DOUBLE NONE 1
0YI C16 C17 SINGLE NONE 2
0YI N9 C7 SINGLE NONE 3
0YI C15 C14 SINGLE NONE 4
0YI C17 C12 DOUBLE NONE 5
0YI C7 O8 DOUBLE NONE 6
0YI C7 C2 SINGLE NONE 7
0YI C2 N1 DOUBLE NONE 8
0YI C2 C3 SINGLE NONE 9
0YI N1 C6 SINGLE NONE 10
0YI C14 C13 DOUBLE NONE 11
0YI C12 C13 SINGLE NONE 12
0YI C12 C11 SINGLE NONE 13
0YI N10 C3 SINGLE NONE 14
0YI N10 C11 SINGLE NONE 15
0YI C3 N4 DOUBLE NONE 16
0YI C6 C5 DOUBLE NONE 17
0YI C13 CL1 SINGLE NONE 18
0YI N4 C5 SINGLE NONE 19
#
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
0YI MurckoScaffold S1 scaffold c1ccc(CNc2cnccn2)cc1 InChI=1S/C11H11N3/c1-2-4-10(5-3-1)8-14-11-9-12-6-7-13-11/h1-7,9H,8H2,(H,13,14) ITELDXFJDCTYAQ-UHFFFAOYSA-N
0YI amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
0YI phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
0YI pyrazine F3 fragment c1cnccn1 InChI=1S/C4H4N2/c1-2-6-4-3-5-1/h1-4H KYQCOXFCLRTKLS-UHFFFAOYSA-N
0YI Z31197063 F4 fragment c1ccc(CNc2cnccn2)cc1 InChI=1S/C11H11N3/c1-2-4-10(5-3-1)8-14-11-9-12-6-7-13-11/h1-7,9H,8H2,(H,13,14) ITELDXFJDCTYAQ-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
0YI C3 S1 1
0YI C5 S1 1
0YI C11 S1 1
0YI C12 S1 1
0YI C13 S1 1
0YI C14 S1 1
0YI C15 S1 1
0YI C16 S1 1
0YI C17 S1 1
0YI C2 S1 1
0YI C6 S1 1
0YI N1 S1 1
0YI N10 S1 1
0YI N4 S1 1
0YI N9 F1 1
0YI C7 F1 1
0YI O8 F1 1
0YI C2 F1 1
0YI C12 F2 1
0YI C17 F2 1
0YI C16 F2 1
0YI C15 F2 1
0YI C14 F2 1
0YI C13 F2 1
0YI C3 F3 1
0YI C2 F3 1
0YI N1 F3 1
0YI C6 F3 1
0YI C5 F3 1
0YI N4 F3 1
0YI C11 F4 1
0YI N10 F4 1
0YI C3 F4 1
0YI C2 F4 1
0YI N1 F4 1
0YI C6 F4 1
0YI C5 F4 1
0YI N4 F4 1
0YI C12 F4 1
0YI C17 F4 1
0YI C16 F4 1
0YI C15 F4 1
0YI C14 F4 1
0YI C13 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 0YI
_pdbe_chem_comp_rdkit_properties.exactmw 262.062
_pdbe_chem_comp_rdkit_properties.amw 262.700
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.083
_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 124.641
_pdbe_chem_comp_rdkit_properties.tpsa 80.900
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.351
_pdbe_chem_comp_rdkit_properties.CrippenMR 67.973
_pdbe_chem_comp_rdkit_properties.chi0v 9.331
_pdbe_chem_comp_rdkit_properties.chi1v 4.836
_pdbe_chem_comp_rdkit_properties.chi2v 1.993
_pdbe_chem_comp_rdkit_properties.chi3v 1.993
_pdbe_chem_comp_rdkit_properties.chi4v 1.103
_pdbe_chem_comp_rdkit_properties.chi0n 19.575
_pdbe_chem_comp_rdkit_properties.chi1n 9.800
_pdbe_chem_comp_rdkit_properties.chi2n 1.709
_pdbe_chem_comp_rdkit_properties.chi3n 1.709
_pdbe_chem_comp_rdkit_properties.chi4n 0.966
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.140
_pdbe_chem_comp_rdkit_properties.kappa1 4.512
_pdbe_chem_comp_rdkit_properties.kappa2 5.463
_pdbe_chem_comp_rdkit_properties.kappa3 2.752
_pdbe_chem_comp_rdkit_properties.Phi 1.369
#
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
0YI UniChem PDBe 0YI
0YI UniChem PubChem 145998486
#
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
0YI C3 -1.659 -0.549 0.118 ETKDGv3 1
0YI C5 -3.457 -2.118 0.320 ETKDGv3 2
0YI C11 0.753 -1.302 0.006 ETKDGv3 3
0YI C12 2.128 -0.708 -0.167 ETKDGv3 4
0YI C13 2.728 0.143 0.902 ETKDGv3 5
0YI C14 3.940 0.687 0.721 ETKDGv3 6
0YI C15 4.682 0.454 -0.533 ETKDGv3 7
0YI C16 4.144 -0.297 -1.500 ETKDGv3 8
0YI N9 -3.233 2.996 0.042 ETKDGv3 9
0YI C17 2.807 -0.898 -1.314 ETKDGv3 10
0YI C2 -2.664 0.549 0.279 ETKDGv3 11
0YI C6 -4.359 -1.140 0.421 ETKDGv3 12
0YI C7 -2.289 1.976 0.373 ETKDGv3 13
0YI N1 -3.921 0.226 0.408 ETKDGv3 14
0YI N10 -0.275 -0.273 -0.149 ETKDGv3 15
0YI N4 -2.072 -1.785 0.152 ETKDGv3 16
0YI O8 -1.148 2.310 0.791 ETKDGv3 17
0YI CL1 1.866 0.462 2.402 ETKDGv3 18
0YI H1 -3.766 -3.155 0.342 ETKDGv3 19
0YI H2 0.572 -2.117 -0.729 ETKDGv3 20
0YI H3 0.678 -1.751 1.020 ETKDGv3 21
0YI H4 4.383 1.307 1.491 ETKDGv3 22
0YI H5 5.661 0.895 -0.670 ETKDGv3 23
0YI H6 4.685 -0.465 -2.422 ETKDGv3 24
0YI H7 -4.183 2.757 -0.319 ETKDGv3 25
0YI H8 -2.974 4.003 0.140 ETKDGv3 26
0YI H9 2.387 -1.492 -2.116 ETKDGv3 27
0YI H10 -5.410 -1.371 0.533 ETKDGv3 28
0YI H11 -0.004 0.656 -0.542 ETKDGv3 29
#