data_Y62
#
_chem_comp.id Y62
_chem_comp.name "2-chloro-N-(5-cyanopyridin-2-yl)-5-nitrobenzamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H7 Cl N4 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-01-05
_chem_comp.pdbx_modified_date 2024-04-12
_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 302.673
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Y62
_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 8FKG
_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
Y62 C14 C1 C 0 1 Y N N N N N -4.585 4.696 9.997 -2.820 -1.817 -0.029 C14 Y62 1
Y62 C13 C2 C 0 1 Y N N N N N -4.716 5.313 8.772 -4.198 -1.787 0.030 C13 Y62 2
Y62 C12 C3 C 0 1 Y N N N N N -5.970 5.741 8.359 -4.838 -0.539 0.032 C12 Y62 3
Y62 C15 C4 C 0 1 N N N N N N -6.156 6.391 7.090 -6.266 -0.455 0.092 C15 Y62 4
Y62 C11 C5 C 0 1 Y N N N N N -7.050 5.535 9.220 -4.062 0.620 -0.025 C11 Y62 5
Y62 C01 C6 C 0 1 Y N N N N N -5.358 2.000 14.114 2.123 -0.738 -0.030 C01 Y62 6
Y62 C02 C7 C 0 1 Y N N N N N -5.002 1.330 15.264 3.501 -0.759 0.022 C02 Y62 7
Y62 C03 C8 C 0 1 Y N N N N N -5.577 1.603 16.482 4.213 0.426 0.074 C03 Y62 8
Y62 C04 C9 C 0 1 Y N N N N N -6.562 2.570 16.537 3.550 1.640 0.073 C04 Y62 9
Y62 C05 C10 C 0 1 Y N N N N N -6.939 3.238 15.381 2.170 1.676 0.021 C05 Y62 10
Y62 C06 C11 C 0 1 Y N N N N N -6.378 2.924 14.145 1.446 0.482 -0.031 C06 Y62 11
Y62 C07 C12 C 0 1 N N N N N N -6.736 3.674 12.895 -0.030 0.512 -0.087 C07 Y62 12
Y62 C09 C13 C 0 1 Y N N N N N -5.721 4.523 10.784 -2.115 -0.618 -0.083 C09 Y62 13
Y62 N08 N1 N 0 1 N N N N N N -5.695 3.901 12.042 -0.726 -0.641 -0.137 N08 Y62 14
Y62 N10 N2 N 0 1 Y N N N N N -6.935 4.941 10.403 -2.749 0.546 -0.079 N10 Y62 15
Y62 N16 N3 N 0 1 N N N N N N -6.303 6.912 6.085 -7.399 -0.388 0.139 N16 Y62 16
Y62 N18 N4 N 1 1 N N N N N N -3.955 0.309 15.190 4.220 -2.053 0.023 N18 Y62 17
Y62 O17 O1 O 0 1 N N N N N N -7.903 3.965 12.648 -0.617 1.577 -0.088 O17 Y62 18
Y62 O19 O2 O -1 1 N N N N N N -3.636 -0.270 16.218 3.595 -3.097 -0.022 O19 Y62 19
Y62 O20 O3 O 0 1 N N N N N N -3.452 0.076 14.101 5.437 -2.073 0.069 O20 Y62 20
Y62 H1 H1 H 0 1 N N N N N N -3.620 4.353 10.340 -2.294 -2.760 -0.028 H1 Y62 21
Y62 H2 H2 H 0 1 N N N N N N -3.853 5.462 8.140 -4.770 -2.702 0.072 H2 Y62 22
Y62 H3 H3 H 0 1 N N N N N N -8.027 5.875 8.909 -4.543 1.587 -0.024 H3 Y62 23
Y62 H4 H4 H 0 1 N N N N N N -4.837 1.801 13.189 1.569 -1.665 -0.074 H4 Y62 24
Y62 H5 H5 H 0 1 N N N N N N -5.267 1.076 17.372 5.292 0.403 0.115 H5 Y62 25
Y62 H6 H6 H 0 1 N N N N N N -7.037 2.805 17.478 4.112 2.561 0.114 H6 Y62 26
Y62 H8 H8 H 0 1 N N N N N N -4.799 3.584 12.353 -0.258 -1.487 -0.211 H8 Y62 27
Y62 CL1 CL1 CL 0 0 N Y N N N N -8.080 4.583 15.498 1.339 3.200 0.021 CL1 Y62 28
#
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
Y62 N16 C15 TRIP N N 1
Y62 C15 C12 SING N N 2
Y62 C12 C13 DOUB Y N 3
Y62 C12 C11 SING Y N 4
Y62 C13 C14 SING Y N 5
Y62 C11 N10 DOUB Y N 6
Y62 C14 C09 DOUB Y N 7
Y62 N10 C09 SING Y N 8
Y62 C09 N08 SING N N 9
Y62 N08 C07 SING N N 10
Y62 O17 C07 DOUB N N 11
Y62 C07 C06 SING N N 12
Y62 O20 N18 DOUB N N 13
Y62 C01 C06 DOUB Y N 14
Y62 C01 C02 SING Y N 15
Y62 C06 C05 SING Y N 16
Y62 N18 C02 SING N N 17
Y62 N18 O19 SING N N 18
Y62 C02 C03 DOUB Y N 19
Y62 C05 C04 DOUB Y N 20
Y62 C03 C04 SING Y N 21
Y62 C14 H1 SING N N 22
Y62 C13 H2 SING N N 23
Y62 C11 H3 SING N N 24
Y62 C01 H4 SING N N 25
Y62 C03 H5 SING N N 26
Y62 C04 H6 SING N N 27
Y62 N08 H8 SING N N 28
Y62 C05 CL1 SING N N 29
#
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
Y62 SMILES ACDLabs 12.01 "O=C(Nc1ccc(cn1)C#N)c1cc(ccc1Cl)[N+]([O-])=O"
Y62 InChI InChI 1.06 "InChI=1S/C13H7ClN4O3/c14-11-3-2-9(18(20)21)5-10(11)13(19)17-12-4-1-8(6-15)7-16-12/h1-5,7H,(H,16,17,19)"
Y62 InChIKey InChI 1.06 WLQNMMZWQLFUOW-UHFFFAOYSA-N
Y62 SMILES_CANONICAL CACTVS 3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2ccc(cn2)C#N"
Y62 SMILES CACTVS 3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2ccc(cn2)C#N"
Y62 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2ccc(cn2)C#N)Cl"
Y62 SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2ccc(cn2)C#N)Cl"
#
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
Y62 "SYSTEMATIC NAME" ACDLabs 12.01 "2-chloro-N-(5-cyanopyridin-2-yl)-5-nitrobenzamide"
Y62 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-chloranyl-~{N}-(5-cyanopyridin-2-yl)-5-nitro-benzamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Y62 'Create component' 2023-01-05 RCSB
Y62 'Initial release' 2024-04-17 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
Y62 C14 C 5.598 1.875 1
Y62 C13 C 5.598 3.375 2
Y62 C12 C 6.897 4.125 3
Y62 C15 C 6.897 5.625 4
Y62 C11 C 8.196 3.375 5
Y62 C01 C 6.897 -3.375 6
Y62 C02 C 6.897 -4.875 7
Y62 C03 C 5.598 -5.625 8
Y62 C04 C 4.299 -4.875 9
Y62 C05 C 4.299 -3.375 10
Y62 C06 C 5.598 -2.625 11
Y62 C07 C 5.598 -1.125 12
Y62 C09 C 6.897 1.125 13
Y62 N08 N 6.897 -0.375 14
Y62 N10 N 8.196 1.875 15
Y62 N16 N 6.897 7.125 16
Y62 N18 N 8.196 -5.625 17
Y62 O17 O 4.299 -0.375 18
Y62 O19 O 9.495 -4.875 19
Y62 O20 O 8.196 -7.125 20
Y62 CL1 Cl 3.000 -2.625 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
Y62 N16 C15 TRIPLE NONE 1
Y62 C15 C12 SINGLE NONE 2
Y62 C12 C13 SINGLE NONE 3
Y62 C12 C11 DOUBLE NONE 4
Y62 C13 C14 DOUBLE NONE 5
Y62 C11 N10 SINGLE NONE 6
Y62 C14 C09 SINGLE NONE 7
Y62 N10 C09 DOUBLE NONE 8
Y62 C09 N08 SINGLE NONE 9
Y62 N08 C07 SINGLE NONE 10
Y62 O17 C07 DOUBLE NONE 11
Y62 C07 C06 SINGLE NONE 12
Y62 O20 N18 DOUBLE NONE 13
Y62 C01 C06 DOUBLE NONE 14
Y62 C01 C02 SINGLE NONE 15
Y62 C06 C05 SINGLE NONE 16
Y62 N18 C02 SINGLE NONE 17
Y62 N18 O19 SINGLE NONE 18
Y62 C02 C03 DOUBLE NONE 19
Y62 C05 C04 DOUBLE NONE 20
Y62 C03 C04 SINGLE NONE 21
Y62 C05 CL1 SINGLE 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
Y62 MurckoScaffold S1 scaffold O=C(Nc1ccccn1)c1ccccc1 InChI=1S/C12H10N2O/c15-12(10-6-2-1-3-7-10)14-11-8-4-5-9-13-11/h1-9H,(H,13,14,15) LZIJKEIPCFEOLH-UHFFFAOYSA-N
Y62 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
Y62 phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
Y62 pyridine F3 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
Y62 Z219104216 F4 fragment 'CCNc1ccc(C#N)cn1' InChI=1S/C8H9N3/c1-2-10-8-4-3-7(5-9)6-11-8/h3-4,6H,2H2,1H3,(H,10,11) MVJDUNKELBBNKM-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
Y62 C14 S1 1
Y62 C13 S1 1
Y62 C12 S1 1
Y62 C11 S1 1
Y62 C01 S1 1
Y62 C02 S1 1
Y62 C03 S1 1
Y62 C04 S1 1
Y62 C05 S1 1
Y62 C06 S1 1
Y62 C07 S1 1
Y62 C09 S1 1
Y62 N08 S1 1
Y62 N10 S1 1
Y62 O17 S1 1
Y62 N08 F1 1
Y62 C07 F1 1
Y62 O17 F1 1
Y62 C06 F1 1
Y62 C01 F2 1
Y62 C06 F2 1
Y62 C05 F2 1
Y62 C04 F2 1
Y62 C03 F2 1
Y62 C02 F2 1
Y62 C11 F3 1
Y62 C12 F3 1
Y62 C13 F3 1
Y62 C14 F3 1
Y62 C09 F3 1
Y62 N10 F3 1
Y62 C06 F4 1
Y62 C07 F4 1
Y62 N08 F4 1
Y62 C09 F4 1
Y62 C14 F4 1
Y62 C13 F4 1
Y62 C12 F4 1
Y62 C15 F4 1
Y62 N16 F4 1
Y62 C11 F4 1
Y62 N10 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id Y62
_pdbe_chem_comp_rdkit_properties.exactmw 302.021
_pdbe_chem_comp_rdkit_properties.amw 302.677
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_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 133.391
_pdbe_chem_comp_rdkit_properties.tpsa 108.920
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.897
_pdbe_chem_comp_rdkit_properties.CrippenMR 72.832
_pdbe_chem_comp_rdkit_properties.chi0v 10.647
_pdbe_chem_comp_rdkit_properties.chi1v 5.478
_pdbe_chem_comp_rdkit_properties.chi2v 2.326
_pdbe_chem_comp_rdkit_properties.chi3v 2.326
_pdbe_chem_comp_rdkit_properties.chi4v 1.336
_pdbe_chem_comp_rdkit_properties.chi0n 16.892
_pdbe_chem_comp_rdkit_properties.chi1n 8.547
_pdbe_chem_comp_rdkit_properties.chi2n 2.042
_pdbe_chem_comp_rdkit_properties.chi3n 2.042
_pdbe_chem_comp_rdkit_properties.chi4n 1.161
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.980
_pdbe_chem_comp_rdkit_properties.kappa1 7.710
_pdbe_chem_comp_rdkit_properties.kappa2 5.983
_pdbe_chem_comp_rdkit_properties.kappa3 3.318
_pdbe_chem_comp_rdkit_properties.Phi 2.197
#
_pdbe_chem_comp_external_mappings.comp_id Y62
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource Mcule
_pdbe_chem_comp_external_mappings.resource_id MCULE-4241847668
#
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
Y62 C14 3.182 0.852 0.354 ETKDGv3 1
Y62 C13 4.382 0.423 0.756 ETKDGv3 2
Y62 C12 4.578 -1.002 1.096 ETKDGv3 3
Y62 C15 5.868 -1.471 1.529 ETKDGv3 4
Y62 C11 3.541 -1.845 0.997 ETKDGv3 5
Y62 C01 -2.529 -0.404 -1.522 ETKDGv3 6
Y62 C02 -3.883 0.171 -1.731 ETKDGv3 7
Y62 C03 -4.301 1.162 -0.922 ETKDGv3 8
Y62 C04 -3.438 1.653 0.168 ETKDGv3 9
Y62 C05 -2.219 1.134 0.358 ETKDGv3 10
Y62 C06 -1.721 0.059 -0.550 ETKDGv3 11
Y62 C07 -0.363 -0.510 -0.399 ETKDGv3 12
Y62 C09 2.060 -0.109 0.252 ETKDGv3 13
Y62 N08 0.764 0.351 -0.165 ETKDGv3 14
Y62 N10 2.258 -1.361 0.564 ETKDGv3 15
Y62 N16 6.905 -1.848 1.876 ETKDGv3 16
Y62 N18 -4.721 -0.327 -2.790 ETKDGv3 17
Y62 O17 -0.197 -1.753 -0.533 ETKDGv3 18
Y62 O19 -4.278 -1.340 -3.608 ETKDGv3 19
Y62 O20 -5.860 0.148 -2.984 ETKDGv3 20
Y62 H1 3.034 1.895 0.105 ETKDGv3 21
Y62 H2 5.207 1.120 0.832 ETKDGv3 22
Y62 H3 3.655 -2.895 1.241 ETKDGv3 23
Y62 H4 -2.181 -1.187 -2.186 ETKDGv3 24
Y62 H5 -5.281 1.606 -1.045 ETKDGv3 25
Y62 H6 -3.815 2.422 0.831 ETKDGv3 26
Y62 H8 0.640 1.376 -0.329 ETKDGv3 27
Y62 CL1 -1.285 1.678 1.748 ETKDGv3 28
#