data_KSX
#
_chem_comp.id KSX
_chem_comp.name 2-(5-cyanopyridin-3-yl)-N-(4-methylpyridin-3-yl)acetamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H12 N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-08-14
_chem_comp.pdbx_modified_date 2023-11-03
_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 252.271
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code KSX
_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 7GBC
_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
KSX N1 N1 N 0 1 N N N N N N 8.177 -0.024 21.044 1.678 0.554 0.934 N1 KSX 1
KSX N3 N2 N 0 1 N N N N N N 15.302 -1.843 19.810 -5.400 1.490 -2.093 N3 KSX 2
KSX C4 C1 C 0 1 Y N N N N N 8.087 0.100 18.581 2.644 -1.137 -0.503 C4 KSX 3
KSX C5 C2 C 0 1 Y N N N N N 7.506 0.288 19.840 2.750 0.069 0.176 C5 KSX 4
KSX C6 C3 C 0 1 N N N N N N 9.498 -0.148 21.174 0.419 0.172 0.641 C6 KSX 5
KSX C7 C4 C 0 1 N N N N N N 9.976 -0.953 22.367 -0.722 0.591 1.532 C7 KSX 6
KSX C8 C5 C 0 1 Y N N N N N 11.471 -0.786 22.518 -2.014 0.038 0.988 C8 KSX 7
KSX C10 C6 C 0 1 Y N N N N N 14.126 -0.134 22.671 -4.340 -1.048 0.058 C10 KSX 8
KSX C13 C7 C 0 1 Y N N N N N 12.348 -1.275 21.556 -2.758 0.768 0.077 C13 KSX 9
KSX C12 C8 C 0 1 N N N N N N 14.607 -1.430 20.615 -4.759 0.925 -1.345 C12 KSX 10
KSX C11 C9 C 0 1 Y N N N N N 13.696 -0.937 21.615 -3.951 0.213 -0.401 C11 KSX 11
KSX N2 N3 N 0 1 Y N N N N N 13.309 0.309 23.635 -3.594 -1.705 0.921 N2 KSX 12
KSX C9 C10 C 0 1 Y N N N N N 12.011 -0.019 23.540 -2.465 -1.206 1.389 C9 KSX 13
KSX O O1 O 0 1 N N N N N N 10.275 0.507 20.494 0.204 -0.508 -0.340 O KSX 14
KSX C1 C11 C 0 1 Y N N N N N 6.193 0.758 19.909 3.940 0.789 0.093 C1 KSX 15
KSX C C12 C 0 1 N N N N N N 5.523 1.039 21.230 4.099 2.102 0.816 C KSX 16
KSX N N4 N 0 1 Y N N N N N 7.480 0.421 17.435 3.653 -1.599 -1.214 N KSX 17
KSX C3 C13 C 0 1 Y N N N N N 6.249 0.937 17.520 4.794 -0.944 -1.309 C3 KSX 18
KSX C2 C14 C 0 1 Y N N N N N 5.574 1.105 18.713 4.972 0.268 -0.669 C2 KSX 19
KSX H1 H1 H 0 1 N N N N N N 7.618 -0.162 21.861 1.841 1.162 1.672 H1 KSX 20
KSX H2 H2 H 0 1 N N N N N N 9.078 -0.327 18.533 1.727 -1.704 -0.446 H2 KSX 21
KSX H3 H3 H 0 1 N N N N N N 9.473 -0.595 23.277 -0.557 0.206 2.539 H3 KSX 22
KSX H4 H4 H 0 1 N N N N N N 9.739 -2.016 22.211 -0.777 1.679 1.564 H4 KSX 23
KSX H5 H5 H 0 1 N N N N N N 15.169 0.144 22.713 -5.258 -1.489 -0.302 H5 KSX 24
KSX H6 H6 H 0 1 N N N N N N 11.984 -1.915 20.766 -2.427 1.740 -0.256 H6 KSX 25
KSX H7 H7 H 0 1 N N N N N N 11.343 0.338 24.310 -1.884 -1.779 2.096 H7 KSX 26
KSX H8 H8 H 0 1 N N N N N N 4.956 0.153 21.550 4.496 1.921 1.814 H8 KSX 27
KSX H9 H9 H 0 1 N N N N N N 6.287 1.278 21.985 4.787 2.740 0.261 H9 KSX 28
KSX H10 H10 H 0 1 N N N N N N 4.838 1.892 21.119 3.130 2.594 0.893 H10 KSX 29
KSX H11 H11 H 0 1 N N N N N N 5.757 1.238 16.607 5.597 -1.357 -1.901 H11 KSX 30
KSX H12 H12 H 0 1 N N N N N N 4.570 1.504 18.717 5.910 0.798 -0.753 H12 KSX 31
#
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
KSX N C3 DOUB Y N 1
KSX N C4 SING Y N 2
KSX C3 C2 SING Y N 3
KSX C4 C5 DOUB Y N 4
KSX C2 C1 DOUB Y N 5
KSX N3 C12 TRIP N N 6
KSX C5 C1 SING Y N 7
KSX C5 N1 SING N N 8
KSX C1 C SING N N 9
KSX O C6 DOUB N N 10
KSX C12 C11 SING N N 11
KSX N1 C6 SING N N 12
KSX C6 C7 SING N N 13
KSX C13 C11 DOUB Y N 14
KSX C13 C8 SING Y N 15
KSX C11 C10 SING Y N 16
KSX C7 C8 SING N N 17
KSX C8 C9 DOUB Y N 18
KSX C10 N2 DOUB Y N 19
KSX C9 N2 SING Y N 20
KSX N1 H1 SING N N 21
KSX C4 H2 SING N N 22
KSX C7 H3 SING N N 23
KSX C7 H4 SING N N 24
KSX C10 H5 SING N N 25
KSX C13 H6 SING N N 26
KSX C9 H7 SING N N 27
KSX C H8 SING N N 28
KSX C H9 SING N N 29
KSX C H10 SING N N 30
KSX C3 H11 SING N N 31
KSX C2 H12 SING N N 32
#
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
KSX SMILES ACDLabs 12.01 "O=C(Nc1cnccc1C)Cc1cc(C#N)cnc1"
KSX InChI InChI 1.06 InChI=1S/C14H12N4O/c1-10-2-3-16-9-13(10)18-14(19)5-11-4-12(6-15)8-17-7-11/h2-4,7-9H,5H2,1H3,(H,18,19)
KSX InChIKey InChI 1.06 MAYMKKDCBJTHBQ-UHFFFAOYSA-N
KSX SMILES_CANONICAL CACTVS 3.385 "Cc1ccncc1NC(=O)Cc2cncc(c2)C#N"
KSX SMILES CACTVS 3.385 "Cc1ccncc1NC(=O)Cc2cncc(c2)C#N"
KSX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1ccncc1NC(=O)Cc2cc(cnc2)C#N"
KSX SMILES "OpenEye OEToolkits" 2.0.7 "Cc1ccncc1NC(=O)Cc2cc(cnc2)C#N"
#
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
KSX "SYSTEMATIC NAME" ACDLabs 12.01 2-(5-cyanopyridin-3-yl)-N-(4-methylpyridin-3-yl)acetamide
KSX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 2-(5-cyanopyridin-3-yl)-~{N}-(4-methylpyridin-3-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
KSX 'Create component' 2023-08-14 RCSB
KSX 'Initial release' 2023-11-08 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
KSX N1 N 5.598 -0.375 1
KSX N3 N 13.392 1.125 2
KSX C4 C 6.897 -2.625 3
KSX C5 C 5.598 -1.875 4
KSX C6 C 6.897 0.375 5
KSX C7 C 6.897 1.875 6
KSX C8 C 8.196 2.625 7
KSX C10 C 10.794 4.125 8
KSX C13 C 9.495 1.875 9
KSX C12 C 12.093 1.875 10
KSX C11 C 10.794 2.625 11
KSX N2 N 9.495 4.875 12
KSX C9 C 8.196 4.125 13
KSX O O 8.196 -0.375 14
KSX C1 C 4.299 -2.625 15
KSX C C 3.000 -1.875 16
KSX N N 6.897 -4.125 17
KSX C3 C 5.598 -4.875 18
KSX C2 C 4.299 -4.125 19
#
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
KSX N C3 SINGLE NONE 1
KSX N C4 DOUBLE NONE 2
KSX C3 C2 DOUBLE NONE 3
KSX C4 C5 SINGLE NONE 4
KSX C2 C1 SINGLE NONE 5
KSX N3 C12 TRIPLE NONE 6
KSX C5 C1 DOUBLE NONE 7
KSX C5 N1 SINGLE NONE 8
KSX C1 C SINGLE NONE 9
KSX O C6 DOUBLE NONE 10
KSX C12 C11 SINGLE NONE 11
KSX N1 C6 SINGLE NONE 12
KSX C6 C7 SINGLE NONE 13
KSX C13 C11 SINGLE NONE 14
KSX C13 C8 DOUBLE NONE 15
KSX C11 C10 DOUBLE NONE 16
KSX C7 C8 SINGLE NONE 17
KSX C8 C9 SINGLE NONE 18
KSX C10 N2 SINGLE NONE 19
KSX C9 N2 DOUBLE NONE 20
#
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
KSX MurckoScaffold S1 scaffold O=C(Cc1cccnc1)Nc1cccnc1 InChI=1S/C12H11N3O/c16-12(7-10-3-1-5-13-8-10)15-11-4-2-6-14-9-11/h1-6,8-9H,7H2,(H,15,16) ZBTJRBRHSBUMTP-UHFFFAOYSA-N
KSX amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
KSX pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
KSX Z1129283193 F3 fragment CC(=O)Nc1cnccc1C InChI=1S/C8H10N2O/c1-6-3-4-9-5-8(6)10-7(2)11/h3-5H,1-2H3,(H,10,11) WRPYDRDMRXJIJA-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
KSX N1 S1 1
KSX C4 S1 1
KSX C5 S1 1
KSX C6 S1 1
KSX C7 S1 1
KSX C8 S1 1
KSX C10 S1 1
KSX C13 S1 1
KSX C11 S1 1
KSX N2 S1 1
KSX C9 S1 1
KSX O S1 1
KSX C1 S1 1
KSX N S1 1
KSX C3 S1 1
KSX C2 S1 1
KSX N1 F1 1
KSX C6 F1 1
KSX O F1 1
KSX C7 F1 1
KSX C4 F2 1
KSX C5 F2 1
KSX C1 F2 1
KSX C2 F2 1
KSX C3 F2 1
KSX N F2 1
KSX C10 F2 2
KSX C11 F2 2
KSX C13 F2 2
KSX C8 F2 2
KSX C9 F2 2
KSX N2 F2 2
KSX C7 F3 1
KSX C6 F3 1
KSX O F3 1
KSX N1 F3 1
KSX C5 F3 1
KSX C4 F3 1
KSX N F3 1
KSX C3 F3 1
KSX C2 F3 1
KSX C1 F3 1
KSX C F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id KSX
_pdbe_chem_comp_rdkit_properties.exactmw 252.101
_pdbe_chem_comp_rdkit_properties.amw 252.277
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.143
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 127.409
_pdbe_chem_comp_rdkit_properties.tpsa 78.670
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.293
_pdbe_chem_comp_rdkit_properties.CrippenMR 68.638
_pdbe_chem_comp_rdkit_properties.chi0v 9.197
_pdbe_chem_comp_rdkit_properties.chi1v 4.769
_pdbe_chem_comp_rdkit_properties.chi2v 1.778
_pdbe_chem_comp_rdkit_properties.chi3v 1.778
_pdbe_chem_comp_rdkit_properties.chi4v 1.030
_pdbe_chem_comp_rdkit_properties.chi0n 21.197
_pdbe_chem_comp_rdkit_properties.chi1n 10.717
_pdbe_chem_comp_rdkit_properties.chi2n 1.778
_pdbe_chem_comp_rdkit_properties.chi3n 1.778
_pdbe_chem_comp_rdkit_properties.chi4n 1.030
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.740
_pdbe_chem_comp_rdkit_properties.kappa1 4.423
_pdbe_chem_comp_rdkit_properties.kappa2 5.736
_pdbe_chem_comp_rdkit_properties.kappa3 3.360
_pdbe_chem_comp_rdkit_properties.Phi 1.335
#
_pdbe_chem_comp_external_mappings.comp_id KSX
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 154875993
#
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
KSX N1 -0.842 0.879 0.264 ETKDGv3 1
KSX N3 5.874 -2.223 0.359 ETKDGv3 2
KSX C4 -1.582 -1.468 0.872 ETKDGv3 3
KSX C5 -1.894 -0.094 0.400 ETKDGv3 4
KSX C6 0.241 1.005 1.198 ETKDGv3 5
KSX C7 1.439 1.832 0.848 ETKDGv3 6
KSX C8 2.336 1.067 -0.085 ETKDGv3 7
KSX C10 3.918 -0.409 -1.870 ETKDGv3 8
KSX C13 3.250 0.204 0.388 ETKDGv3 9
KSX C12 5.079 -1.486 -0.046 ETKDGv3 10
KSX C11 4.091 -0.569 -0.550 ETKDGv3 11
KSX N2 2.923 0.506 -2.360 ETKDGv3 12
KSX C9 2.175 1.201 -1.552 ETKDGv3 13
KSX O 0.196 0.419 2.313 ETKDGv3 14
KSX C1 -3.168 0.198 0.053 ETKDGv3 15
KSX C -3.559 1.560 -0.454 ETKDGv3 16
KSX N -2.521 -2.364 0.960 ETKDGv3 17
KSX C3 -3.881 -2.068 0.611 ETKDGv3 18
KSX C2 -4.210 -0.851 0.169 ETKDGv3 19
KSX H1 -0.870 1.544 -0.542 ETKDGv3 20
KSX H2 -0.567 -1.745 1.120 ETKDGv3 21
KSX H3 1.109 2.778 0.369 ETKDGv3 22
KSX H4 1.993 2.111 1.771 ETKDGv3 23
KSX H5 4.520 -0.965 -2.579 ETKDGv3 24
KSX H6 3.374 0.065 1.456 ETKDGv3 25
KSX H7 1.434 1.875 -1.960 ETKDGv3 26
KSX H8 -3.154 1.709 -1.477 ETKDGv3 27
KSX H9 -4.663 1.669 -0.495 ETKDGv3 28
KSX H10 -3.164 2.349 0.221 ETKDGv3 29
KSX H11 -4.637 -2.837 0.700 ETKDGv3 30
KSX H12 -5.237 -0.638 -0.100 ETKDGv3 31
#