data_YG5
#
_chem_comp.id YG5
_chem_comp.name 2-(1H-indazol-1-yl)-N,N-dimethylacetamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H13 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-01-27
_chem_comp.pdbx_modified_date 2023-02-10
_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 203.240
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YG5
_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 7FSY
_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
YG5 C10 C1 C 0 1 Y N N N N N -36.442 -0.153 -20.337 -2.361 -0.689 0.128 C10 YG5 1
YG5 C13 C2 C 0 1 Y N N N N N -34.065 -0.167 -18.823 -2.637 2.047 -0.149 C13 YG5 2
YG5 C15 C3 C 0 1 Y N N N N N -35.284 -0.686 -20.878 -1.273 0.094 -0.306 C15 YG5 3
YG5 C01 C4 C 0 1 N N N N N N -31.516 -0.325 -24.785 4.105 0.614 1.204 C01 YG5 4
YG5 N02 N1 N 0 1 N N N N N N -32.461 -1.247 -24.185 3.261 0.311 0.046 N02 YG5 5
YG5 C03 C5 C 0 1 N N N N N N -32.129 -2.665 -24.121 3.809 0.421 -1.308 C03 YG5 6
YG5 C04 C6 C 0 1 N N N N N N -33.701 -0.743 -23.641 1.980 -0.068 0.225 C04 YG5 7
YG5 O05 O1 O 0 1 N N N N N N -33.964 0.421 -23.700 1.526 -0.159 1.346 O05 YG5 8
YG5 C06 C7 C 0 1 N N N N N N -34.650 -1.757 -23.007 1.112 -0.379 -0.967 C06 YG5 9
YG5 N07 N2 N 0 1 Y N N N N N -35.593 -1.116 -22.121 -0.225 -0.765 -0.510 N07 YG5 10
YG5 N08 N3 N 0 1 Y N N N N N -36.884 -0.884 -22.410 -0.637 -2.068 -0.212 N08 YG5 11
YG5 C09 C8 C 0 1 Y N N N N N -37.446 -0.298 -21.368 -1.883 -2.068 0.167 C09 YG5 12
YG5 C11 C9 C 0 1 Y N N N N N -36.410 0.381 -19.024 -3.585 -0.076 0.414 C11 YG5 13
YG5 C12 C10 C 0 1 Y N N N N N -35.228 0.375 -18.276 -3.712 1.276 0.273 C12 YG5 14
YG5 C14 C11 C 0 1 Y N N N N N -34.084 -0.697 -20.111 -1.434 1.471 -0.441 C14 YG5 15
YG5 H131 H1 H 0 0 N N N N N N -33.151 -0.176 -18.248 -2.756 3.116 -0.255 H131 YG5 16
YG5 H012 H2 H 0 0 N N N N N N -31.925 0.695 -24.749 4.017 1.672 1.451 H012 YG5 17
YG5 H011 H3 H 0 0 N N N N N N -30.567 -0.359 -24.229 3.782 0.014 2.056 H011 YG5 18
YG5 H013 H4 H 0 0 N N N N N N -31.338 -0.612 -25.832 5.143 0.381 0.969 H013 YG5 19
YG5 H032 H5 H 0 0 N N N N N N -32.952 -3.213 -23.639 4.242 -0.534 -1.604 H032 YG5 20
YG5 H033 H6 H 0 0 N N N N N N -31.978 -3.052 -25.139 3.013 0.689 -2.002 H033 YG5 21
YG5 H031 H7 H 0 0 N N N N N N -31.207 -2.800 -23.537 4.581 1.191 -1.326 H031 YG5 22
YG5 H061 H8 H 0 0 N N N N N N -35.203 -2.276 -23.804 1.039 0.503 -1.603 H061 YG5 23
YG5 H062 H9 H 0 0 N N N N N N -34.061 -2.488 -22.434 1.553 -1.200 -1.533 H062 YG5 24
YG5 H091 H10 H 0 0 N N N N N N -38.476 0.018 -21.298 -2.460 -2.933 0.457 H091 YG5 25
YG5 H111 H11 H 0 0 N N N N N N -37.310 0.798 -18.596 -4.426 -0.669 0.742 H111 YG5 26
YG5 H121 H12 H 0 0 N N N N N N -35.216 0.789 -17.278 -4.656 1.751 0.499 H121 YG5 27
YG5 H141 H13 H 0 0 N N N N N N -33.183 -1.119 -20.531 -0.607 2.082 -0.774 H141 YG5 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
YG5 N02 C01 SING N N 1
YG5 C03 N02 SING N N 2
YG5 C04 N02 SING N N 3
YG5 O05 C04 DOUB N N 4
YG5 C06 C04 SING N N 5
YG5 N07 C06 SING N N 6
YG5 N08 N07 SING Y N 7
YG5 C09 N08 DOUB Y N 8
YG5 C10 C09 SING Y N 9
YG5 C11 C10 DOUB Y N 10
YG5 C12 C11 SING Y N 11
YG5 C13 C12 DOUB Y N 12
YG5 C14 C13 SING Y N 13
YG5 C15 C14 DOUB Y N 14
YG5 N07 C15 SING Y N 15
YG5 C10 C15 SING Y N 16
YG5 C13 H131 SING N N 17
YG5 C01 H012 SING N N 18
YG5 C01 H011 SING N N 19
YG5 C01 H013 SING N N 20
YG5 C03 H032 SING N N 21
YG5 C03 H033 SING N N 22
YG5 C03 H031 SING N N 23
YG5 C06 H061 SING N N 24
YG5 C06 H062 SING N N 25
YG5 C09 H091 SING N N 26
YG5 C11 H111 SING N N 27
YG5 C12 H121 SING N N 28
YG5 C14 H141 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
YG5 SMILES ACDLabs 12.01 CN(C)C(=O)Cn1ncc2ccccc21
YG5 InChI InChI 1.06 InChI=1S/C11H13N3O/c1-13(2)11(15)8-14-10-6-4-3-5-9(10)7-12-14/h3-7H,8H2,1-2H3
YG5 InChIKey InChI 1.06 AOLISVCNSODKGB-UHFFFAOYSA-N
YG5 SMILES_CANONICAL CACTVS 3.385 CN(C)C(=O)Cn1ncc2ccccc12
YG5 SMILES CACTVS 3.385 CN(C)C(=O)Cn1ncc2ccccc12
YG5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CN(C)C(=O)Cn1c2ccccc2cn1
YG5 SMILES "OpenEye OEToolkits" 2.0.7 CN(C)C(=O)Cn1c2ccccc2cn1
#
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
YG5 "SYSTEMATIC NAME" ACDLabs 12.01 2-(1H-indazol-1-yl)-N,N-dimethylacetamide
YG5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 2-indazol-1-yl-~{N},~{N}-dimethyl-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
YG5 'Create component' 2023-01-27 RCSB
YG5 'Initial release' 2023-02-15 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
YG5 C10 C 5.598 2.742 1
YG5 C13 C 3.000 1.242 2
YG5 C15 C 5.598 1.242 3
YG5 C01 C 10.885 -2.685 4
YG5 N02 N 9.417 -2.376 5
YG5 C03 C 8.415 -3.492 6
YG5 C04 C 8.951 -0.950 7
YG5 O05 O 9.953 0.167 8
YG5 C06 C 7.483 -0.641 9
YG5 N07 N 7.018 0.785 10
YG5 N08 N 7.893 1.992 11
YG5 C09 C 7.018 3.199 12
YG5 C11 C 4.299 3.492 13
YG5 C12 C 3.000 2.742 14
YG5 C14 C 4.299 0.492 15
#
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
YG5 N02 C01 SINGLE NONE 1
YG5 C03 N02 SINGLE NONE 2
YG5 C04 N02 SINGLE NONE 3
YG5 O05 C04 DOUBLE NONE 4
YG5 C06 C04 SINGLE NONE 5
YG5 N07 C06 SINGLE NONE 6
YG5 N08 N07 SINGLE NONE 7
YG5 C09 N08 DOUBLE NONE 8
YG5 C10 C09 SINGLE NONE 9
YG5 C11 C10 DOUBLE NONE 10
YG5 C12 C11 SINGLE NONE 11
YG5 C13 C12 DOUBLE NONE 12
YG5 C14 C13 SINGLE NONE 13
YG5 C15 C14 DOUBLE NONE 14
YG5 N07 C15 SINGLE NONE 15
YG5 C10 C15 SINGLE NONE 16
#
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
YG5 MurckoScaffold S1 scaffold 'c1ccc2[nH]ncc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)5-8-9-7/h1-5H,(H,8,9) BAXOFTOLAUCFNW-UHFFFAOYSA-N
YG5 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YG5 peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
YG5 phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
YG5 pyrazole F4 fragment 'c1cn[nH]c1' InChI=1S/C3H4N2/c1-2-4-5-3-1/h1-3H,(H,4,5) WTKZEGDFNFYCGP-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
YG5 C10 S1 1
YG5 C13 S1 1
YG5 C15 S1 1
YG5 N07 S1 1
YG5 N08 S1 1
YG5 C09 S1 1
YG5 C11 S1 1
YG5 C12 S1 1
YG5 C14 S1 1
YG5 N02 F1 1
YG5 C04 F1 1
YG5 O05 F1 1
YG5 C06 F1 1
YG5 O05 F2 1
YG5 C04 F2 1
YG5 C06 F2 1
YG5 N07 F2 1
YG5 C10 F3 1
YG5 C11 F3 1
YG5 C12 F3 1
YG5 C13 F3 1
YG5 C14 F3 1
YG5 C15 F3 1
YG5 C15 F4 1
YG5 C10 F4 1
YG5 C09 F4 1
YG5 N08 F4 1
YG5 N07 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YG5
_pdbe_chem_comp_rdkit_properties.exactmw 203.106
_pdbe_chem_comp_rdkit_properties.amw 203.245
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 106.366
_pdbe_chem_comp_rdkit_properties.tpsa 38.130
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.696
_pdbe_chem_comp_rdkit_properties.CrippenMR 56.221
_pdbe_chem_comp_rdkit_properties.chi0v 7.250
_pdbe_chem_comp_rdkit_properties.chi1v 3.746
_pdbe_chem_comp_rdkit_properties.chi2v 1.546
_pdbe_chem_comp_rdkit_properties.chi3v 1.546
_pdbe_chem_comp_rdkit_properties.chi4v 0.917
_pdbe_chem_comp_rdkit_properties.chi0n 20.250
_pdbe_chem_comp_rdkit_properties.chi1n 10.246
_pdbe_chem_comp_rdkit_properties.chi2n 1.546
_pdbe_chem_comp_rdkit_properties.chi3n 1.546
_pdbe_chem_comp_rdkit_properties.chi4n 0.917
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 2.638
_pdbe_chem_comp_rdkit_properties.kappa2 3.726
_pdbe_chem_comp_rdkit_properties.kappa3 1.834
_pdbe_chem_comp_rdkit_properties.Phi 0.655
#
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
YG5 UniChem ChEMBL CHEMBL4540215
YG5 UniChem PDBe YG5
YG5 UniChem ZINC ZINC000096404712
YG5 UniChem PubChem 84583666
#
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
YG5 C10 2.558 1.085 0.893 ETKDGv3 1
YG5 C13 3.211 -1.256 -0.468 ETKDGv3 2
YG5 C15 1.563 0.074 0.686 ETKDGv3 3
YG5 C01 -3.197 0.093 -2.178 ETKDGv3 4
YG5 N02 -2.723 -0.272 -0.839 ETKDGv3 5
YG5 C03 -3.466 -1.250 -0.036 ETKDGv3 6
YG5 C04 -1.529 0.353 -0.322 ETKDGv3 7
YG5 O05 -0.944 1.239 -1.006 ETKDGv3 8
YG5 C06 -0.989 0.001 1.042 ETKDGv3 9
YG5 N07 0.349 0.551 1.243 ETKDGv3 10
YG5 N08 0.599 1.841 1.747 ETKDGv3 11
YG5 C09 1.850 2.164 1.575 ETKDGv3 12
YG5 C11 3.810 0.956 0.453 ETKDGv3 13
YG5 C12 4.152 -0.303 -0.266 ETKDGv3 14
YG5 C14 1.820 -1.060 0.030 ETKDGv3 15
YG5 H131 3.466 -2.165 -0.997 ETKDGv3 16
YG5 H012 -4.112 -0.469 -2.460 ETKDGv3 17
YG5 H011 -3.432 1.178 -2.209 ETKDGv3 18
YG5 H013 -2.410 -0.132 -2.928 ETKDGv3 19
YG5 H032 -4.395 -1.580 -0.546 ETKDGv3 20
YG5 H033 -3.754 -0.799 0.936 ETKDGv3 21
YG5 H031 -2.836 -2.147 0.141 ETKDGv3 22
YG5 H061 -0.946 -1.102 1.161 ETKDGv3 23
YG5 H062 -1.671 0.407 1.819 ETKDGv3 24
YG5 H091 2.271 3.112 1.881 ETKDGv3 25
YG5 H111 4.542 1.738 0.601 ETKDGv3 26
YG5 H121 5.159 -0.452 -0.635 ETKDGv3 27
YG5 H141 1.055 -1.806 -0.138 ETKDGv3 28
#