data_YDG
#
_chem_comp.id YDG
_chem_comp.name N,N-dimethyl-2-(1H-pyrazol-1-yl)acetamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H11 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-01-25
_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 153.182
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YDG
_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 7FSN
_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
YDG C10 C1 C 0 1 Y N N N N N -37.065 0.899 -21.094 3.034 0.798 -0.417 C10 YDG 1
YDG C01 C2 C 0 1 N N N N N N -31.800 0.580 -24.396 -3.363 1.034 0.305 C01 YDG 2
YDG N02 N1 N 0 1 N N N N N N -32.623 -0.535 -23.968 -2.422 -0.049 0.009 N02 YDG 3
YDG C03 C3 C 0 1 N N N N N N -32.224 -1.897 -24.281 -2.924 -1.380 -0.344 C03 YDG 4
YDG C04 C4 C 0 1 N N N N N N -33.820 -0.236 -23.224 -1.095 0.178 0.062 C04 YDG 5
YDG O05 O1 O 0 1 N N N N N N -34.069 0.906 -23.011 -0.679 1.279 0.355 O05 YDG 6
YDG C06 C5 C 0 1 N N N N N N -34.762 -1.325 -22.723 -0.127 -0.937 -0.242 C06 YDG 7
YDG N07 N2 N 0 1 Y N N N N N -35.767 -0.664 -21.921 1.245 -0.440 -0.116 N07 YDG 8
YDG C08 C6 C 0 1 Y N N N N N -36.441 -1.243 -20.960 2.214 -0.970 0.658 C08 YDG 9
YDG C09 C7 C 0 1 Y N N N N N -37.269 -0.295 -20.431 3.329 -0.221 0.495 C09 YDG 10
YDG N11 N3 N 0 1 Y N N N N N -36.139 0.678 -22.025 1.785 0.668 -0.784 N11 YDG 11
YDG H101 H1 H 0 0 N N N N N N -37.563 1.836 -20.895 3.717 1.562 -0.755 H101 YDG 12
YDG H012 H2 H 0 0 N N N N N N -32.261 1.524 -24.069 -3.591 1.037 1.371 H012 YDG 13
YDG H011 H3 H 0 0 N N N N N N -30.798 0.488 -23.951 -2.917 1.989 0.026 H011 YDG 14
YDG H013 H4 H 0 0 N N N N N N -31.716 0.574 -25.493 -4.281 0.883 -0.262 H013 YDG 15
YDG H032 H5 H 0 0 N N N N N N -32.968 -2.600 -23.877 -3.055 -1.443 -1.424 H032 YDG 16
YDG H033 H6 H 0 0 N N N N N N -32.160 -2.018 -25.372 -2.210 -2.136 -0.019 H033 YDG 17
YDG H031 H7 H 0 0 N N N N N N -31.242 -2.104 -23.831 -3.882 -1.549 0.148 H031 YDG 18
YDG H061 H8 H 0 0 N N N N N N -35.233 -1.840 -23.573 -0.283 -1.755 0.461 H061 YDG 19
YDG H062 H9 H 0 0 N N N N N N -34.209 -2.054 -22.113 -0.293 -1.294 -1.258 H062 YDG 20
YDG H081 H10 H 0 0 N N N N N N -36.358 -2.273 -20.646 2.117 -1.836 1.296 H081 YDG 21
YDG H091 H11 H 0 0 N N N N N N -37.970 -0.453 -19.625 4.280 -0.381 0.983 H091 YDG 22
#
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
YDG N02 C01 SING N N 1
YDG C03 N02 SING N N 2
YDG C04 N02 SING N N 3
YDG O05 C04 DOUB N N 4
YDG C06 C04 SING N N 5
YDG N07 C06 SING N N 6
YDG C08 N07 SING Y N 7
YDG C09 C08 DOUB Y N 8
YDG C10 C09 SING Y N 9
YDG N11 C10 DOUB Y N 10
YDG N07 N11 SING Y N 11
YDG C10 H101 SING N N 12
YDG C01 H012 SING N N 13
YDG C01 H011 SING N N 14
YDG C01 H013 SING N N 15
YDG C03 H032 SING N N 16
YDG C03 H033 SING N N 17
YDG C03 H031 SING N N 18
YDG C06 H061 SING N N 19
YDG C06 H062 SING N N 20
YDG C08 H081 SING N N 21
YDG C09 H091 SING N N 22
#
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
YDG SMILES ACDLabs 12.01 O=C(Cn1cccn1)N(C)C
YDG InChI InChI 1.06 InChI=1S/C7H11N3O/c1-9(2)7(11)6-10-5-3-4-8-10/h3-5H,6H2,1-2H3
YDG InChIKey InChI 1.06 HTIDWWCOZGRQRN-UHFFFAOYSA-N
YDG SMILES_CANONICAL CACTVS 3.385 CN(C)C(=O)Cn1cccn1
YDG SMILES CACTVS 3.385 CN(C)C(=O)Cn1cccn1
YDG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CN(C)C(=O)Cn1cccn1
YDG SMILES "OpenEye OEToolkits" 2.0.7 CN(C)C(=O)Cn1cccn1
#
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
YDG "SYSTEMATIC NAME" ACDLabs 12.01 N,N-dimethyl-2-(1H-pyrazol-1-yl)acetamide
YDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N},~{N}-dimethyl-2-pyrazol-1-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
YDG 'Create component' 2023-01-25 RCSB
YDG '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
YDG C10 C 4.848 3.404 1
YDG C01 C 3.000 -3.404 2
YDG N02 N 4.299 -2.654 3
YDG C03 C 5.598 -3.404 4
YDG C04 C 4.299 -1.154 5
YDG O05 O 3.000 -0.404 6
YDG C06 C 5.598 -0.404 7
YDG N07 N 5.598 1.096 8
YDG C08 C 6.812 1.978 9
YDG C09 C 6.348 3.404 10
YDG N11 N 4.385 1.978 11
#
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
YDG N02 C01 SINGLE NONE 1
YDG C03 N02 SINGLE NONE 2
YDG C04 N02 SINGLE NONE 3
YDG O05 C04 DOUBLE NONE 4
YDG C06 C04 SINGLE NONE 5
YDG N07 C06 SINGLE NONE 6
YDG C08 N07 SINGLE NONE 7
YDG C09 C08 DOUBLE NONE 8
YDG C10 C09 SINGLE NONE 9
YDG N11 C10 DOUBLE NONE 10
YDG N07 N11 SINGLE NONE 11
#
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
YDG MurckoScaffold S1 scaffold 'c1cn[nH]c1' InChI=1S/C3H4N2/c1-2-4-5-3-1/h1-3H,(H,4,5) WTKZEGDFNFYCGP-UHFFFAOYSA-N
YDG amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YDG peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
YDG pyrazole F3 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
YDG C10 S1 1
YDG N07 S1 1
YDG C08 S1 1
YDG C09 S1 1
YDG N11 S1 1
YDG N02 F1 1
YDG C04 F1 1
YDG O05 F1 1
YDG C06 F1 1
YDG O05 F2 1
YDG C04 F2 1
YDG C06 F2 1
YDG N07 F2 1
YDG C10 F3 1
YDG C09 F3 1
YDG C08 F3 1
YDG N07 F3 1
YDG N11 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YDG
_pdbe_chem_comp_rdkit_properties.exactmw 153.090
_pdbe_chem_comp_rdkit_properties.amw 153.185
_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 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 80.874
_pdbe_chem_comp_rdkit_properties.tpsa 38.130
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.029
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.921
_pdbe_chem_comp_rdkit_properties.chi0v 5.250
_pdbe_chem_comp_rdkit_properties.chi1v 2.496
_pdbe_chem_comp_rdkit_properties.chi2v 0.772
_pdbe_chem_comp_rdkit_properties.chi3v 0.772
_pdbe_chem_comp_rdkit_properties.chi4v 0.371
_pdbe_chem_comp_rdkit_properties.chi0n 16.250
_pdbe_chem_comp_rdkit_properties.chi1n 7.996
_pdbe_chem_comp_rdkit_properties.chi2n 0.772
_pdbe_chem_comp_rdkit_properties.chi3n 0.772
_pdbe_chem_comp_rdkit_properties.chi4n 0.371
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.320
_pdbe_chem_comp_rdkit_properties.kappa1 1.705
_pdbe_chem_comp_rdkit_properties.kappa2 3.184
_pdbe_chem_comp_rdkit_properties.kappa3 2.070
_pdbe_chem_comp_rdkit_properties.Phi 0.494
#
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
YDG UniChem PDBe YDG
YDG UniChem ZINC ZINC000041367139
YDG UniChem SureChEMBL SCHEMBL17399639
YDG UniChem PubChem 52141969
YDG UniChem Mcule MCULE-6682455234
#
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
YDG C10 2.946 0.592 1.048 ETKDGv3 1
YDG C01 -2.915 0.877 0.832 ETKDGv3 2
YDG N02 -1.791 0.197 0.181 ETKDGv3 3
YDG C03 -1.586 -1.242 0.385 ETKDGv3 4
YDG C04 -0.898 0.963 -0.658 ETKDGv3 5
YDG O05 -1.101 2.197 -0.824 ETKDGv3 6
YDG C06 0.301 0.341 -1.319 ETKDGv3 7
YDG N07 1.346 0.089 -0.335 ETKDGv3 8
YDG C08 2.270 -0.989 -0.364 ETKDGv3 9
YDG C09 3.251 -0.724 0.483 ETKDGv3 10
YDG N11 1.847 1.052 0.546 ETKDGv3 11
YDG H101 3.549 1.133 1.764 ETKDGv3 12
YDG H012 -2.532 1.679 1.498 ETKDGv3 13
YDG H011 -3.577 1.328 0.062 ETKDGv3 14
YDG H013 -3.523 0.180 1.445 ETKDGv3 15
YDG H032 -0.589 -1.422 0.839 ETKDGv3 16
YDG H033 -2.349 -1.674 1.065 ETKDGv3 17
YDG H031 -1.656 -1.775 -0.586 ETKDGv3 18
YDG H061 0.700 1.020 -2.103 ETKDGv3 19
YDG H062 0.008 -0.606 -1.818 ETKDGv3 20
YDG H081 2.187 -1.869 -0.989 ETKDGv3 21
YDG H091 4.113 -1.346 0.683 ETKDGv3 22
#