data_S0G
#
_chem_comp.id S0G
_chem_comp.name 6-amino-1-methyl-5-(piperidin-1-yl)pyrimidine-2,4(1H,3H)-dione
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 N4 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-11-06
_chem_comp.pdbx_modified_date 2014-04-11
_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 224.260
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S0G
_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 3WKA
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
S0G C3 C3 C 0 1 N N N N N N -16.454 -9.494 70.678 0.050 0.010 0.088 C3 S0G 1
S0G C1 C1 C 0 1 N N N N N N -16.255 -9.859 71.953 1.015 0.977 0.157 C1 S0G 2
S0G C6 C6 C 0 1 N N N N N N -16.109 -8.094 70.277 0.438 -1.330 -0.094 C6 S0G 3
S0G C4 C4 C 0 1 N N N N N N -15.390 -7.663 72.563 2.682 -0.672 -0.126 C4 S0G 4
S0G C16 C16 C 0 1 N N N N N N -17.905 -12.156 67.597 -4.114 0.112 -0.145 C16 S0G 5
S0G C15 C15 C 0 1 N N N N N N -16.545 -12.355 68.254 -3.214 0.482 -1.326 C15 S0G 6
S0G C14 C14 C 0 1 N N N N N N -18.861 -11.394 68.485 -3.365 -0.839 0.791 C14 S0G 7
S0G C12 C12 C 0 1 N N N N N N -15.966 -11.083 68.886 -1.965 1.200 -0.806 C12 S0G 8
S0G C13 C13 C 0 1 N N N N N N -18.253 -10.123 69.068 -2.118 -0.135 1.336 C13 S0G 9
S0G C11 C11 C 0 1 N N N N N N -15.522 -9.452 74.280 3.381 1.645 0.119 C11 S0G 10
S0G N5 N5 N 0 1 N N N N N N -15.614 -7.281 71.264 1.746 -1.635 -0.196 N5 S0G 11
S0G N7 N7 N 0 1 N N N N N N -16.960 -10.371 69.721 -1.318 0.352 0.204 N7 S0G 12
S0G N2 N2 N 0 1 N N N N N N -15.727 -8.985 72.902 2.339 0.618 0.047 N2 S0G 13
S0G N10 N10 N 0 1 N N N N N N -16.584 -11.142 72.295 0.666 2.296 0.334 N10 S0G 14
S0G O9 O9 O 0 1 N N N N N N -16.261 -7.649 69.147 -0.405 -2.209 -0.157 O9 S0G 15
S0G O8 O8 O 0 1 N N N N N N -14.920 -6.842 73.333 3.857 -0.971 -0.221 O8 S0G 16
S0G H1 H1 H 0 1 N N N N N N -17.768 -11.595 66.661 -4.389 1.015 0.399 H1 S0G 17
S0G H2 H2 H 0 1 N N N N N N -18.338 -13.142 67.374 -5.015 -0.378 -0.515 H2 S0G 18
S0G H3 H3 H 0 1 N N N N N N -16.649 -13.116 69.041 -2.919 -0.424 -1.856 H3 S0G 19
S0G H4 H4 H 0 1 N N N N N N -15.840 -12.713 67.489 -3.757 1.140 -2.005 H4 S0G 20
S0G H5 H5 H 0 1 N N N N N N -19.746 -11.119 67.892 -4.015 -1.121 1.620 H5 S0G 21
S0G H6 H6 H 0 1 N N N N N N -19.165 -12.049 69.315 -3.068 -1.732 0.242 H6 S0G 22
S0G H7 H7 H 0 1 N N N N N N -15.107 -11.359 69.516 -1.276 1.378 -1.631 H7 S0G 23
S0G H8 H8 H 0 1 N N N N N N -15.630 -10.410 68.083 -2.252 2.151 -0.355 H8 S0G 24
S0G H9 H9 H 0 1 N N N N N N -18.105 -9.397 68.255 -2.417 0.706 1.961 H9 S0G 25
S0G H10 H10 H 0 1 N N N N N N -18.950 -9.706 69.810 -1.529 -0.839 1.924 H10 S0G 26
S0G H11 H11 H 0 1 N N N N N N -15.101 -8.636 74.886 3.691 1.777 1.156 H11 S0G 27
S0G H12 H12 H 0 1 N N N N N N -16.485 -9.767 74.708 4.238 1.336 -0.479 H12 S0G 28
S0G H13 H13 H 0 1 N N N N N N -14.826 -10.304 74.279 2.990 2.587 -0.266 H13 S0G 29
S0G H14 H14 H 0 1 N N N N N N -15.399 -6.336 71.018 2.015 -2.559 -0.321 H14 S0G 30
S0G H15 H15 H 0 1 N N N N N N -16.390 -11.289 73.265 -0.260 2.535 0.497 H15 S0G 31
S0G H16 H16 H 0 1 N N N N N N -17.557 -11.294 72.123 1.346 2.987 0.295 H16 S0G 32
#
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
S0G C16 C15 SING N N 1
S0G C16 C14 SING N N 2
S0G C15 C12 SING N N 3
S0G C14 C13 SING N N 4
S0G C12 N7 SING N N 5
S0G C13 N7 SING N N 6
S0G O9 C6 DOUB N N 7
S0G N7 C3 SING N N 8
S0G C6 C3 SING N N 9
S0G C6 N5 SING N N 10
S0G C3 C1 DOUB N N 11
S0G N5 C4 SING N N 12
S0G C1 N10 SING N N 13
S0G C1 N2 SING N N 14
S0G C4 N2 SING N N 15
S0G C4 O8 DOUB N N 16
S0G N2 C11 SING N N 17
S0G C16 H1 SING N N 18
S0G C16 H2 SING N N 19
S0G C15 H3 SING N N 20
S0G C15 H4 SING N N 21
S0G C14 H5 SING N N 22
S0G C14 H6 SING N N 23
S0G C12 H7 SING N N 24
S0G C12 H8 SING N N 25
S0G C13 H9 SING N N 26
S0G C13 H10 SING N N 27
S0G C11 H11 SING N N 28
S0G C11 H12 SING N N 29
S0G C11 H13 SING N N 30
S0G N5 H14 SING N N 31
S0G N10 H15 SING N N 32
S0G N10 H16 SING N N 33
#
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
S0G SMILES ACDLabs 12.01 O=C1C(=C(N)N(C(=O)N1)C)N2CCCCC2
S0G InChI InChI 1.03 InChI=1S/C10H16N4O2/c1-13-8(11)7(9(15)12-10(13)16)14-5-3-2-4-6-14/h2-6,11H2,1H3,(H,12,15,16)
S0G InChIKey InChI 1.03 ABFVQIXFKQQEOF-UHFFFAOYSA-N
S0G SMILES_CANONICAL CACTVS 3.385 CN1C(=C(N2CCCCC2)C(=O)NC1=O)N
S0G SMILES CACTVS 3.385 CN1C(=C(N2CCCCC2)C(=O)NC1=O)N
S0G SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CN1C(=C(C(=O)NC1=O)N2CCCCC2)N
S0G SMILES "OpenEye OEToolkits" 1.7.6 CN1C(=C(C(=O)NC1=O)N2CCCCC2)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
S0G "SYSTEMATIC NAME" ACDLabs 12.01 6-amino-1-methyl-5-(piperidin-1-yl)pyrimidine-2,4(1H,3H)-dione
S0G "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 6-azanyl-1-methyl-5-piperidin-1-yl-pyrimidine-2,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S0G 'Create component' 2013-11-06 PDBJ
S0G 'Initial release' 2014-04-16 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
S0G C3 C 6.897 0.375 1
S0G C1 C 6.897 -1.125 2
S0G C6 C 8.196 1.125 3
S0G C4 C 9.495 -1.125 4
S0G C16 C 3.000 2.625 5
S0G C15 C 4.299 3.375 6
S0G C14 C 3.000 1.125 7
S0G C12 C 5.598 2.625 8
S0G C13 C 4.299 0.375 9
S0G C11 C 8.196 -3.375 10
S0G N5 N 9.495 0.375 11
S0G N7 N 5.598 1.125 12
S0G N2 N 8.196 -1.875 13
S0G N10 N 5.598 -1.875 14
S0G O9 O 8.196 2.625 15
S0G O8 O 10.794 -1.875 16
#
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
S0G C16 C15 SINGLE NONE 1
S0G C16 C14 SINGLE NONE 2
S0G C15 C12 SINGLE NONE 3
S0G C14 C13 SINGLE NONE 4
S0G C12 N7 SINGLE NONE 5
S0G C13 N7 SINGLE NONE 6
S0G O9 C6 DOUBLE NONE 7
S0G N7 C3 SINGLE NONE 8
S0G C6 C3 SINGLE NONE 9
S0G C6 N5 SINGLE NONE 10
S0G C3 C1 DOUBLE NONE 11
S0G N5 C4 SINGLE NONE 12
S0G C1 N10 SINGLE NONE 13
S0G C1 N2 SINGLE NONE 14
S0G C4 N2 SINGLE NONE 15
S0G C4 O8 DOUBLE NONE 16
S0G N2 C11 SINGLE NONE 17
#
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
S0G MurckoScaffold S1 scaffold 'O=c1[nH]cc(N2CCCCC2)c(=O)[nH]1' InChI=1S/C9H13N3O2/c13-8-7(6-10-9(14)11-8)12-4-2-1-3-5-12/h6H,1-5H2,(H2,10,11,13,14) FBTCYHWAZUTCFE-UHFFFAOYSA-N
S0G pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
S0G C3 S1 1
S0G C1 S1 1
S0G C6 S1 1
S0G C4 S1 1
S0G C16 S1 1
S0G C15 S1 1
S0G C14 S1 1
S0G C12 S1 1
S0G C13 S1 1
S0G N5 S1 1
S0G N7 S1 1
S0G N2 S1 1
S0G O9 S1 1
S0G O8 S1 1
S0G C3 F1 1
S0G C6 F1 1
S0G N5 F1 1
S0G C4 F1 1
S0G N2 F1 1
S0G C1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id S0G
_pdbe_chem_comp_rdkit_properties.exactmw 224.127
_pdbe_chem_comp_rdkit_properties.amw 224.264
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 115.341
_pdbe_chem_comp_rdkit_properties.tpsa 84.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.685
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.348
_pdbe_chem_comp_rdkit_properties.chi0v 7.605
_pdbe_chem_comp_rdkit_properties.chi1v 3.921
_pdbe_chem_comp_rdkit_properties.chi2v 1.699
_pdbe_chem_comp_rdkit_properties.chi3v 1.699
_pdbe_chem_comp_rdkit_properties.chi4v 1.016
_pdbe_chem_comp_rdkit_properties.chi0n 23.605
_pdbe_chem_comp_rdkit_properties.chi1n 11.762
_pdbe_chem_comp_rdkit_properties.chi2n 1.699
_pdbe_chem_comp_rdkit_properties.chi3n 1.699
_pdbe_chem_comp_rdkit_properties.chi4n 1.016
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.720
_pdbe_chem_comp_rdkit_properties.kappa1 2.574
_pdbe_chem_comp_rdkit_properties.kappa2 4.034
_pdbe_chem_comp_rdkit_properties.kappa3 1.704
_pdbe_chem_comp_rdkit_properties.Phi 0.649
#
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
S0G UniChem ChEMBL CHEMBL3233607
S0G UniChem PDBe S0G
S0G UniChem ZINC ZINC000003379396
S0G UniChem BindingDb 50002344
S0G UniChem BRENDA 199919
S0G UniChem eMolecules 2861607
S0G UniChem PubChem 2497562
S0G UniChem Mcule MCULE-8375985990
#
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
S0G C3 -0.582 0.256 -0.309 ETKDGv3 1
S0G C1 -1.595 -0.212 0.457 ETKDGv3 2
S0G C6 -0.863 1.058 -1.513 ETKDGv3 3
S0G C4 -3.272 0.889 -1.046 ETKDGv3 4
S0G C16 3.669 0.036 -0.080 ETKDGv3 5
S0G C15 2.922 0.452 1.197 ETKDGv3 6
S0G C14 2.831 -0.845 -1.037 ETKDGv3 7
S0G C12 1.510 0.954 0.876 ETKDGv3 8
S0G C13 1.450 -1.209 -0.479 ETKDGv3 9
S0G C11 -4.074 -0.532 0.875 ETKDGv3 10
S0G N5 -2.207 1.379 -1.857 ETKDGv3 11
S0G N7 0.786 -0.006 0.034 ETKDGv3 12
S0G N2 -2.978 0.047 0.088 ETKDGv3 13
S0G N10 -1.296 -0.964 1.648 ETKDGv3 14
S0G O9 0.083 1.469 -2.237 ETKDGv3 15
S0G O8 -4.460 1.199 -1.334 ETKDGv3 16
S0G H1 4.593 -0.509 0.212 ETKDGv3 17
S0G H2 3.989 0.954 -0.620 ETKDGv3 18
S0G H3 3.492 1.252 1.719 ETKDGv3 19
S0G H4 2.854 -0.419 1.885 ETKDGv3 20
S0G H5 2.687 -0.300 -1.996 ETKDGv3 21
S0G H6 3.385 -1.780 -1.269 ETKDGv3 22
S0G H7 0.956 1.109 1.827 ETKDGv3 23
S0G H8 1.577 1.928 0.346 ETKDGv3 24
S0G H9 1.562 -1.947 0.345 ETKDGv3 25
S0G H10 0.843 -1.682 -1.282 ETKDGv3 26
S0G H11 -3.932 -1.629 0.972 ETKDGv3 27
S0G H12 -4.101 -0.065 1.882 ETKDGv3 28
S0G H13 -5.062 -0.376 0.394 ETKDGv3 29
S0G H14 -2.410 1.969 -2.695 ETKDGv3 30
S0G H15 -2.042 -1.271 2.308 ETKDGv3 31
S0G H16 -0.318 -1.206 1.920 ETKDGv3 32
#