data_XOB
#
_chem_comp.id XOB
_chem_comp.name "1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]pyrimidine-2,4-dione"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H12 N2 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-06-08
_chem_comp.pdbx_modified_date 2024-02-16
_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 332.331
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XOB
_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 8CG9
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
XOB C1 C1 C 0 1 Y N N N N N 0.898 18.568 20.211 5.496 0.487 -1.393 C1 XOB 1
XOB C2 C2 C 0 1 Y N N N N N 2.104 18.816 19.587 4.652 1.580 -1.456 C2 XOB 2
XOB C3 C3 C 0 1 Y N N N N N 3.283 18.765 20.309 3.403 1.526 -0.865 C3 XOB 3
XOB C4 C4 C 0 1 Y N N N N N 3.244 18.476 21.666 2.995 0.376 -0.207 C4 XOB 4
XOB C5 C5 C 0 1 Y N N N N N 2.035 18.208 22.291 3.843 -0.724 -0.146 C5 XOB 5
XOB C6 C6 C 0 1 Y N N N N N 0.858 18.274 21.564 5.094 -0.663 -0.740 C6 XOB 6
XOB O7 O1 O 0 1 N N N N N N 1.967 17.912 23.636 3.460 -1.864 0.491 O7 XOB 7
XOB C8 C7 C 0 1 N N N N N N 3.237 17.527 24.200 2.356 -1.756 1.396 C8 XOB 8
XOB C9 C8 C 0 1 N N R N N N 4.324 18.478 23.771 1.246 -0.952 0.705 C9 XOB 9
XOB O10 O2 O 0 1 N N N N N N 4.444 18.439 22.341 1.766 0.341 0.377 O10 XOB 10
XOB C11 C9 C 0 1 N N N N N N 5.715 18.120 24.316 0.052 -0.804 1.650 C11 XOB 11
XOB N12 N1 N 0 1 N N N N N N 5.867 18.208 25.783 -1.049 -0.141 0.946 N12 XOB 12
XOB C13 C10 C 0 1 Y N N N N N 6.086 19.400 26.428 -1.992 -0.910 0.251 C13 XOB 13
XOB C14 C11 C 0 1 Y N N N N N 6.182 20.752 25.850 -2.078 -2.288 0.098 C14 XOB 14
XOB C15 C12 C 0 1 Y N N N N N 6.403 21.696 26.804 -3.103 -2.723 -0.631 C15 XOB 15
XOB S16 S1 S 0 1 Y N N N N N 6.501 21.061 28.402 -4.057 -1.427 -1.191 S16 XOB 16
XOB C17 C13 C 0 1 Y N N N N N 6.242 19.442 27.812 -3.017 -0.249 -0.402 C17 XOB 17
XOB C18 C14 C 0 1 N N N N N N 6.183 18.274 28.559 -3.077 1.167 -0.346 C18 XOB 18
XOB O19 O3 O 0 1 N N N N N N 6.316 18.238 29.779 -3.973 1.765 -0.915 O19 XOB 19
XOB N20 N2 N 0 1 N N N N N N 5.968 17.105 27.876 -2.138 1.846 0.339 N20 XOB 20
XOB C21 C15 C 0 1 N N N N N N 5.809 17.049 26.511 -1.149 1.197 0.977 C21 XOB 21
XOB O22 O4 O 0 1 N N N N N N 5.621 15.987 25.939 -0.320 1.839 1.593 O22 XOB 22
XOB O23 O5 O 0 1 N N N N N N 5.900 15.916 28.579 -2.197 3.259 0.395 O23 XOB 23
XOB H1 H1 H 0 1 N N N N N N -0.019 18.603 19.641 6.469 0.531 -1.859 H1 XOB 24
XOB H2 H2 H 0 1 N N N N N N 2.127 19.050 18.533 4.968 2.477 -1.968 H2 XOB 25
XOB H3 H3 H 0 1 N N N N N N 4.228 18.949 19.820 2.746 2.382 -0.915 H3 XOB 26
XOB H4 H4 H 0 1 N N N N N N -0.089 18.097 22.051 5.754 -1.517 -0.697 H4 XOB 27
XOB H5 H5 H 0 1 N N N N N N 3.162 17.537 25.297 1.988 -2.750 1.647 H5 XOB 28
XOB H6 H6 H 0 1 N N N N N N 3.490 16.512 23.859 2.673 -1.241 2.303 H6 XOB 29
XOB H7 H7 H 0 1 N N N N N N 4.065 19.495 24.102 0.933 -1.465 -0.205 H7 XOB 30
XOB H8 H8 H 0 1 N N N N N N 5.942 17.087 24.013 -0.272 -1.789 1.984 H8 XOB 31
XOB H9 H9 H 0 1 N N N N N N 6.444 18.804 23.858 0.344 -0.205 2.513 H9 XOB 32
XOB H10 H10 H 0 1 N N N N N N 6.088 20.967 24.796 -1.359 -2.962 0.540 H10 XOB 33
XOB H11 H11 H 0 1 N N N N N N 6.507 22.747 26.580 -3.305 -3.763 -0.840 H11 XOB 34
XOB H12 H12 H 0 1 N N N N N N 6.023 16.088 29.505 -2.944 3.641 -0.087 H12 XOB 35
#
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
XOB C2 C1 DOUB Y N 1
XOB C2 C3 SING Y N 2
XOB C1 C6 SING Y N 3
XOB C3 C4 DOUB Y N 4
XOB C6 C5 DOUB Y N 5
XOB C4 C5 SING Y N 6
XOB C4 O10 SING N N 7
XOB C5 O7 SING N N 8
XOB O10 C9 SING N N 9
XOB O7 C8 SING N N 10
XOB C9 C8 SING N N 11
XOB C9 C11 SING N N 12
XOB C11 N12 SING N N 13
XOB N12 C13 SING N N 14
XOB N12 C21 SING N N 15
XOB C14 C13 SING Y N 16
XOB C14 C15 DOUB Y N 17
XOB O22 C21 DOUB N N 18
XOB C13 C17 DOUB Y N 19
XOB C21 N20 SING N N 20
XOB C15 S16 SING Y N 21
XOB C17 S16 SING Y N 22
XOB C17 C18 SING N N 23
XOB N20 C18 SING N N 24
XOB N20 O23 SING N N 25
XOB C18 O19 DOUB N N 26
XOB C1 H1 SING N N 27
XOB C2 H2 SING N N 28
XOB C3 H3 SING N N 29
XOB C6 H4 SING N N 30
XOB C8 H5 SING N N 31
XOB C8 H6 SING N N 32
XOB C9 H7 SING N N 33
XOB C11 H8 SING N N 34
XOB C11 H9 SING N N 35
XOB C14 H10 SING N N 36
XOB C15 H11 SING N N 37
XOB O23 H12 SING N N 38
#
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
XOB InChI InChI 1.06 "InChI=1S/C15H12N2O5S/c18-14-13-10(5-6-23-13)16(15(19)17(14)20)7-9-8-21-11-3-1-2-4-12(11)22-9/h1-6,9,20H,7-8H2/t9-/m1/s1"
XOB InChIKey InChI 1.06 MXQGCMQXTPTJJT-SECBINFHSA-N
XOB SMILES_CANONICAL CACTVS 3.385 "ON1C(=O)N(C[C@@H]2COc3ccccc3O2)c4ccsc4C1=O"
XOB SMILES CACTVS 3.385 "ON1C(=O)N(C[CH]2COc3ccccc3O2)c4ccsc4C1=O"
XOB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)OC[C@H](O2)CN3c4ccsc4C(=O)N(C3=O)O"
XOB SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)OCC(O2)CN3c4ccsc4C(=O)N(C3=O)O"
#
_pdbx_chem_comp_identifier.comp_id XOB
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
"1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]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
XOB 'Create component' 2023-06-08 PDBE
XOB 'Initial release' 2024-02-21 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
XOB C1 C 3.000 0.605 1
XOB C2 C 3.000 -0.958 2
XOB C3 C 4.359 -1.728 3
XOB C4 C 5.700 -0.926 4
XOB C5 C 5.700 0.574 5
XOB C6 C 4.359 1.376 6
XOB O7 O 6.999 1.324 7
XOB C8 C 8.298 0.574 8
XOB C9 C 8.298 -0.926 9
XOB O10 O 6.999 -1.676 10
XOB C11 C 9.597 -1.676 11
XOB N12 N 10.896 -0.926 12
XOB C13 C 12.195 -1.676 13
XOB C14 C 12.509 -3.134 14
XOB C15 C 13.992 -3.289 15
XOB S16 S 14.600 -1.927 16
XOB C17 C 13.494 -0.926 17
XOB C18 C 13.494 0.574 18
XOB O19 O 14.793 1.324 19
XOB N20 N 12.195 1.324 20
XOB C21 C 10.896 0.574 21
XOB O22 O 9.597 1.324 22
XOB O23 O 12.195 2.824 23
#
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
XOB C2 C1 DOUBLE NONE 1
XOB C2 C3 SINGLE NONE 2
XOB C1 C6 SINGLE NONE 3
XOB C3 C4 DOUBLE NONE 4
XOB C6 C5 DOUBLE NONE 5
XOB C4 C5 SINGLE NONE 6
XOB C4 O10 SINGLE NONE 7
XOB C5 O7 SINGLE NONE 8
XOB O10 C9 SINGLE NONE 9
XOB O7 C8 SINGLE NONE 10
XOB C9 C8 SINGLE NONE 11
XOB C9 C11 SINGLE BEGINWEDGE 12
XOB C11 N12 SINGLE NONE 13
XOB N12 C13 SINGLE NONE 14
XOB N12 C21 SINGLE NONE 15
XOB C14 C13 SINGLE NONE 16
XOB C14 C15 DOUBLE NONE 17
XOB O22 C21 DOUBLE NONE 18
XOB C13 C17 DOUBLE NONE 19
XOB C21 N20 SINGLE NONE 20
XOB C15 S16 SINGLE NONE 21
XOB C17 S16 SINGLE NONE 22
XOB C17 C18 SINGLE NONE 23
XOB N20 C18 SINGLE NONE 24
XOB N20 O23 SINGLE NONE 25
XOB C18 O19 DOUBLE NONE 26
#
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
XOB MurckoScaffold S1 scaffold 'O=c1[nH]c(=O)n(C[C@@H]2COc3ccccc3O2)c2ccsc12' InChI=1S/C15H12N2O4S/c18-14-13-10(5-6-22-13)17(15(19)16-14)7-9-8-20-11-3-1-2-4-12(11)21-9/h1-6,9H,7-8H2,(H,16,18,19)/t9-/m1/s1 MMUHNMSJKZWUND-SECBINFHSA-N
XOB phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
XOB pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
XOB thiophen F3 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
XOB C1 S1 1
XOB C2 S1 1
XOB C3 S1 1
XOB C4 S1 1
XOB C5 S1 1
XOB C6 S1 1
XOB O7 S1 1
XOB C8 S1 1
XOB C9 S1 1
XOB O10 S1 1
XOB C11 S1 1
XOB N12 S1 1
XOB C13 S1 1
XOB C14 S1 1
XOB C15 S1 1
XOB S16 S1 1
XOB C17 S1 1
XOB C18 S1 1
XOB O19 S1 1
XOB N20 S1 1
XOB C21 S1 1
XOB O22 S1 1
XOB C1 F1 1
XOB C2 F1 1
XOB C3 F1 1
XOB C4 F1 1
XOB C5 F1 1
XOB C6 F1 1
XOB C17 F2 1
XOB C13 F2 1
XOB N12 F2 1
XOB C21 F2 1
XOB N20 F2 1
XOB C18 F2 1
XOB C15 F3 1
XOB C14 F3 1
XOB C13 F3 1
XOB C17 F3 1
XOB S16 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id XOB
_pdbe_chem_comp_rdkit_properties.exactmw 332.047
_pdbe_chem_comp_rdkit_properties.amw 332.337
_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 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 150.003
_pdbe_chem_comp_rdkit_properties.tpsa 82.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.749
_pdbe_chem_comp_rdkit_properties.CrippenMR 80.673
_pdbe_chem_comp_rdkit_properties.chi0v 11.660
_pdbe_chem_comp_rdkit_properties.chi1v 6.750
_pdbe_chem_comp_rdkit_properties.chi2v 3.565
_pdbe_chem_comp_rdkit_properties.chi3v 3.565
_pdbe_chem_comp_rdkit_properties.chi4v 2.461
_pdbe_chem_comp_rdkit_properties.chi0n 22.844
_pdbe_chem_comp_rdkit_properties.chi1n 11.842
_pdbe_chem_comp_rdkit_properties.chi2n 2.789
_pdbe_chem_comp_rdkit_properties.chi3n 2.789
_pdbe_chem_comp_rdkit_properties.chi4n 1.802
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.740
_pdbe_chem_comp_rdkit_properties.kappa1 6.045
_pdbe_chem_comp_rdkit_properties.kappa2 5.165
_pdbe_chem_comp_rdkit_properties.kappa3 2.184
_pdbe_chem_comp_rdkit_properties.Phi 1.358
#
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
XOB UniChem ZINC ZINC000028362665
XOB UniChem SureChEMBL SCHEMBL20856907
XOB UniChem PubChem 138506135
#
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
XOB C1 5.461 -0.200 -0.269 ETKDGv3 1
XOB C2 5.242 0.135 -1.550 ETKDGv3 2
XOB C3 3.860 0.337 -2.040 ETKDGv3 3
XOB C4 2.832 0.182 -1.197 ETKDGv3 4
XOB C5 3.074 -0.148 0.221 ETKDGv3 5
XOB C6 4.321 -0.350 0.663 ETKDGv3 6
XOB O7 1.975 -0.239 1.077 ETKDGv3 7
XOB C8 0.691 0.246 0.671 ETKDGv3 8
XOB C9 0.420 -0.110 -0.808 ETKDGv3 9
XOB O10 1.511 0.324 -1.629 ETKDGv3 10
XOB C11 -0.883 0.516 -1.331 ETKDGv3 11
XOB N12 -2.060 -0.031 -0.637 ETKDGv3 12
XOB C13 -2.693 0.666 0.465 ETKDGv3 13
XOB C14 -2.285 1.993 1.002 ETKDGv3 14
XOB C15 -3.025 2.415 2.026 ETKDGv3 15
XOB S16 -4.283 1.215 2.412 ETKDGv3 16
XOB C17 -3.731 0.138 1.111 ETKDGv3 17
XOB C18 -4.293 -1.163 0.755 ETKDGv3 18
XOB O19 -5.275 -1.633 1.388 ETKDGv3 19
XOB N20 -3.704 -1.892 -0.325 ETKDGv3 20
XOB C21 -2.580 -1.326 -1.026 ETKDGv3 21
XOB O22 -2.054 -1.963 -1.979 ETKDGv3 22
XOB O23 -4.221 -3.123 -0.675 ETKDGv3 23
XOB H1 6.471 -0.353 0.087 ETKDGv3 24
XOB H2 6.076 0.250 -2.231 ETKDGv3 25
XOB H3 3.686 0.586 -3.079 ETKDGv3 26
XOB H4 4.502 -0.599 1.701 ETKDGv3 27
XOB H5 0.675 1.349 0.799 ETKDGv3 28
XOB H6 -0.084 -0.201 1.328 ETKDGv3 29
XOB H7 0.347 -1.216 -0.890 ETKDGv3 30
XOB H8 -0.968 0.305 -2.420 ETKDGv3 31
XOB H9 -0.839 1.620 -1.254 ETKDGv3 32
XOB H10 -1.465 2.584 0.622 ETKDGv3 33
XOB H11 -2.873 3.353 2.544 ETKDGv3 34
XOB H12 -3.828 -3.667 -1.434 ETKDGv3 35
#