data_OD2
#
_chem_comp.id OD2
_chem_comp.name "2-[6-(4-methylsulfanylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H12 N2 O2 S3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-02-27
_chem_comp.pdbx_modified_date 2020-03-06
_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 348.463
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OD2
_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 6Y6F
_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
OD2 C C1 C 0 1 N N N N N N 58.968 3.834 -0.888 6.211 -1.542 0.001 C OD2 1
OD2 O O1 O 0 1 N N N N N N 57.889 4.358 -0.698 5.740 -2.655 -0.000 O OD2 2
OD2 O1 O2 O 0 1 N N N N N N 59.987 3.984 -0.113 7.543 -1.378 -0.004 O1 OD2 3
OD2 C1 C2 C 0 1 N N N N N N 59.283 2.950 -2.063 5.303 -0.340 0.002 C1 OD2 4
OD2 S S1 S 0 1 N N N N N N 61.029 2.502 -2.140 3.578 -0.886 0.000 S OD2 5
OD2 C2 C3 C 0 1 Y N N N N N 61.122 1.569 -3.617 2.762 0.675 0.001 C2 OD2 6
OD2 N1 N1 N 0 1 Y N N N N N 60.035 1.404 -4.383 3.463 1.804 0.002 N1 OD2 7
OD2 C14 C4 C 0 1 Y N N N N N 60.246 0.762 -5.534 2.857 2.977 0.003 C14 OD2 8
OD2 N N2 N 0 1 Y N N N N N 61.383 0.235 -5.998 1.553 3.097 0.003 N OD2 9
OD2 C4 C5 C 0 1 Y N N N N N 62.454 0.398 -5.178 0.750 2.006 0.002 C4 OD2 10
OD2 C5 C6 C 0 1 Y N N N N N 63.804 -0.026 -5.430 -0.648 1.928 0.001 C5 OD2 11
OD2 C6 C7 C 0 1 Y N N N N N 64.687 0.350 -4.492 -1.157 0.691 0.000 C6 OD2 12
OD2 S1 S2 S 0 1 Y N N N N N 63.915 1.223 -3.209 0.128 -0.506 -0.001 S1 OD2 13
OD2 C3 C8 C 0 1 Y N N N N N 62.365 1.084 -3.967 1.359 0.748 -0.005 C3 OD2 14
OD2 C7 C9 C 0 1 Y N N N N N 66.142 0.163 -4.471 -2.601 0.375 -0.000 C7 OD2 15
OD2 C12 C10 C 0 1 Y N N N N N 66.793 -0.506 -5.506 -3.543 1.406 -0.005 C12 OD2 16
OD2 C11 C11 C 0 1 Y N N N N N 68.153 -0.757 -5.439 -4.888 1.109 -0.005 C11 OD2 17
OD2 C10 C12 C 0 1 Y N N N N N 68.886 -0.350 -4.335 -5.309 -0.217 -0.001 C10 OD2 18
OD2 S2 S3 S 0 1 N N N N N N 70.590 -0.793 -4.342 -7.030 -0.594 -0.001 S2 OD2 19
OD2 C13 C13 C 0 1 N N N N N N 71.127 -0.491 -2.655 -7.051 -2.408 0.006 C13 OD2 20
OD2 C9 C14 C 0 1 Y N N N N N 68.253 0.339 -3.311 -4.373 -1.247 0.004 C9 OD2 21
OD2 C8 C15 C 0 1 Y N N N N N 66.898 0.597 -3.381 -3.026 -0.955 -0.002 C8 OD2 22
OD2 H1 H1 H 0 1 N N N N N N 59.755 4.557 0.609 8.085 -2.179 -0.008 H1 OD2 23
OD2 H2 H2 H 0 1 N N N N N N 59.014 3.482 -2.987 5.494 0.259 0.892 H2 OD2 24
OD2 H3 H3 H 0 1 N N N N N N 58.686 2.030 -1.983 5.495 0.261 -0.888 H3 OD2 25
OD2 H4 H4 H 0 1 N N N N N N 59.384 0.654 -6.175 3.460 3.873 0.005 H4 OD2 26
OD2 H5 H5 H 0 1 N N N N N N 64.084 -0.599 -6.301 -1.274 2.809 0.002 H5 OD2 27
OD2 H6 H6 H 0 1 N N N N N N 66.231 -0.832 -6.369 -3.217 2.436 -0.008 H6 OD2 28
OD2 H7 H7 H 0 1 N N N N N N 68.645 -1.272 -6.251 -5.616 1.906 -0.009 H7 OD2 29
OD2 H8 H8 H 0 1 N N N N N N 72.194 -0.742 -2.559 -6.540 -2.780 -0.882 H8 OD2 30
OD2 H9 H9 H 0 1 N N N N N N 70.976 0.570 -2.407 -6.542 -2.773 0.898 H9 OD2 31
OD2 H10 H10 H 0 1 N N N N N N 70.540 -1.116 -1.966 -8.083 -2.759 0.006 H10 OD2 32
OD2 H11 H11 H 0 1 N N N N N N 68.821 0.675 -2.456 -4.702 -2.275 0.007 H11 OD2 33
OD2 H12 H12 H 0 1 N N N N N N 66.417 1.142 -2.582 -2.300 -1.755 -0.002 H12 OD2 34
#
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
OD2 N C14 DOUB Y N 1
OD2 N C4 SING Y N 2
OD2 C14 N1 SING Y N 3
OD2 C12 C11 DOUB Y N 4
OD2 C12 C7 SING Y N 5
OD2 C11 C10 SING Y N 6
OD2 C5 C4 SING Y N 7
OD2 C5 C6 DOUB Y N 8
OD2 C4 C3 DOUB Y N 9
OD2 C6 C7 SING N N 10
OD2 C6 S1 SING Y N 11
OD2 C7 C8 DOUB Y N 12
OD2 N1 C2 DOUB Y N 13
OD2 S2 C10 SING N N 14
OD2 S2 C13 SING N N 15
OD2 C10 C9 DOUB Y N 16
OD2 C3 C2 SING Y N 17
OD2 C3 S1 SING Y N 18
OD2 C2 S SING N N 19
OD2 C8 C9 SING Y N 20
OD2 S C1 SING N N 21
OD2 C1 C SING N N 22
OD2 C O DOUB N N 23
OD2 C O1 SING N N 24
OD2 O1 H1 SING N N 25
OD2 C1 H2 SING N N 26
OD2 C1 H3 SING N N 27
OD2 C14 H4 SING N N 28
OD2 C5 H5 SING N N 29
OD2 C12 H6 SING N N 30
OD2 C11 H7 SING N N 31
OD2 C13 H8 SING N N 32
OD2 C13 H9 SING N N 33
OD2 C13 H10 SING N N 34
OD2 C9 H11 SING N N 35
OD2 C8 H12 SING N N 36
#
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
OD2 InChI InChI 1.03 InChI=1S/C15H12N2O2S3/c1-20-10-4-2-9(3-5-10)12-6-11-14(22-12)15(17-8-16-11)21-7-13(18)19/h2-6,8H,7H2,1H3,(H,18,19)
OD2 InChIKey InChI 1.03 KJCQGDBVLKOAHP-UHFFFAOYSA-N
OD2 SMILES_CANONICAL CACTVS 3.385 CSc1ccc(cc1)c2sc3c(SCC(O)=O)ncnc3c2
OD2 SMILES CACTVS 3.385 CSc1ccc(cc1)c2sc3c(SCC(O)=O)ncnc3c2
OD2 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CSc1ccc(cc1)c2cc3c(s2)c(ncn3)SCC(=O)O
OD2 SMILES "OpenEye OEToolkits" 2.0.7 CSc1ccc(cc1)c2cc3c(s2)c(ncn3)SCC(=O)O
#
_pdbx_chem_comp_identifier.comp_id OD2
_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 "2-[6-(4-methylsulfanylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
OD2 'Create component' 2020-02-27 PDBE
OD2 'Initial release' 2020-03-11 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
OD2 C C 4.299 -2.535 1
OD2 O O 3.000 -3.285 2
OD2 O1 O 5.598 -3.285 3
OD2 C1 C 4.299 -1.035 4
OD2 S S 5.598 -0.285 5
OD2 C2 C 5.598 1.215 6
OD2 N1 N 4.299 1.965 7
OD2 C14 C 4.299 3.465 8
OD2 N N 5.598 4.215 9
OD2 C4 C 6.897 3.465 10
OD2 C5 C 8.316 3.922 11
OD2 C6 C 9.192 2.715 12
OD2 S1 S 8.316 1.508 13
OD2 C3 C 6.897 1.965 14
OD2 C7 C 10.692 2.715 15
OD2 C12 C 11.442 4.014 16
OD2 C11 C 12.942 4.014 17
OD2 C10 C 13.692 2.715 18
OD2 S2 S 15.192 2.715 19
OD2 C13 C 15.942 4.014 20
OD2 C9 C 12.942 1.416 21
OD2 C8 C 11.442 1.416 22
#
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
OD2 N C14 DOUBLE NONE 1
OD2 N C4 SINGLE NONE 2
OD2 C14 N1 SINGLE NONE 3
OD2 C12 C11 DOUBLE NONE 4
OD2 C12 C7 SINGLE NONE 5
OD2 C11 C10 SINGLE NONE 6
OD2 C5 C4 SINGLE NONE 7
OD2 C5 C6 DOUBLE NONE 8
OD2 C4 C3 DOUBLE NONE 9
OD2 C6 C7 SINGLE NONE 10
OD2 C6 S1 SINGLE NONE 11
OD2 C7 C8 DOUBLE NONE 12
OD2 N1 C2 DOUBLE NONE 13
OD2 S2 C10 SINGLE NONE 14
OD2 S2 C13 SINGLE NONE 15
OD2 C10 C9 DOUBLE NONE 16
OD2 C3 C2 SINGLE NONE 17
OD2 C3 S1 SINGLE NONE 18
OD2 C2 S SINGLE NONE 19
OD2 C8 C9 SINGLE NONE 20
OD2 S C1 SINGLE NONE 21
OD2 C1 C SINGLE NONE 22
OD2 C O DOUBLE NONE 23
OD2 C O1 SINGLE NONE 24
#
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
OD2 MurckoScaffold S1 scaffold c1ccc(-c2cc3ncncc3s2)cc1 InChI=1S/C12H8N2S/c1-2-4-9(5-3-1)11-6-10-12(15-11)7-13-8-14-10/h1-8H AVGKRRPAWDSBPE-UHFFFAOYSA-N
OD2 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
OD2 pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
OD2 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
OD2 C2 S1 1
OD2 N1 S1 1
OD2 C14 S1 1
OD2 N S1 1
OD2 C4 S1 1
OD2 C5 S1 1
OD2 C6 S1 1
OD2 S1 S1 1
OD2 C3 S1 1
OD2 C7 S1 1
OD2 C12 S1 1
OD2 C11 S1 1
OD2 C10 S1 1
OD2 C9 S1 1
OD2 C8 S1 1
OD2 C7 F1 1
OD2 C12 F1 1
OD2 C11 F1 1
OD2 C10 F1 1
OD2 C9 F1 1
OD2 C8 F1 1
OD2 C3 F2 1
OD2 C4 F2 1
OD2 N F2 1
OD2 C14 F2 1
OD2 N1 F2 1
OD2 C2 F2 1
OD2 C6 F3 1
OD2 C5 F3 1
OD2 C4 F3 1
OD2 C3 F3 1
OD2 S1 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id OD2
_pdbe_chem_comp_rdkit_properties.exactmw 348.006
_pdbe_chem_comp_rdkit_properties.amw 348.474
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.133
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_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 156.493
_pdbe_chem_comp_rdkit_properties.tpsa 63.080
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.232
_pdbe_chem_comp_rdkit_properties.CrippenMR 90.604
_pdbe_chem_comp_rdkit_properties.chi0v 12.885
_pdbe_chem_comp_rdkit_properties.chi1v 7.977
_pdbe_chem_comp_rdkit_properties.chi2v 4.717
_pdbe_chem_comp_rdkit_properties.chi3v 4.717
_pdbe_chem_comp_rdkit_properties.chi4v 3.266
_pdbe_chem_comp_rdkit_properties.chi0n 22.436
_pdbe_chem_comp_rdkit_properties.chi1n 11.436
_pdbe_chem_comp_rdkit_properties.chi2n 2.321
_pdbe_chem_comp_rdkit_properties.chi3n 2.321
_pdbe_chem_comp_rdkit_properties.chi4n 1.473
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.570
_pdbe_chem_comp_rdkit_properties.kappa1 6.506
_pdbe_chem_comp_rdkit_properties.kappa2 6.681
_pdbe_chem_comp_rdkit_properties.kappa3 3.262
_pdbe_chem_comp_rdkit_properties.Phi 1.976
#
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
OD2 UniChem ChEMBL CHEMBL1836719
OD2 UniChem PDBe OD2
OD2 UniChem ChEBI 143111
OD2 UniChem ZINC ZINC000072123072
OD2 UniChem 'Probes And Drugs' PD076620
OD2 UniChem BindingDb 50354565
OD2 UniChem PubChem 56675920
#
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
OD2 C 5.669 0.750 -1.079 ETKDGv3 1
OD2 O 6.832 0.539 -1.516 ETKDGv3 2
OD2 O1 5.487 1.205 0.223 ETKDGv3 3
OD2 C1 4.483 0.481 -1.947 ETKDGv3 4
OD2 S 4.162 -1.313 -2.055 ETKDGv3 5
OD2 C2 3.500 -1.447 -0.394 ETKDGv3 6
OD2 N1 4.281 -1.766 0.600 ETKDGv3 7
OD2 C14 3.770 -1.878 1.947 ETKDGv3 8
OD2 N 2.506 -1.662 2.194 ETKDGv3 9
OD2 C4 1.620 -1.314 1.120 ETKDGv3 10
OD2 C5 0.179 -1.037 1.273 ETKDGv3 11
OD2 C6 -0.430 -0.723 0.119 ETKDGv3 12
OD2 S1 0.767 -0.753 -1.223 ETKDGv3 13
OD2 C3 2.077 -1.210 -0.118 ETKDGv3 14
OD2 C7 -1.869 -0.389 -0.037 ETKDGv3 15
OD2 C12 -2.854 -0.720 1.030 ETKDGv3 16
OD2 C11 -4.148 -0.410 0.879 ETKDGv3 17
OD2 C10 -4.613 0.265 -0.349 ETKDGv3 18
OD2 S2 -6.348 0.674 -0.541 ETKDGv3 19
OD2 C13 -6.172 2.311 0.233 ETKDGv3 20
OD2 C9 -3.738 0.555 -1.320 ETKDGv3 21
OD2 C8 -2.309 0.214 -1.159 ETKDGv3 22
OD2 H1 6.280 1.377 0.829 ETKDGv3 23
OD2 H2 3.590 1.010 -1.554 ETKDGv3 24
OD2 H3 4.684 0.866 -2.969 ETKDGv3 25
OD2 H4 4.438 -2.142 2.755 ETKDGv3 26
OD2 H5 -0.314 -1.065 2.234 ETKDGv3 27
OD2 H6 -2.546 -1.231 1.931 ETKDGv3 28
OD2 H7 -4.857 -0.659 1.659 ETKDGv3 29
OD2 H8 -5.808 2.202 1.276 ETKDGv3 30
OD2 H9 -5.461 2.934 -0.349 ETKDGv3 31
OD2 H10 -7.161 2.814 0.248 ETKDGv3 32
OD2 H11 -4.068 1.045 -2.227 ETKDGv3 33
OD2 H12 -1.629 0.476 -1.959 ETKDGv3 34
#