data_4SU # _chem_comp.id 4SU _chem_comp.name "4-THIOURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P S" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces S4U _chem_comp.formula_weight 340.247 _chem_comp.one_letter_code U _chem_comp.three_letter_code 4SU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1C0A _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 4SU N1 N1 N 0 1 N N N N N N 63.154 13.727 18.838 0.383 0.505 2.126 N1 4SU 1 4SU C2 C2 C 0 1 N N N N N N 64.392 13.288 19.235 -0.353 -0.614 2.243 C2 4SU 2 4SU N3 N3 N 0 1 N N N N N N 65.444 13.734 18.479 -1.082 -0.849 3.350 N3 4SU 3 4SU C4 C4 C 0 1 N N N N N N 65.393 14.561 17.376 -1.093 0.043 4.359 C4 4SU 4 4SU C5 C5 C 0 1 N N N N N N 64.064 14.981 17.022 -0.328 1.228 4.248 C5 4SU 5 4SU C6 C6 C 0 1 N N N N N N 63.015 14.557 17.746 0.398 1.438 3.130 C6 4SU 6 4SU O2 O2 O 0 1 N N N N N N 64.547 12.555 20.187 -0.353 -1.429 1.341 O2 4SU 7 4SU S4 S4 S 0 1 N N N N N N 66.471 14.892 16.753 -2.026 -0.252 5.764 S4 4SU 8 4SU "C1'" C1* C 0 1 N N R N N N 61.999 13.272 19.625 1.171 0.732 0.912 "C1'" 4SU 9 4SU "C2'" C2* C 0 1 N N R N N N 61.785 14.056 20.917 2.207 -0.397 0.724 "C2'" 4SU 10 4SU "O2'" O2* O 0 1 N N N N N N 61.255 13.167 21.876 3.490 0.011 1.201 "O2'" 4SU 11 4SU "C3'" C3* C 0 1 N N S N N N 60.724 15.065 20.500 2.244 -0.622 -0.803 "C3'" 4SU 12 4SU "C4'" C4* C 0 1 N N R N N N 59.879 14.273 19.518 1.225 0.396 -1.361 "C4'" 4SU 13 4SU "O3'" O3* O 0 1 N N N N N N 59.926 15.428 21.608 3.551 -0.356 -1.317 "O3'" 4SU 14 4SU "O4'" O4* O 0 1 N N N N N N 60.827 13.409 18.838 0.328 0.658 -0.258 "O4'" 4SU 15 4SU "C5'" C5* C 0 1 N N N N N N 59.164 15.117 18.500 0.458 -0.200 -2.542 "C5'" 4SU 16 4SU "O5'" O5* O 0 1 N N N N N N 60.122 15.869 17.763 -0.525 0.734 -2.991 "O5'" 4SU 17 4SU P P P 0 1 N N N N N N 59.736 17.216 17.019 -1.291 0.045 -4.229 P 4SU 18 4SU OP1 O1P O 0 1 N N N N N N 61.010 17.801 16.545 -1.928 -1.211 -3.777 OP1 4SU 19 4SU OP2 O2P O 0 1 N N N N N N 58.830 18.014 17.876 -2.420 1.048 -4.787 OP2 4SU 20 4SU OP3 O3P O 0 1 N Y N N N N 58.930 16.738 15.732 -0.235 -0.279 -5.400 OP3 4SU 21 4SU HN3 HN3 H 0 1 N N N N N N 66.368 13.414 18.769 -1.604 -1.664 3.420 HN3 4SU 22 4SU H5 H5 H 0 1 N N N N N N 63.843 15.647 16.171 -0.325 1.954 5.047 H5 4SU 23 4SU H6 H6 H 0 1 N N N N N N 62.013 14.899 17.435 0.988 2.336 3.027 H6 4SU 24 4SU "H1'" H1* H 0 1 N N N N N N 62.207 12.213 19.905 1.669 1.700 0.959 "H1'" 4SU 25 4SU "H2'" H2* H 0 1 N N N N N N 62.698 14.527 21.348 1.881 -1.303 1.235 "H2'" 4SU 26 4SU "HO2'" *HO2 H 0 0 N N N N N N 61.121 13.655 22.680 4.105 -0.708 1.002 "HO2'" 4SU 27 4SU "H3'" H3* H 0 1 N N N N N N 61.154 16.005 20.082 1.939 -1.640 -1.047 "H3'" 4SU 28 4SU "H4'" H4* H 0 1 N N N N N N 59.071 13.735 20.067 1.733 1.312 -1.663 "H4'" 4SU 29 4SU "HO3'" *HO3 H 0 0 N Y N N N N 59.263 16.057 21.347 4.147 -1.001 -0.913 "HO3'" 4SU 30 4SU "H5'" 1H5* H 0 1 N N N N N N 58.500 14.512 17.839 1.151 -0.415 -3.355 "H5'" 4SU 31 4SU "H5''" 2H5* H 0 0 N N N N N N 58.380 15.763 18.960 -0.032 -1.121 -2.229 "H5''" 4SU 32 4SU HOP2 2HOP H 0 0 N N N N N N 58.598 18.820 17.430 -2.853 0.598 -5.525 HOP2 4SU 33 4SU HOP3 3HOP H 0 0 N N N N N N 58.698 17.544 15.286 0.156 0.564 -5.665 HOP3 4SU 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 4SU N1 C2 SING N N 1 4SU N1 C6 SING N N 2 4SU N1 "C1'" SING N N 3 4SU C2 N3 SING N N 4 4SU C2 O2 DOUB N N 5 4SU N3 C4 SING N N 6 4SU N3 HN3 SING N N 7 4SU C4 C5 SING N N 8 4SU C4 S4 DOUB N N 9 4SU C5 C6 DOUB N N 10 4SU C5 H5 SING N N 11 4SU C6 H6 SING N N 12 4SU "C1'" "C2'" SING N N 13 4SU "C1'" "O4'" SING N N 14 4SU "C1'" "H1'" SING N N 15 4SU "C2'" "O2'" SING N N 16 4SU "C2'" "C3'" SING N N 17 4SU "C2'" "H2'" SING N N 18 4SU "O2'" "HO2'" SING N N 19 4SU "C3'" "C4'" SING N N 20 4SU "C3'" "O3'" SING N N 21 4SU "C3'" "H3'" SING N N 22 4SU "C4'" "O4'" SING N N 23 4SU "C4'" "C5'" SING N N 24 4SU "C4'" "H4'" SING N N 25 4SU "O3'" "HO3'" SING N N 26 4SU "C5'" "O5'" SING N N 27 4SU "C5'" "H5'" SING N N 28 4SU "C5'" "H5''" SING N N 29 4SU "O5'" P SING N N 30 4SU P OP1 DOUB N N 31 4SU P OP2 SING N N 32 4SU P OP3 SING N N 33 4SU OP2 HOP2 SING N N 34 4SU OP3 HOP3 SING N N 35 # 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 4SU SMILES ACDLabs 10.04 S=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O 4SU SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=S)NC2=O 4SU SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=S)NC2=O 4SU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=S)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O 4SU SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=S)C2C(C(C(O2)COP(=O)(O)O)O)O 4SU InChI InChI 1.03 InChI=1S/C9H13N2O8PS/c12-6-4(3-18-20(15,16)17)19-8(7(6)13)11-2-1-5(21)10-9(11)14/h1-2,4,6-8,12-13H,3H2,(H,10,14,21)(H2,15,16,17)/t4-,6-,7-,8-/m1/s1 4SU InChIKey InChI 1.03 CKTAUHRBDDXUDJ-XVFCMESISA-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 4SU "SYSTEMATIC NAME" ACDLabs 10.04 1-(5-O-phosphono-beta-D-ribofuranosyl)-4-thioxo-3,4-dihydropyrimidin-2(1H)-one 4SU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxo-4-sulfanylidene-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 4SU 'Create component' 1999-07-08 RCSB 4SU 'Modify descriptor' 2011-06-04 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 4SU N1 N 6.331 1.396 1 4SU C2 C 7.630 2.146 2 4SU N3 N 7.630 3.646 3 4SU C4 C 6.331 4.396 4 4SU C5 C 5.032 3.646 5 4SU C6 C 5.032 2.146 6 4SU O2 O 8.929 1.396 7 4SU S4 S 6.331 5.896 8 4SU "C1'" C 6.331 -0.104 9 4SU "C2'" C 5.118 -0.986 10 4SU "O2'" O 3.691 -0.522 11 4SU "C3'" C 5.581 -2.412 12 4SU "C4'" C 7.081 -2.412 13 4SU "O3'" O 4.699 -3.626 14 4SU "O4'" O 7.545 -0.986 15 4SU "C5'" C 7.963 -3.626 16 4SU "O5'" O 9.455 -3.469 17 4SU P P 10.336 -4.683 18 4SU OP1 O 11.218 -5.896 19 4SU OP2 O 11.550 -3.801 20 4SU OP3 O 9.123 -5.564 21 # 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 4SU N1 C2 SINGLE NONE 1 4SU N1 C6 SINGLE NONE 2 4SU "C1'" N1 SINGLE BEGINDASH 3 4SU C2 N3 SINGLE NONE 4 4SU C2 O2 DOUBLE NONE 5 4SU N3 C4 SINGLE NONE 6 4SU C4 C5 SINGLE NONE 7 4SU C4 S4 DOUBLE NONE 8 4SU C5 C6 DOUBLE NONE 9 4SU "C1'" "C2'" SINGLE NONE 10 4SU "C1'" "O4'" SINGLE NONE 11 4SU "C2'" "O2'" SINGLE BEGINWEDGE 12 4SU "C2'" "C3'" SINGLE NONE 13 4SU "C3'" "C4'" SINGLE NONE 14 4SU "C3'" "O3'" SINGLE BEGINWEDGE 15 4SU "C4'" "O4'" SINGLE NONE 16 4SU "C4'" "C5'" SINGLE BEGINDASH 17 4SU "C5'" "O5'" SINGLE NONE 18 4SU "O5'" P SINGLE NONE 19 4SU P OP1 DOUBLE NONE 20 4SU P OP2 SINGLE NONE 21 4SU P OP3 SINGLE NONE 22 # 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 4SU MurckoScaffold S1 scaffold 'O=c1[nH]c(=S)ccn1[C@H]1CCCO1' InChI=1S/C8H10N2O2S/c11-8-9-6(13)3-4-10(8)7-2-1-5-12-7/h3-4,7H,1-2,5H2,(H,9,11,13)/t7-/m1/s1 AMZPSBSOLHJAED-SSDOTTSWSA-N 4SU phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N 4SU pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N 4SU ribose F3 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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 4SU N1 S1 1 4SU C2 S1 1 4SU N3 S1 1 4SU C4 S1 1 4SU C5 S1 1 4SU C6 S1 1 4SU O2 S1 1 4SU S4 S1 1 4SU "C1'" S1 1 4SU "C2'" S1 1 4SU "C3'" S1 1 4SU "C4'" S1 1 4SU "O4'" S1 1 4SU "O5'" F1 1 4SU P F1 1 4SU OP1 F1 1 4SU OP2 F1 1 4SU OP3 F1 1 4SU C5 F2 1 4SU C4 F2 1 4SU N3 F2 1 4SU C2 F2 1 4SU N1 F2 1 4SU C6 F2 1 4SU "C2'" F3 1 4SU "C3'" F3 1 4SU "C4'" F3 1 4SU "O4'" F3 1 4SU "C1'" F3 1 4SU "C5'" F3 1 4SU "O5'" F3 1 4SU "O3'" F3 1 4SU "O2'" F3 1 # _pdbe_chem_comp_rdkit_properties.comp_id 4SU _pdbe_chem_comp_rdkit_properties.exactmw 340.013 _pdbe_chem_comp_rdkit_properties.amw 340.250 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 10 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 5 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8 _pdbe_chem_comp_rdkit_properties.NumHBD 5 _pdbe_chem_comp_rdkit_properties.NumHBA 10 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21 _pdbe_chem_comp_rdkit_properties.NumAtoms 34 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556 _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 4 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 141.043 _pdbe_chem_comp_rdkit_properties.tpsa 154.240 _pdbe_chem_comp_rdkit_properties.CrippenClogP -0.466 _pdbe_chem_comp_rdkit_properties.CrippenMR 69.914 _pdbe_chem_comp_rdkit_properties.chi0v 11.227 _pdbe_chem_comp_rdkit_properties.chi1v 6.646 _pdbe_chem_comp_rdkit_properties.chi2v 2.430 _pdbe_chem_comp_rdkit_properties.chi3v 2.430 _pdbe_chem_comp_rdkit_properties.chi4v 1.474 _pdbe_chem_comp_rdkit_properties.chi0n 22.516 _pdbe_chem_comp_rdkit_properties.chi1n 10.857 _pdbe_chem_comp_rdkit_properties.chi2n 1.922 _pdbe_chem_comp_rdkit_properties.chi3n 1.922 _pdbe_chem_comp_rdkit_properties.chi4n 1.155 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.910 _pdbe_chem_comp_rdkit_properties.kappa1 6.300 _pdbe_chem_comp_rdkit_properties.kappa2 6.067 _pdbe_chem_comp_rdkit_properties.kappa3 3.843 _pdbe_chem_comp_rdkit_properties.Phi 1.820 # 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 4SU UniChem ChEMBL CHEMBL1230331 4SU UniChem PDBe 4SU 4SU UniChem ZINC ZINC000013518042 4SU UniChem SureChEMBL SCHEMBL1402556 4SU UniChem 'PubChem TPHARMA' 123104125 4SU UniChem BindingDb 50341895 4SU UniChem BRENDA 112682 4SU UniChem BRENDA 145354 4SU UniChem BRENDA 211141 4SU UniChem BRENDA 33835 4SU UniChem Nikkaji J756.680H 4SU UniChem 'PubChem TPHARMA' 26514762 4SU UniChem PubChem 16655024 # 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 4SU N1 -2.121 0.239 0.825 ETKDGv3 1 4SU C2 -1.904 1.555 0.269 ETKDGv3 2 4SU N3 -3.000 2.465 0.164 ETKDGv3 3 4SU C4 -4.301 2.046 0.581 ETKDGv3 4 4SU C5 -4.492 0.685 1.100 ETKDGv3 5 4SU C6 -3.457 -0.154 1.203 ETKDGv3 6 4SU O2 -0.762 1.909 -0.131 ETKDGv3 7 4SU S4 -5.573 3.069 0.465 ETKDGv3 8 4SU "C1'" -1.035 -0.750 0.928 ETKDGv3 9 4SU "C2'" -0.743 -1.385 -0.420 ETKDGv3 10 4SU "O2'" -1.579 -2.489 -0.649 ETKDGv3 11 4SU "C3'" 0.714 -1.773 -0.287 ETKDGv3 12 4SU "C4'" 1.239 -0.820 0.805 ETKDGv3 13 4SU "O3'" 0.875 -3.121 0.091 ETKDGv3 14 4SU "O4'" 0.147 -0.146 1.401 ETKDGv3 15 4SU "C5'" 2.217 0.216 0.241 ETKDGv3 16 4SU "O5'" 3.376 -0.437 -0.221 ETKDGv3 17 4SU P 4.466 0.739 -0.805 ETKDGv3 18 4SU OP1 4.914 1.639 0.325 ETKDGv3 19 4SU OP2 5.818 -0.046 -1.451 ETKDGv3 20 4SU OP3 3.742 1.664 -2.026 ETKDGv3 21 4SU HN3 -2.849 3.424 -0.224 ETKDGv3 22 4SU H5 -5.479 0.354 1.399 ETKDGv3 23 4SU H6 -3.637 -1.152 1.584 ETKDGv3 24 4SU "H1'" -1.316 -1.544 1.659 ETKDGv3 25 4SU "H2'" -0.859 -0.632 -1.235 ETKDGv3 26 4SU "HO2'" -1.435 -2.758 -1.593 ETKDGv3 27 4SU "H3'" 1.229 -1.624 -1.262 ETKDGv3 28 4SU "H4'" 1.769 -1.394 1.598 ETKDGv3 29 4SU "HO3'" 0.410 -3.258 0.958 ETKDGv3 30 4SU "H5'" 2.470 0.930 1.058 ETKDGv3 31 4SU "H5''" 1.714 0.766 -0.586 ETKDGv3 32 4SU HOP2 6.144 -0.631 -0.721 ETKDGv3 33 4SU HOP3 3.297 2.414 -1.556 ETKDGv3 34 #