data_SSU # _chem_comp.id SSU _chem_comp.name "URIDINE-5'-PHOSPHOROTHIOATE" _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 "SP-SULFUR-SUBSTITUTED URIDINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-04-09 _chem_comp.pdbx_modified_date 2020-06-17 _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 340.247 _chem_comp.one_letter_code U _chem_comp.three_letter_code SSU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1NZ1 _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 SSU "O2'" O2* O 0 1 N N N N N N -2.068 -3.875 -14.864 0.137 -0.058 2.041 "O2'" SSU 1 SSU "C2'" C2* C 0 1 N N R N N N -2.623 -3.836 -13.545 0.748 0.163 0.786 "C2'" SSU 2 SSU "C1'" C1* C 0 1 N N R N N N -2.568 -2.425 -12.958 1.373 1.543 0.675 "C1'" SSU 3 SSU "O4'" O4* O 0 1 N N N N N N -3.898 -1.884 -13.034 2.470 1.422 -0.246 "O4'" SSU 4 SSU "C4'" C4* C 0 1 N N R N N N -4.743 -2.785 -13.748 2.725 0.023 -0.498 "C4'" SSU 5 SSU "C5'" C5* C 0 1 N N N N N N -6.170 -2.758 -13.209 2.282 -0.292 -1.921 "C5'" SSU 6 SSU "O5'" O5* O 0 1 N N N N N N -6.201 -2.919 -11.788 3.063 0.476 -2.819 "O5'" SSU 7 SSU P P P 0 1 N N N N N N -7.477 -2.424 -10.939 2.812 0.347 -4.417 P SSU 8 SSU S1P S1P S 0 1 N N N N N N -9.119 -2.439 -12.265 1.133 1.036 -5.105 S1P SSU 9 SSU OP2 O2P O 0 1 N N N N N N -7.467 -3.134 -9.641 3.104 -1.222 -4.708 OP2 SSU 10 SSU OP3 O3P O 0 1 N Y N N N N ? ? ? 4.136 1.046 -5.041 OP3 SSU 11 SSU "C3'" C3* C 0 1 N N S N N N -4.109 -4.150 -13.556 1.940 -0.742 0.560 "C3'" SSU 12 SSU "O3'" O3* O 0 1 N N N N N N -4.392 -4.958 -14.704 2.742 -0.809 1.739 "O3'" SSU 13 SSU N1 N1 N 0 1 N N N N N N -2.082 -2.466 -11.566 0.452 2.524 0.177 N1 SSU 14 SSU C6 C6 C 0 1 N N N N N N -2.941 -2.668 -10.520 0.308 2.664 -1.199 C6 SSU 15 SSU C5 C5 C 0 1 N N N N N N -2.491 -2.729 -9.242 -0.516 3.539 -1.779 C5 SSU 16 SSU C4 C4 C 0 1 N N N N N N -1.085 -2.578 -8.941 -1.338 4.427 -0.933 C4 SSU 17 SSU O4 O4 O 0 1 N N N N N N -0.591 -2.621 -7.817 -2.105 5.242 -1.435 O4 SSU 18 SSU N3 N3 N 0 1 N N N N N N -0.290 -2.378 -10.056 -1.161 4.252 0.431 N3 SSU 19 SSU C2 C2 C 0 1 N N N N N N -0.724 -2.312 -11.367 -0.301 3.338 1.055 C2 SSU 20 SSU O2 O2 O 0 1 N N N N N N 0.055 -2.128 -12.299 -0.226 3.271 2.284 O2 SSU 21 SSU "HO2'" 2HO* H 0 0 N N N N N N -1.583 -3.057 -14.993 -0.494 0.669 2.185 "HO2'" SSU 22 SSU "H2'" H2* H 0 1 N N N N N N -2.106 -4.531 -12.884 -0.000 0.004 -0.000 "H2'" SSU 23 SSU "H1'" H1* H 0 1 N N N N N N -1.895 -1.813 -13.557 1.754 1.910 1.633 "H1'" SSU 24 SSU "H4'" H4* H 0 1 N N N N N N -4.742 -2.521 -14.804 3.804 -0.139 -0.410 "H4'" SSU 25 SSU "H5'" 1H5* H 0 1 N N N N N N -6.630 -1.805 -13.470 1.229 -0.035 -2.051 "H5'" SSU 26 SSU "H5''" 2H5* H 0 0 N N N N N N -6.738 -3.565 -13.671 2.428 -1.352 -2.133 "H5''" SSU 27 SSU H2P H2P H 0 1 N N N N N N -8.219 -2.842 -9.140 3.952 -1.609 -4.402 H2P SSU 28 SSU H3P H3P H 0 1 N N N N N N -0.752 0.292 0.500 4.167 1.222 -6.006 H3P SSU 29 SSU "H3'" H3* H 0 1 N N N N N N -4.433 -4.622 -12.630 1.675 -1.764 0.277 "H3'" SSU 30 SSU "HO3'" H3T H 0 0 N Y N N N N -5.321 -5.154 -14.710 3.447 -0.153 1.628 "HO3'" SSU 31 SSU H6 6H H 0 1 N N N N N N -4.006 -2.784 -10.719 0.921 2.002 -1.802 H6 SSU 32 SSU H5 5H H 0 1 N N N N N N -3.199 -2.895 -8.430 -0.601 3.619 -2.856 H5 SSU 33 SSU H3 3H H 0 1 N N N N N N 0.701 -2.269 -9.897 -1.712 4.848 1.042 H3 SSU 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 SSU "O2'" "C2'" SING N N 1 SSU "O2'" "HO2'" SING N N 2 SSU "C2'" "C1'" SING N N 3 SSU "C2'" "C3'" SING N N 4 SSU "C2'" "H2'" SING N N 5 SSU "C1'" "O4'" SING N N 6 SSU "C1'" N1 SING N N 7 SSU "C1'" "H1'" SING N N 8 SSU "O4'" "C4'" SING N N 9 SSU "C4'" "C5'" SING N N 10 SSU "C4'" "C3'" SING N N 11 SSU "C4'" "H4'" SING N N 12 SSU "C5'" "O5'" SING N N 13 SSU "C5'" "H5'" SING N N 14 SSU "C5'" "H5''" SING N N 15 SSU "O5'" P SING N N 16 SSU P S1P DOUB N N 17 SSU P OP2 SING N N 18 SSU P OP3 SING N N 19 SSU OP2 H2P SING N N 20 SSU OP3 H3P SING N N 21 SSU "C3'" "O3'" SING N N 22 SSU "C3'" "H3'" SING N N 23 SSU "O3'" "HO3'" SING N N 24 SSU N1 C6 SING N N 25 SSU N1 C2 SING N N 26 SSU C6 C5 DOUB N N 27 SSU C6 H6 SING N N 28 SSU C5 C4 SING N N 29 SSU C5 H5 SING N N 30 SSU C4 O4 DOUB N N 31 SSU C4 N3 SING N N 32 SSU N3 C2 SING N N 33 SSU N3 H3 SING N N 34 SSU C2 O2 DOUB 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 SSU SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=S)(O)O SSU SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O SSU SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O SSU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=S)(O)O)O)O SSU SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=S)(O)O)O)O SSU InChI InChI 1.03 InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1 SSU InChIKey InChI 1.03 NSEBKRRODBXALJ-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 SSU "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-thiophosphonouridine" SSU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1-[(2R,3R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-3,4-dihydroxy-oxolan-2-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 SSU 'Create component' 2003-04-09 RCSB SSU 'Modify descriptor' 2011-06-04 RCSB SSU 'Modify synonyms' 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SSU _pdbx_chem_comp_synonyms.name "SP-SULFUR-SUBSTITUTED URIDINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbe_chem_comp_synonyms.comp_id SSU _pdbe_chem_comp_synonyms.name 'SP-SULFUR-SUBSTITUTED URIDINE' _pdbe_chem_comp_synonyms.provenance wwPDB _pdbe_chem_comp_synonyms.type ? # loop_ _software.name _software.version _software.description rdkit 2025.03.3 'Core functionality.' pdbeccdutils 1.0.0 '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 SSU "O2'" O 3.691 -0.522 1 SSU "C2'" C 5.118 -0.986 2 SSU "C1'" C 6.331 -0.104 3 SSU "O4'" O 7.545 -0.986 4 SSU "C4'" C 7.081 -2.412 5 SSU "C5'" C 7.963 -3.626 6 SSU "O5'" O 9.455 -3.469 7 SSU P P 10.336 -4.683 8 SSU S1P S 11.218 -5.896 9 SSU OP2 O 11.550 -3.801 10 SSU OP3 O 9.123 -5.564 11 SSU "C3'" C 5.581 -2.412 12 SSU "O3'" O 4.699 -3.626 13 SSU N1 N 6.331 1.396 14 SSU C6 C 5.032 2.146 15 SSU C5 C 5.032 3.646 16 SSU C4 C 6.331 4.396 17 SSU O4 O 6.331 5.896 18 SSU N3 N 7.630 3.646 19 SSU C2 C 7.630 2.146 20 SSU O2 O 8.929 1.396 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 SSU "C2'" "O2'" SINGLE BEGINWEDGE 1 SSU "C2'" "C1'" SINGLE NONE 2 SSU "C2'" "C3'" SINGLE NONE 3 SSU "C1'" "O4'" SINGLE NONE 4 SSU "C1'" N1 SINGLE BEGINDASH 5 SSU "O4'" "C4'" SINGLE NONE 6 SSU "C4'" "C5'" SINGLE BEGINDASH 7 SSU "C4'" "C3'" SINGLE NONE 8 SSU "C5'" "O5'" SINGLE NONE 9 SSU "O5'" P SINGLE NONE 10 SSU P S1P DOUBLE NONE 11 SSU P OP2 SINGLE NONE 12 SSU P OP3 SINGLE NONE 13 SSU "C3'" "O3'" SINGLE BEGINWEDGE 14 SSU N1 C6 SINGLE NONE 15 SSU N1 C2 SINGLE NONE 16 SSU C6 C5 DOUBLE NONE 17 SSU C5 C4 SINGLE NONE 18 SSU C4 O4 DOUBLE NONE 19 SSU C4 N3 SINGLE NONE 20 SSU N3 C2 SINGLE NONE 21 SSU C2 O2 DOUBLE 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 SSU MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N SSU pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N SSU ribose F2 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 SSU "C2'" S1 1 SSU "C1'" S1 1 SSU "O4'" S1 1 SSU "C4'" S1 1 SSU "C3'" S1 1 SSU N1 S1 1 SSU C6 S1 1 SSU C5 S1 1 SSU C4 S1 1 SSU O4 S1 1 SSU N3 S1 1 SSU C2 S1 1 SSU O2 S1 1 SSU C5 F1 1 SSU C6 F1 1 SSU N1 F1 1 SSU C2 F1 1 SSU N3 F1 1 SSU C4 F1 1 SSU "C2'" F2 1 SSU "C3'" F2 1 SSU "C4'" F2 1 SSU "O4'" F2 1 SSU "C1'" F2 1 SSU "C5'" F2 1 SSU "O5'" F2 1 SSU "O3'" F2 1 SSU "O2'" F2 1 # _pdbe_chem_comp_rdkit_properties.comp_id SSU _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 140.676 _pdbe_chem_comp_rdkit_properties.tpsa 154.240 _pdbe_chem_comp_rdkit_properties.CrippenClogP -0.819 _pdbe_chem_comp_rdkit_properties.CrippenMR 72.137 _pdbe_chem_comp_rdkit_properties.chi0v 11.227 _pdbe_chem_comp_rdkit_properties.chi1v 7.333 _pdbe_chem_comp_rdkit_properties.chi2v 2.460 _pdbe_chem_comp_rdkit_properties.chi3v 2.460 _pdbe_chem_comp_rdkit_properties.chi4v 1.462 _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 SSU UniChem eMolecules 1933569 SSU UniChem SureChEMBL SCHEMBL2706641 SSU UniChem 'PubChem TPHARMA' 15422183 SSU UniChem PubChem 10404968 SSU UniChem Nikkaji J2.178.151G SSU UniChem BRENDA 101699 # 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 SSU "O2'" -1.331 -2.937 0.153 ETKDGv3 1 SSU "C2'" -0.944 -1.641 -0.243 ETKDGv3 2 SSU "C1'" -1.320 -0.594 0.820 ETKDGv3 3 SSU "O4'" -0.150 0.057 1.269 ETKDGv3 4 SSU "C4'" 0.938 -0.760 0.907 ETKDGv3 5 SSU "C5'" 2.194 0.101 0.736 ETKDGv3 6 SSU "O5'" 3.289 -0.726 0.420 ETKDGv3 7 SSU P 4.648 0.268 0.150 ETKDGv3 8 SSU S1P 6.022 -0.735 -0.151 ETKDGv3 9 SSU OP2 4.381 1.265 -1.193 ETKDGv3 10 SSU OP3 4.948 1.224 1.516 ETKDGv3 11 SSU "C3'" 0.561 -1.495 -0.374 ETKDGv3 12 SSU "O3'" 1.220 -2.733 -0.455 ETKDGv3 13 SSU N1 -2.272 0.389 0.275 ETKDGv3 14 SSU C6 -3.673 0.255 0.593 ETKDGv3 15 SSU C5 -4.589 1.094 0.100 ETKDGv3 16 SSU C4 -4.193 2.182 -0.802 ETKDGv3 17 SSU O4 -5.060 2.976 -1.255 ETKDGv3 18 SSU N3 -2.821 2.334 -1.167 ETKDGv3 19 SSU C2 -1.853 1.424 -0.642 ETKDGv3 20 SSU O2 -0.647 1.532 -0.990 ETKDGv3 21 SSU "HO2'" -0.884 -3.142 1.017 ETKDGv3 22 SSU "H2'" -1.425 -1.419 -1.222 ETKDGv3 23 SSU "H1'" -1.774 -1.096 1.705 ETKDGv3 24 SSU "H4'" 1.117 -1.492 1.728 ETKDGv3 25 SSU "H5'" 2.377 0.633 1.697 ETKDGv3 26 SSU "H5''" 2.006 0.852 -0.066 ETKDGv3 27 SSU H2P 3.992 0.668 -1.881 ETKDGv3 28 SSU H3P 5.552 1.941 1.198 ETKDGv3 29 SSU "H3'" 0.799 -0.868 -1.266 ETKDGv3 30 SSU "HO3'" 1.058 -3.076 -1.372 ETKDGv3 31 SSU H6 -4.004 -0.542 1.249 ETKDGv3 32 SSU H5 -5.632 0.967 0.363 ETKDGv3 33 SSU H3 -2.530 3.096 -1.820 ETKDGv3 34 #