data_RSP # _chem_comp.id RSP _chem_comp.name "4-amino-1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidine-2(1H)-thione" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O7 P S" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-01-11 _chem_comp.pdbx_modified_date 2019-12-05 _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 339.262 _chem_comp.one_letter_code C _chem_comp.three_letter_code RSP _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 2KRV _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.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 RSP P P P 0 1 N N N 5.049 -9.227 -0.867 -4.098 -0.946 0.156 P RSP 1 RSP N1 N1 N 0 1 N N N 1.303 -6.593 1.269 2.394 0.106 0.534 N1 RSP 2 RSP C2 C2 C 0 1 N N N 0.039 -5.998 1.348 2.293 -0.823 -0.434 C2 RSP 3 RSP S2 S2 S 0 1 N N N -0.346 -5.088 2.702 0.920 -0.829 -1.456 S2 RSP 4 RSP N3 N3 N 0 1 N N N -0.838 -6.172 0.332 3.245 -1.737 -0.611 N3 RSP 5 RSP C4 C4 C 0 1 N N N -0.494 -6.908 -0.728 4.320 -1.755 0.166 C4 RSP 6 RSP N4 N4 N 0 1 N N N -1.386 -7.042 -1.711 5.297 -2.704 -0.026 N4 RSP 7 RSP C5 C5 C 0 1 N N N 0.781 -7.537 -0.827 4.456 -0.795 1.191 C5 RSP 8 RSP C6 C6 C 0 1 N N N 1.639 -7.355 0.184 3.482 0.132 1.354 C6 RSP 9 RSP "C1'" "C1'" C 0 1 N N R 2.262 -6.374 2.365 1.330 1.100 0.704 "C1'" RSP 10 RSP "C2'" "C2'" C 0 1 N N R 2.089 -7.323 3.552 1.208 1.990 -0.559 "C2'" RSP 11 RSP "O2'" "O2'" O 0 1 N N N 2.384 -6.603 4.734 2.114 3.093 -0.495 "O2'" RSP 12 RSP "C3'" "C3'" C 0 1 N N S 3.146 -8.387 3.262 -0.260 2.474 -0.474 "C3'" RSP 13 RSP "O3'" "O3'" O 0 1 N N N 3.627 -9.019 4.446 -0.323 3.779 0.105 "O3'" RSP 14 RSP "C4'" "C4'" C 0 1 N N R 4.255 -7.594 2.585 -0.945 1.442 0.443 "C4'" RSP 15 RSP "O4'" "O4'" O 0 1 N N N 3.569 -6.547 1.850 0.041 0.455 0.791 "O4'" RSP 16 RSP "C5'" "C5'" C 0 1 N N N 5.116 -8.381 1.624 -2.111 0.783 -0.296 "C5'" RSP 17 RSP "O5'" "O5'" O 0 1 N N N 4.345 -8.789 0.494 -2.811 -0.085 0.598 "O5'" RSP 18 RSP OP1 OP1 O 0 1 N N N 3.985 -9.618 -1.827 -5.123 -0.043 -0.414 OP1 RSP 19 RSP OP2 OP2 O 0 1 N N N 6.133 -10.190 -0.543 -3.664 -2.031 -0.951 OP2 RSP 20 RSP OP3 O3P O 0 1 N Y N 5.726 -7.874 -1.414 -4.705 -1.702 1.441 OP3 RSP 21 RSP H5 H5 H 0 1 N N N 1.045 -8.138 -1.685 5.325 -0.796 1.832 H5 RSP 22 RSP H6 H6 H 0 1 N N N 2.614 -7.818 0.142 3.563 0.877 2.132 H6 RSP 23 RSP "H5'" "H5'" H 0 1 N N N 5.509 -9.272 2.136 -2.791 1.552 -0.663 "H5'" RSP 24 RSP "H1'" "H1'" H 0 1 N N N 2.081 -5.357 2.744 1.515 1.711 1.587 "H1'" RSP 25 RSP "H2'" "H2'" H 0 1 N N N 1.084 -7.752 3.681 1.373 1.405 -1.464 "H2'" RSP 26 RSP "HO2'" "HO2'" H 0 0 N N N 2.283 -7.174 5.487 2.075 3.679 -1.263 "HO2'" RSP 27 RSP "H3'" "H3'" H 0 1 N N N 2.748 -9.210 2.650 -0.720 2.473 -1.463 "H3'" RSP 28 RSP "H4'" "H4'" H 0 1 N N N 4.954 -7.239 3.357 -1.309 1.933 1.346 "H4'" RSP 29 RSP HN4 HN4 H 0 1 N N N -2.279 -6.598 -1.639 6.082 -2.715 0.544 HN4 RSP 30 RSP HN4A HN4A H 0 0 N N N -1.161 -7.586 -2.519 5.201 -3.363 -0.732 HN4A RSP 31 RSP "H5'A" "H5'A" H 0 0 N N N 5.951 -7.750 1.285 -1.728 0.205 -1.137 "H5'A" RSP 32 RSP "HO3'" H3T H 0 0 N Y N 4.279 -9.670 4.215 0.143 4.457 -0.402 "HO3'" RSP 33 RSP HOP2 HOP2 H 0 0 N N N 5.997 -10.995 -1.028 -2.993 -2.658 -0.646 HOP2 RSP 34 RSP HOP3 HOP3 H 0 0 N N N 5.306 -7.615 -2.226 -5.484 -2.241 1.248 HOP3 RSP 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 RSP OP1 P DOUB N N 1 RSP OP3 P SING N N 2 RSP P OP2 SING N N 3 RSP P "O5'" SING N N 4 RSP C6 N1 SING N N 5 RSP N1 C2 SING N N 6 RSP N1 "C1'" SING N N 7 RSP N3 C2 SING N N 8 RSP C2 S2 DOUB N N 9 RSP C4 N3 DOUB N N 10 RSP N4 C4 SING N N 11 RSP C5 C4 SING N N 12 RSP HN4 N4 SING N N 13 RSP N4 HN4A SING N N 14 RSP H5 C5 SING N N 15 RSP C5 C6 DOUB N N 16 RSP H6 C6 SING N N 17 RSP "O4'" "C1'" SING N N 18 RSP "C1'" "H1'" SING N N 19 RSP "C1'" "C2'" SING N N 20 RSP "C3'" "C2'" SING N N 21 RSP "C2'" "H2'" SING N N 22 RSP "C2'" "O2'" SING N N 23 RSP "O2'" "HO2'" SING N N 24 RSP "C4'" "C3'" SING N N 25 RSP "H3'" "C3'" SING N N 26 RSP "C3'" "O3'" SING N N 27 RSP "O3'" "HO3'" SING N N 28 RSP "C5'" "C4'" SING N N 29 RSP "O4'" "C4'" SING N N 30 RSP "C4'" "H4'" SING N N 31 RSP "O5'" "C5'" SING N N 32 RSP "H5'A" "C5'" SING N N 33 RSP "C5'" "H5'" SING N N 34 RSP OP2 HOP2 SING N N 35 RSP OP3 HOP3 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 RSP SMILES_CANONICAL CACTVS 3.352 "NC1=NC(=S)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" RSP SMILES CACTVS 3.352 "NC1=NC(=S)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" RSP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=S)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" RSP SMILES "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=S)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O" RSP InChI InChI 1.03 "InChI=1S/C9H14N3O7PS/c10-5-1-2-12(9(21)11-5)8-7(14)6(13)4(19-8)3-18-20(15,16)17/h1-2,4,6-8,13-14H,3H2,(H2,10,11,21)(H2,15,16,17)/t4-,6-,7-,8-/m1/s1" RSP InChIKey InChI 1.03 BPWVHBCPZTVLLY-XVFCMESISA-N # _pdbx_chem_comp_identifier.comp_id RSP _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.6.1 _pdbx_chem_comp_identifier.identifier "[(2R,3S,4R,5R)-5-(4-azanyl-2-sulfanylidene-pyrimidin-1-yl)-3,4-dihydroxy-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 RSP "Create component" 2010-01-11 RCSB RSP "Modify descriptor" 2011-06-04 RCSB RSP "Modify parent residue" 2019-12-05 PDBE ##