data_4SC # _chem_comp.id 4SC _chem_comp.name "2'-deoxy-5-methyl-4'-thiocytidine 5'-(dihydrogen phosphate)" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O6 P S" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2022-04-07 _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 337.289 _chem_comp.one_letter_code C _chem_comp.three_letter_code 4SC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6MHT _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 4SC P P P 0 1 N N N -19.306 45.420 87.739 -3.784 1.166 -0.065 P 4SC 1 4SC OP1 O1P O 0 1 N N N -19.710 45.872 86.370 -4.967 0.544 0.570 OP1 4SC 2 4SC OP2 O2P O 0 1 N N N -17.881 45.200 87.986 -3.352 2.473 0.771 OP2 4SC 3 4SC "O5'" "O5'" O 0 1 N N N -20.057 43.953 87.967 -2.566 0.113 -0.080 "O5'" 4SC 4 4SC "C5'" "C5'" C 0 1 N N N -19.584 42.997 88.988 -2.672 -1.191 -0.654 "C5'" 4SC 5 4SC "C4'" "C4'" C 0 1 N N R -20.227 41.613 88.748 -1.340 -1.927 -0.499 "C4'" 4SC 6 4SC "S4'" "S4'" S 0 1 N N N -19.615 41.206 87.075 -0.001 -1.078 -1.434 "S4'" 4SC 7 4SC "C3'" "C3'" C 0 1 N N S -19.735 40.545 89.724 -0.803 -1.812 0.952 "C3'" 4SC 8 4SC "O3'" "O3'" O 0 1 N N N -20.543 40.545 91.028 -1.461 -2.769 1.785 "O3'" 4SC 9 4SC "C2'" "C2'" C 0 1 N N N -20.000 39.193 88.937 0.702 -2.085 0.948 "C2'" 4SC 10 4SC "C1'" "C1'" C 0 1 N N R -19.633 39.423 87.466 1.372 -1.668 -0.371 "C1'" 4SC 11 4SC N1 N1 N 0 1 N N N -18.565 38.656 86.776 2.333 -0.587 -0.135 N1 4SC 12 4SC C2 C2 C 0 1 N N N -18.515 38.779 85.376 1.949 0.516 0.534 C2 4SC 13 4SC O2 O2 O 0 1 N N N -19.412 39.394 84.818 0.801 0.604 0.936 O2 4SC 14 4SC N3 N3 N 0 1 N N N -17.482 38.177 84.665 2.802 1.513 0.763 N3 4SC 15 4SC C4 C4 C 0 1 N N N -16.486 37.441 85.286 4.056 1.442 0.336 C4 4SC 16 4SC N4 N4 N 0 1 N N N -15.388 36.985 84.562 4.929 2.478 0.578 N4 4SC 17 4SC C5 C5 C 0 1 N N N -16.569 37.288 86.760 4.490 0.300 -0.368 C5 4SC 18 4SC C6 C6 C 0 1 N N N -17.601 37.907 87.431 3.612 -0.707 -0.588 C6 4SC 19 4SC C5M C5M C 0 1 N N N -16.750 35.700 86.690 5.910 0.199 -0.863 C5M 4SC 20 4SC "H5'" "H5'" H 0 1 N N N -18.490 42.907 88.925 -3.457 -1.750 -0.143 "H5'" 4SC 21 4SC "H5''" "H5''" H 0 0 N N N -19.865 43.362 89.987 -2.919 -1.104 -1.712 "H5''" 4SC 22 4SC "H4'" "H4'" H 0 1 N N N -21.325 41.670 88.712 -1.431 -2.969 -0.803 "H4'" 4SC 23 4SC "H3'" "H3'" H 0 1 N N N -18.660 40.662 89.928 -0.988 -0.807 1.332 "H3'" 4SC 24 4SC "HO3'" "HO3'" H 0 0 N Y N -20.209 39.870 91.608 -1.173 -2.752 2.707 "HO3'" 4SC 25 4SC "H2'" "H2'" H 0 1 N N N -19.377 38.389 89.356 1.163 -1.533 1.768 "H2'" 4SC 26 4SC "H2''" "H2''" H 0 0 N N N -21.061 38.915 89.018 0.868 -3.151 1.107 "H2''" 4SC 27 4SC "H1'" "H1'" H 0 1 N N N -20.546 39.109 86.938 1.867 -2.523 -0.831 "H1'" 4SC 28 4SC HN41 HN41 H 0 0 N N N -15.314 37.188 83.586 4.627 3.262 1.063 HN41 4SC 29 4SC HN42 HN42 H 0 0 N N N -14.674 36.454 85.018 5.845 2.424 0.265 HN42 4SC 30 4SC H61 H61 H 0 1 N N N -17.660 37.805 88.505 3.922 -1.595 -1.120 H61 4SC 31 4SC H71 H71 H 0 1 N N N -16.842 35.296 87.709 6.456 1.101 -0.585 H71 4SC 32 4SC H72 H72 H 0 1 N N N -17.658 35.459 86.117 6.391 -0.669 -0.413 H72 4SC 33 4SC H73 H73 H 0 1 N N N -15.875 35.253 86.196 5.910 0.094 -1.947 H73 4SC 34 4SC OP3 OP3 O 0 1 N Y N ? ? ? -4.146 1.590 -1.575 OP3 4SC 35 4SC HOP2 H1 H 0 0 N N N -17.389 45.387 87.195 -4.039 3.152 0.821 HOP2 4SC 36 4SC HOP3 H2 H 0 0 N Y N ? ? ? -3.415 2.006 -2.053 HOP3 4SC 37 # # 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 4SC P OP1 DOUB N N 1 4SC P OP2 SING N N 2 4SC P "O5'" SING N N 3 4SC "O5'" "C5'" SING N N 4 4SC "C5'" "C4'" SING N N 5 4SC "C5'" "H5'" SING N N 6 4SC "C5'" "H5''" SING N N 7 4SC "C4'" "S4'" SING N N 8 4SC "C4'" "C3'" SING N N 9 4SC "C4'" "H4'" SING N N 10 4SC "S4'" "C1'" SING N N 11 4SC "C3'" "O3'" SING N N 12 4SC "C3'" "C2'" SING N N 13 4SC "C3'" "H3'" SING N N 14 4SC "O3'" "HO3'" SING N N 15 4SC "C2'" "C1'" SING N N 16 4SC "C2'" "H2'" SING N N 17 4SC "C2'" "H2''" SING N N 18 4SC "C1'" N1 SING N N 19 4SC "C1'" "H1'" SING N N 20 4SC N1 C2 SING N N 21 4SC N1 C6 SING N N 22 4SC C2 O2 DOUB N N 23 4SC C2 N3 SING N N 24 4SC N3 C4 DOUB N N 25 4SC C4 N4 SING N N 26 4SC C4 C5 SING N N 27 4SC N4 HN41 SING N N 28 4SC N4 HN42 SING N N 29 4SC C5 C6 DOUB N N 30 4SC C5 C5M SING N N 31 4SC C6 H61 SING N N 32 4SC C5M H71 SING N N 33 4SC C5M H72 SING N N 34 4SC C5M H73 SING N N 35 4SC P OP3 SING N N 36 4SC OP2 HOP2 SING N N 37 4SC OP3 HOP3 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 4SC SMILES ACDLabs 12.01 "O=P(O)(O)OCC1SC(CC1O)N1C=C(C)C(N)=NC1=O" 4SC InChI InChI 1.03 "InChI=1S/C10H16N3O6PS/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(21-8)4-19-20(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" 4SC InChIKey InChI 1.03 GBRJOHLRKRNNCY-XLPZGREQSA-N 4SC SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)S2)C(=O)N=C1N" 4SC SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)S2)C(=O)N=C1N" 4SC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](S2)COP(=O)(O)O)O" 4SC SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)C2CC(C(S2)COP(=O)(O)O)O" # # 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 4SC "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5-methyl-4'-thiocytidine 5'-(dihydrogen phosphate)" 4SC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-thiolan-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 4SC "Create component" 1999-07-08 RCSB 4SC "Modify descriptor" 2011-06-04 RCSB 4SC "Other modification" 2022-04-07 RCSB ##