data_CSL # _chem_comp.id CSL _chem_comp.name "(D)-2'-METHYLSELENYL-2'-DEOXYCYTIDINE-5'-PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P Se" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "(D)-2'-DEOXY-2'-SE-METHYLCYTIDINE-5'-PHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-02-15 _chem_comp.pdbx_modified_date 2021-03-01 _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 400.184 _chem_comp.one_letter_code C _chem_comp.three_letter_code CSL _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 1YLS _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 CSL P P P 0 1 N N N 62.884 18.223 24.845 4.724 0.598 0.168 P CSL 1 CSL O2P O2P O 0 1 N N N 63.739 18.040 23.643 5.473 0.922 1.556 O2P CSL 2 CSL O1P O1P O 0 1 N N N 62.269 19.540 25.164 5.457 -0.467 -0.552 O1P CSL 3 CSL "O5'" "O5'" O 0 1 N N N 61.730 17.186 24.799 3.222 0.104 0.472 "O5'" CSL 4 CSL "C5'" "C5'" C 0 1 N N N 61.962 15.986 24.246 2.334 -0.359 -0.547 "C5'" CSL 5 CSL "C4'" "C4'" C 0 1 N N R 60.664 15.284 24.226 0.995 -0.749 0.083 "C4'" CSL 6 CSL "O4'" "O4'" O 0 1 N N N 60.150 15.181 25.563 0.325 0.414 0.614 "O4'" CSL 7 CSL "C1'" "C1'" C 0 1 N N R 58.746 15.230 25.512 -1.071 0.086 0.712 "C1'" CSL 8 CSL N1 N1 N 0 1 N N N 58.294 16.334 26.307 -1.882 1.277 0.445 N1 CSL 9 CSL C2 C2 C 0 1 N N N 56.972 16.365 26.765 -1.689 1.979 -0.687 C2 CSL 10 CSL O2 O2 O 0 1 N N N 56.195 15.436 26.508 -0.837 1.614 -1.481 O2 CSL 11 CSL N3 N3 N 0 1 N N N 56.586 17.407 27.506 -2.412 3.064 -0.955 N3 CSL 12 CSL C4 C4 C 0 1 N N N 57.437 18.380 27.755 -3.345 3.483 -0.109 C4 CSL 13 CSL N4 N4 N 0 1 N N N 57.013 19.396 28.491 -4.086 4.606 -0.397 N4 CSL 14 CSL C5 C5 C 0 1 N N N 58.775 18.363 27.286 -3.572 2.770 1.086 C5 CSL 15 CSL C6 C6 C 0 1 N N N 59.159 17.337 26.563 -2.832 1.665 1.341 C6 CSL 16 CSL "C2'" "C2'" C 0 1 N N R 58.362 15.387 24.053 -1.363 -0.994 -0.347 "C2'" CSL 17 CSL "SE2'" "SE2'" SE 0 0 N N N 57.938 13.703 23.330 -2.054 -2.619 0.504 "SE2'" CSL 18 CSL "CA'" "CA'" C 0 1 N N N 59.189 12.355 23.778 -2.321 -3.774 -1.057 "CA'" CSL 19 CSL "C3'" "C3'" C 0 1 N N R 59.610 16.051 23.497 0.014 -1.268 -1.000 "C3'" CSL 20 CSL "O3'" "O3'" O 0 1 N N N 59.811 15.935 22.120 0.201 -2.666 -1.229 "O3'" CSL 21 CSL O3P O3P O 0 1 N Y N ? ? ? 4.678 1.927 -0.739 O3P CSL 22 CSL HOP2 HOP2 H 0 0 N N N 63.192 18.001 22.867 6.385 1.226 1.449 HOP2 CSL 23 CSL "H5'1" "H5'1" H 0 0 N N N 62.355 16.100 23.225 2.174 0.434 -1.277 "H5'1" CSL 24 CSL "H5'2" "H5'2" H 0 0 N N N 62.713 15.421 24.818 2.769 -1.227 -1.042 "H5'2" CSL 25 CSL "H4'" "H4'" H 0 1 N N N 60.859 14.315 23.744 1.141 -1.497 0.862 "H4'" CSL 26 CSL "H1'" "H1'" H 0 1 N N N 58.279 14.319 25.915 -1.293 -0.297 1.707 "H1'" CSL 27 CSL HN41 HN41 H 0 0 N N N 57.742 20.069 28.612 -3.927 5.094 -1.220 HN41 CSL 28 CSL HN42 HN42 H 0 0 N N N 56.092 19.478 28.872 -4.767 4.909 0.223 HN42 CSL 29 CSL H5 H5 H 0 1 N N N 59.456 19.169 27.516 -4.327 3.098 1.785 H5 CSL 30 CSL H6 H6 H 0 1 N N N 60.166 17.296 26.174 -2.991 1.099 2.247 H6 CSL 31 CSL "H2'" "H2'" H 0 1 N N N 57.464 15.981 23.829 -2.071 -0.622 -1.087 "H2'" CSL 32 CSL "HA'1" "HA'1" H 0 0 N N N 59.432 11.766 22.881 -1.370 -3.921 -1.567 "HA'1" CSL 33 CSL "HA'2" "HA'2" H 0 0 N N N 60.105 12.821 24.170 -2.713 -4.739 -0.733 "HA'2" CSL 34 CSL "HA'3" "HA'3" H 0 0 N N N 58.757 11.694 24.544 -3.031 -3.305 -1.739 "HA'3" CSL 35 CSL "H3'" "H3'" H 0 1 N N N 59.580 17.142 23.636 0.124 -0.705 -1.926 "H3'" CSL 36 CSL H3T H3T H 0 1 N Y N 58.971 15.909 21.678 1.082 -2.897 -1.553 H3T CSL 37 CSL HOP3 HOP3 H 0 0 N N N -0.546 0.117 0.768 4.211 2.668 -0.329 HOP3 CSL 38 # # 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 CSL P O2P SING N N 1 CSL P O1P DOUB N N 2 CSL P "O5'" SING N N 3 CSL P O3P SING N N 4 CSL O2P HOP2 SING N N 5 CSL "O5'" "C5'" SING N N 6 CSL "C5'" "C4'" SING N N 7 CSL "C5'" "H5'1" SING N N 8 CSL "C5'" "H5'2" SING N N 9 CSL "C4'" "O4'" SING N N 10 CSL "C4'" "C3'" SING N N 11 CSL "C4'" "H4'" SING N N 12 CSL "O4'" "C1'" SING N N 13 CSL "C1'" N1 SING N N 14 CSL "C1'" "C2'" SING N N 15 CSL "C1'" "H1'" SING N N 16 CSL N1 C2 SING N N 17 CSL N1 C6 SING N N 18 CSL C2 O2 DOUB N N 19 CSL C2 N3 SING N N 20 CSL N3 C4 DOUB N N 21 CSL C4 N4 SING N N 22 CSL C4 C5 SING N N 23 CSL N4 HN41 SING N N 24 CSL N4 HN42 SING N N 25 CSL C5 C6 DOUB N N 26 CSL C5 H5 SING N N 27 CSL C6 H6 SING N N 28 CSL "C2'" "SE2'" SING N N 29 CSL "C2'" "C3'" SING N N 30 CSL "C2'" "H2'" SING N N 31 CSL "SE2'" "CA'" SING N N 32 CSL "CA'" "HA'1" SING N N 33 CSL "CA'" "HA'2" SING N N 34 CSL "CA'" "HA'3" SING N N 35 CSL "C3'" "O3'" SING N N 36 CSL "C3'" "H3'" SING N N 37 CSL "O3'" H3T SING N N 38 CSL O3P HOP3 SING N N 39 # # 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 CSL SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2[Se]C)COP(=O)(O)O" CSL SMILES_CANONICAL CACTVS 3.341 "C[Se][C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N" CSL SMILES CACTVS 3.341 "C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N" CSL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[Se][C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" CSL SMILES "OpenEye OEToolkits" 1.5.0 "C[Se]C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" CSL InChI InChI 1.03 "InChI=1S/C10H16N3O7PSe/c1-22-8-7(14)5(4-19-21(16,17)18)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1" CSL InChIKey InChI 1.03 INVVCVIDTHAWAJ-ZOQUXTDFSA-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 CSL "SYSTEMATIC NAME" ACDLabs 10.04 "2'-Se-methyl-2'-selenocytidine 5'-(dihydrogen phosphate)" CSL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-4-methylselanyl-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 CSL "Create component" 2005-02-15 RCSB CSL "Modify descriptor" 2011-06-04 RCSB CSL "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id CSL _pdbx_chem_comp_synonyms.name "(D)-2'-DEOXY-2'-SE-METHYLCYTIDINE-5'-PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##