data_2YR
# 
_chem_comp.id                                    2YR 
_chem_comp.name                                  
;2'-deoxy-N-(2-sulfanylethyl)cytidine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H18 N3 O7 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-04-28 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        367.315 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     2YR 
_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        4MGT 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
2YR P     P     P 0 1 N N N N N N 39.797 -19.542 12.242 4.782  -1.832 -0.240 P     2YR 1  
2YR OP1   OP1   O 0 1 N N N N N N 39.227 -18.478 13.104 3.964  -2.884 0.404  OP1   2YR 2  
2YR OP2   OP2   O 0 1 N N N N N N 39.140 -20.869 12.193 5.268  -2.341 -1.687 OP2   2YR 3  
2YR "O5'" "O5'" O 0 1 N N N N N N 39.918 -18.945 10.773 3.901  -0.495 -0.409 "O5'" 2YR 4  
2YR "C5'" "C5'" C 0 1 N N N N N N 39.659 -17.550 10.536 3.238  0.144  0.684  "C5'" 2YR 5  
2YR "C4'" "C4'" C 0 1 N N R N N N 40.942 -16.751 10.518 2.495  1.381  0.176  "C4'" 2YR 6  
2YR "O4'" "O4'" O 0 1 N N N N N N 42.088 -17.600 10.279 1.384  0.999  -0.662 "O4'" 2YR 7  
2YR "C3'" "C3'" C 0 1 N N S N N N 41.002 -15.709 9.410  1.823  2.135  1.352  "C3'" 2YR 8  
2YR "O3'" "O3'" O 0 1 N N N N N N 40.288 -14.530 9.799  2.736  3.052  1.958  "O3'" 2YR 9  
2YR "C2'" "C2'" C 0 1 N N N N N N 42.495 -15.506 9.232  0.674  2.888  0.640  "C2'" 2YR 10 
2YR "C1'" "C1'" C 0 1 N N R N N N 43.091 -16.873 9.567  0.468  2.107  -0.677 "C1'" 2YR 11 
2YR N1    N1    N 0 1 N N N N N N 43.503 -17.676 8.399  -0.909 1.615  -0.754 N1    2YR 12 
2YR C2    C2    C 0 1 N N N N N N 44.577 -17.229 7.617  -1.344 0.701  0.133  C2    2YR 13 
2YR O2    O2    O 0 1 N N N N N N 45.150 -16.179 7.931  -0.584 0.292  0.995  O2    2YR 14 
2YR N3    N3    N 0 1 N N N N N N 44.971 -17.961 6.550  -2.592 0.236  0.086  N3    2YR 15 
2YR C4    C4    C 0 1 N N N N N N 44.331 -19.093 6.246  -3.439 0.664  -0.841 C4    2YR 16 
2YR N4    N4    N 0 1 N N N N N N 44.757 -19.786 5.188  -4.725 0.178  -0.879 N4    2YR 17 
2YR C5    C5    C 0 1 N N N N N N 43.229 -19.567 7.018  -3.014 1.621  -1.785 C5    2YR 18 
2YR C6    C6    C 0 1 N N N N N N 42.858 -18.839 8.081  -1.745 2.088  -1.720 C6    2YR 19 
2YR S     S     S 0 1 N N N N N N 45.398 -23.248 3.658  -7.165 -2.416 1.059  S     2YR 20 
2YR C8    C8    C 0 1 N N N N N N 46.075 -22.466 5.146  -6.623 -1.186 -0.159 C8    2YR 21 
2YR C9    C9    C 0 1 N N N N N N 45.553 -21.041 5.233  -5.162 -0.816 0.104  C9    2YR 22 
2YR H2    H2    H 0 1 N N N N N N 38.380 -20.868 12.763 5.805  -3.145 -1.661 H2    2YR 23 
2YR H3    H3    H 0 1 N N N N N N 39.008 -17.165 11.335 2.525  -0.550 1.131  H3    2YR 24 
2YR H4    H4    H 0 1 N N N N N N 39.153 -17.439 9.565  3.973  0.442  1.431  H4    2YR 25 
2YR H5    H5    H 0 1 N N N N N N 41.055 -16.241 11.486 3.175  2.041  -0.364 H5    2YR 26 
2YR H6    H6    H 0 1 N N N N N N 40.578 -16.133 8.488  1.432  1.434  2.090  H6    2YR 27 
2YR H7    H7    H 0 1 N Y N N N N 39.365 -14.734 9.890  2.362  3.548  2.699  H7    2YR 28 
2YR H8    H8    H 0 1 N N N N N N 42.731 -15.219 8.197  -0.232 2.862  1.246  H8    2YR 29 
2YR H9    H9    H 0 1 N N N N N N 42.871 -14.735 9.921  0.964  3.918  0.431  H9    2YR 30 
2YR H10   H10   H 0 1 N N N N N N 43.964 -16.717 10.218 0.681  2.754  -1.528 H10   2YR 31 
2YR H11   H11   H 0 1 N N N N N N 44.520 -19.429 4.284  -5.343 0.493  -1.558 H11   2YR 32 
2YR H12   H12   H 0 1 N N N N N N 42.713 -20.479 6.756  -3.692 1.979  -2.546 H12   2YR 33 
2YR H13   H13   H 0 1 N N N N N N 42.037 -19.176 8.696  -1.396 2.822  -2.432 H13   2YR 34 
2YR H14   H14   H 0 1 N Y N N N N 45.921 -24.437 3.716  -8.444 -2.644 0.711  H14   2YR 35 
2YR H15   H15   H 0 1 N N N N N N 45.759 -23.030 6.036  -6.718 -1.602 -1.162 H15   2YR 36 
2YR H16   H16   H 0 1 N N N N N N 47.174 -22.454 5.090  -7.245 -0.294 -0.076 H16   2YR 37 
2YR H17   H17   H 0 1 N N N N N N 45.781 -20.945 6.305  -4.541 -1.707 0.021  H17   2YR 38 
2YR H18   H18   H 0 1 N N N N N N 46.382 -20.623 4.643  -5.068 -0.400 1.107  H18   2YR 39 
2YR OP3   OP3   O 0 1 N Y N N N N ?      ?       ?      6.067  -1.516 0.678  OP3   2YR 40 
2YR H20   H20   H 0 1 N Y N N N N ?      ?       ?      6.650  -0.834 0.316  H20   2YR 41 
# 
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 
2YR S     C8    SING N N 1  
2YR C8    C9    SING N N 2  
2YR N4    C9    SING N N 3  
2YR N4    C4    SING N N 4  
2YR C4    N3    DOUB N N 5  
2YR C4    C5    SING N N 6  
2YR N3    C2    SING N N 7  
2YR C5    C6    DOUB N N 8  
2YR C2    O2    DOUB N N 9  
2YR C2    N1    SING N N 10 
2YR C6    N1    SING N N 11 
2YR N1    "C1'" SING N N 12 
2YR "C2'" "C3'" SING N N 13 
2YR "C2'" "C1'" SING N N 14 
2YR "C3'" "O3'" SING N N 15 
2YR "C3'" "C4'" SING N N 16 
2YR "C1'" "O4'" SING N N 17 
2YR "O4'" "C4'" SING N N 18 
2YR "C4'" "C5'" SING N N 19 
2YR "C5'" "O5'" SING N N 20 
2YR "O5'" P     SING N N 21 
2YR OP2   P     SING N N 22 
2YR P     OP1   DOUB N N 23 
2YR OP2   H2    SING N N 24 
2YR "C5'" H3    SING N N 25 
2YR "C5'" H4    SING N N 26 
2YR "C4'" H5    SING N N 27 
2YR "C3'" H6    SING N N 28 
2YR "O3'" H7    SING N N 29 
2YR "C2'" H8    SING N N 30 
2YR "C2'" H9    SING N N 31 
2YR "C1'" H10   SING N N 32 
2YR N4    H11   SING N N 33 
2YR C5    H12   SING N N 34 
2YR C6    H13   SING N N 35 
2YR S     H14   SING N N 36 
2YR C8    H15   SING N N 37 
2YR C8    H16   SING N N 38 
2YR C9    H17   SING N N 39 
2YR C9    H18   SING N N 40 
2YR P     OP3   SING N N 41 
2YR OP3   H20   SING N N 42 
# 
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 
2YR SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(NCCS)C=C1)CC2O"                                                                                                                     
2YR InChI            InChI                1.03  "InChI=1S/C11H18N3O7PS/c15-7-5-10(21-8(7)6-20-22(17,18)19)14-3-1-9(12-2-4-23)13-11(14)16/h1,3,7-8,10,15,23H,2,4-6H2,(H,12,13,16)(H2,17,18,19)/t7-,8+,10+/m0/s1" 
2YR InChIKey         InChI                1.03  OJZURBTUERORPR-QXFUBDJGSA-N                                                                                                                                     
2YR SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCCS"                                                                                                       
2YR SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCCS"                                                                                                            
2YR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)NCCS)COP(=O)(O)O)O"                                                                                                        
2YR SMILES           "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=NC2=O)NCCS)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 
2YR "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-deoxy-N-(2-sulfanylethyl)cytidine 5'-(dihydrogen phosphate)
;
2YR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-3-oxidanyl-5-[2-oxidanylidene-4-(2-sulfanylethylamino)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 
2YR "Create component"         2014-04-28 RCSB 
2YR "Modify leaving atom flag" 2014-05-14 RCSB 
2YR "Initial release"          2014-05-21 RCSB 
2YR "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            2YR 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               S 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
