data_08Q
# 
_chem_comp.id                                    08Q 
_chem_comp.name                                  "5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H20 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                     2011-10-15 
_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                        381.342 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     08Q 
_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        3U6D 
_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 
08Q P     P     P 0 1 N N N N N N 4.255 -8.547  16.061 3.176  1.672  -0.914 P     08Q 1  
08Q OP1   OP1   O 0 1 N N N N N N 3.332 -8.497  17.195 2.956  2.043  -2.330 OP1   08Q 2  
08Q "C8'" "C8'" C 0 1 N N N N N N 4.196 -5.161  14.105 5.221  -1.111 0.666  "C8'" 08Q 3  
08Q "C7'" "C7'" C 0 1 N N N N N N 4.782 -6.345  14.823 4.832  0.367  0.609  "C7'" 08Q 4  
08Q "C5'" "C5'" C 0 1 N N N N N N 4.457 -11.249 15.793 1.402  -0.319 -1.088 "C5'" 08Q 5  
08Q "O5'" "O5'" O 0 1 N N N N N N 4.160 -9.919  15.224 1.923  0.811  -0.384 "O5'" 08Q 6  
08Q "C4'" "C4'" C 0 1 N N R N N N 3.448 -11.983 16.802 0.219  -0.902 -0.312 "C4'" 08Q 7  
08Q "O4'" "O4'" O 0 1 N N N N N N 3.239 -11.271 18.185 -0.867 0.033  -0.307 "O4'" 08Q 8  
08Q "C3'" "C3'" C 0 1 N N S N N N 2.093 -12.502 16.736 -0.277 -2.190 -1.003 "C3'" 08Q 9  
08Q "O3'" "O3'" O 0 1 N N N N N N 1.989 -13.564 15.795 0.207  -3.350 -0.325 "O3'" 08Q 10 
08Q "C2'" "C2'" C 0 1 N N N N N N 2.010 -13.033 18.198 -1.819 -2.069 -0.859 "C2'" 08Q 11 
08Q "C1'" "C1'" C 0 1 N N S N N N 2.197 -11.963 19.041 -2.006 -0.535 -0.974 "C1'" 08Q 12 
08Q N1    N1    N 0 1 N N N N N N 2.331 -11.149 20.228 -3.243 -0.122 -0.307 N1    08Q 13 
08Q C2    C2    C 0 1 N N N N N N 2.252 -11.896 21.415 -4.426 -0.576 -0.758 C2    08Q 14 
08Q O2    O2    O 0 1 N N N N N N 2.176 -13.122 21.352 -4.456 -1.325 -1.715 O2    08Q 15 
08Q N3    N3    N 0 1 N N N N N N 2.294 -11.270 22.644 -5.578 -0.213 -0.164 N3    08Q 16 
08Q C4    C4    C 0 1 N N N N N N 2.378 -9.878  22.689 -5.563 0.617  0.899  C4    08Q 17 
08Q N4    N4    N 0 1 N N N N N N 3.716 -7.286  15.178 4.581  0.755  -0.786 N4    08Q 18 
08Q O4    O4    O 0 1 N N N N N N 2.424 -9.294  23.773 -6.605 0.946  1.437  O4    08Q 19 
08Q C5    C5    C 0 1 N N N N N N 2.416 -9.133  21.508 -4.325 1.103  1.383  C5    08Q 20 
08Q C7    C7    C 0 1 N N N N N N 2.510 -7.615  21.579 -4.280 2.032  2.569  C7    08Q 21 
08Q C6    C6    C 0 1 N N N N N N 2.369 -9.750  20.262 -3.184 0.718  0.771  C6    08Q 22 
08Q S     S     S 0 1 N N N N N N 3.024 -4.339  15.256 5.530  -1.589 2.388  S     08Q 23 
08Q OP3   O1    O 0 1 N Y N N N N 5.661 -8.938  16.688 3.323  3.007  -0.026 OP3   08Q 24 
08Q H1    H1    H 0 1 N N N N N N 4.994 -4.462  13.815 4.410  -1.716 0.261  H1    08Q 25 
08Q H2    H2    H 0 1 N N N N N N 3.667 -5.492  13.199 6.123  -1.272 0.076  H2    08Q 26 
08Q H3    H3    H 0 1 N N N N N N 5.508 -6.847  14.167 3.929  0.528  1.198  H3    08Q 27 
08Q H4    H4    H 0 1 N N N N N N 5.287 -6.003  15.738 5.643  0.972  1.014  H4    08Q 28 
08Q H5    H5    H 0 1 N N N N N N 4.553 -11.924 14.930 1.069  -0.009 -2.078 H5    08Q 29 
08Q H6    H6    H 0 1 N N N N N N 5.396 -11.127 16.352 2.180  -1.076 -1.186 H6    08Q 30 
08Q H7    H7    H 0 1 N N N N N N 4.102 -12.811 16.492 0.521  -1.123 0.712  H7    08Q 31 
08Q H8    H8    H 0 1 N N N N N N 1.311 -11.794 16.423 0.014  -2.203 -2.054 H8    08Q 32 
08Q H9    H9    H 0 1 N N N N N N 1.094 -13.882 15.774 -0.077 -4.185 -0.722 H9    08Q 33 
08Q H10   H10   H 0 1 N N N N N N 1.025 -13.489 18.379 -2.332 -2.589 -1.668 H10   08Q 34 
08Q H11   H11   H 0 1 N N N N N N 2.789 -13.790 18.370 -2.152 -2.433 0.113  H11   08Q 35 
08Q H12   H12   H 0 1 N N N N N N 1.283 -12.306 19.547 -2.020 -0.233 -2.021 H12   08Q 36 
08Q H13   H13   H 0 1 N N N N N N 2.265 -11.805 23.488 -6.423 -0.550 -0.501 H13   08Q 37 
08Q H14   H14   H 0 1 N N N N N N 3.029 -6.796  15.714 5.372  1.249  -1.171 H14   08Q 38 
08Q H15   H15   H 0 1 N N N N N N 2.537 -7.298  22.632 -5.294 2.219  2.922  H15   08Q 39 
08Q H16   H16   H 0 1 N N N N N N 3.427 -7.280  21.072 -3.695 1.574  3.367  H16   08Q 40 
08Q H17   H17   H 0 1 N N N N N N 1.634 -7.170  21.085 -3.818 2.974  2.274  H17   08Q 41 
08Q H18   H18   H 0 1 N N N N N N 2.362 -9.169  19.351 -2.229 1.075  1.129  H18   08Q 42 
08Q H19   H19   H 0 1 N N N N N N 2.589 -3.348  14.536 5.856  -2.890 2.287  H19   08Q 43 
08Q HOP3  H20   H 0 0 N Y N N N N 5.571 -9.044  17.628 3.470  2.839  0.915  HOP3  08Q 44 
# 
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 
08Q "C8'" "C7'" SING N N 1  
08Q "C8'" S     SING N N 2  
08Q "C7'" N4    SING N N 3  
08Q N4    P     SING N N 4  
08Q "O5'" "C5'" SING N N 5  
08Q "O5'" P     SING N N 6  
08Q "C5'" "C4'" SING N N 7  
08Q "O3'" "C3'" SING N N 8  
08Q P     OP1   DOUB N N 9  
08Q "C3'" "C4'" SING N N 10 
08Q "C3'" "C2'" SING N N 11 
08Q "C4'" "O4'" SING N N 12 
08Q "O4'" "C1'" SING N N 13 
08Q "C2'" "C1'" SING N N 14 
08Q "C1'" N1    SING N N 15 
08Q N1    C6    SING N N 16 
08Q N1    C2    SING N N 17 
08Q C6    C5    DOUB N N 18 
08Q O2    C2    DOUB N N 19 
08Q C2    N3    SING N N 20 
08Q C5    C7    SING N N 21 
08Q C5    C4    SING N N 22 
08Q N3    C4    SING N N 23 
08Q C4    O4    DOUB N N 24 
08Q P     OP3   SING N N 25 
08Q "C8'" H1    SING N N 26 
08Q "C8'" H2    SING N N 27 
08Q "C7'" H3    SING N N 28 
08Q "C7'" H4    SING N N 29 
08Q "C5'" H5    SING N N 30 
08Q "C5'" H6    SING N N 31 
08Q "C4'" H7    SING N N 32 
08Q "C3'" H8    SING N N 33 
08Q "O3'" H9    SING N N 34 
08Q "C2'" H10   SING N N 35 
08Q "C2'" H11   SING N N 36 
08Q "C1'" H12   SING N N 37 
08Q N3    H13   SING N N 38 
08Q N4    H14   SING N N 39 
08Q C7    H15   SING N N 40 
08Q C7    H16   SING N N 41 
08Q C7    H17   SING N N 42 
08Q C6    H18   SING N N 43 
08Q S     H19   SING N N 44 
08Q OP3   HOP3  SING N N 45 
# 
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 
08Q SMILES           ACDLabs              12.01 "O=P(O)(OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O)NCCS"                                                                                                                     
08Q InChI            InChI                1.03  "InChI=1S/C12H20N3O7PS/c1-7-5-15(12(18)14-11(7)17)10-4-8(16)9(22-10)6-21-23(19,20)13-2-3-24/h5,8-10,16,24H,2-4,6H2,1H3,(H2,13,19,20)(H,14,17,18)/t8-,9+,10-/m0/s1" 
08Q InChIKey         InChI                1.03  NNHLQGCWACQGSN-AEJSXWLSSA-N                                                                                                                                        
08Q SMILES_CANONICAL CACTVS               3.370 "CC1=CN([C@@H]2C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O"                                                                                                     
08Q SMILES           CACTVS               3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O"                                                                                                          
08Q SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@@H]([C@H](O2)COP(=O)(NCCS)O)O"                                                                                                       
08Q SMILES           "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NCCS)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 
08Q "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine"                                                                       
08Q "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
08Q "Create component" 2011-10-15 RCSB 
08Q "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            08Q 
_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      ? 
# 
