data_TX2
# 
_chem_comp.id                                    TX2 
_chem_comp.name                                  "5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_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                     2009-10-01 
_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                     TX2 
_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        3JY4 
_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 
TX2 P      P      P 0 1 N N N N N N 4.784  -9.939  17.019 -3.786 0.826  0.045  P      TX2 1  
TX2 S      S      S 0 1 N N N N N N 3.075  -5.106  16.065 -3.081 -4.321 0.358  S      TX2 2  
TX2 N1     N1     N 0 1 N N N N N N 1.604  -11.276 21.398 2.886  0.295  0.414  N1     TX2 3  
TX2 C2     C2     C 0 1 N N N N N N 1.265  -11.681 22.693 2.762  -0.094 -0.868 C2     TX2 4  
TX2 O2     O2     O 0 1 N N N N N N 1.162  -12.876 22.961 1.909  0.416  -1.570 O2     TX2 5  
TX2 N3     N3     N 0 1 N N N N N N 1.045  -10.723 23.688 3.568  -1.039 -1.386 N3     TX2 6  
TX2 C4     C4     C 0 1 N N N N N N 1.161  -9.361  23.389 4.519  -1.614 -0.622 C4     TX2 7  
TX2 N4     N4     N 0 1 N N N N N N 4.529  -8.879  15.835 -3.665 -0.525 -0.953 N4     TX2 8  
TX2 O4     O4     O 0 1 N N N N N N 0.965  -8.533  24.279 5.249  -2.469 -1.089 O4     TX2 9  
TX2 C5     C5     C 0 1 N N N N N N 1.498  -8.958  22.094 4.660  -1.214 0.729  C5     TX2 10 
TX2 C6     C6     C 0 1 N N N N N N 1.720  -9.909  21.103 3.838  -0.263 1.222  C6     TX2 11 
TX2 C7     C7     C 0 1 N N N N N N 1.628  -7.466  21.760 5.714  -1.841 1.605  C7     TX2 12 
TX2 "C1'"  "C1'"  C 0 1 N N R N N N 1.839  -12.304 20.356 1.997  1.331  0.947  "C1'"  TX2 13 
TX2 "C2'"  "C2'"  C 0 1 N N N N N N 0.945  -12.109 19.139 2.262  2.668  0.229  "C2'"  TX2 14 
TX2 "C3'"  "C3'"  C 0 1 N N S N N N 1.687  -12.918 18.072 0.895  3.041  -0.394 "C3'"  TX2 15 
TX2 "O3'"  "O3'"  O 0 1 N N N N N N 1.203  -14.274 18.030 0.634  4.439  -0.253 "O3'"  TX2 16 
TX2 "C4'"  "C4'"  C 0 1 N N R N N N 3.142  -12.943 18.579 -0.091 2.205  0.461  "C4'"  TX2 17 
TX2 "O4'"  "O4'"  O 0 1 N N N N N N 3.156  -12.155 19.806 0.627  0.975  0.697  "O4'"  TX2 18 
TX2 "C5'"  "C5'"  C 0 1 N N N N N N 4.112  -12.391 17.512 -1.382 1.935  -0.315 "C5'"  TX2 19 
TX2 "O5'"  "O5'"  O 0 1 N N N N N N 3.699  -11.119 16.975 -2.317 1.266  0.534  "O5'"  TX2 20 
TX2 "C7'"  "C7'"  C 0 1 N N N N N N 3.479  -7.867  15.967 -3.048 -1.652 -0.240 "C7'"  TX2 21 
TX2 "C8'"  "C8'"  C 0 1 N N N N N N 3.971  -6.546  15.375 -3.842 -2.929 -0.522 "C8'"  TX2 22 
TX2 OP1    OP1    O 0 1 N N N N N N 6.128  -10.547 16.910 -4.410 1.938  -0.706 OP1    TX2 23 
TX2 HS     HS     H 0 1 N N N N N N 3.637  -4.114  15.441 -3.869 -5.358 0.023  HS     TX2 24 
TX2 HN3    HN3    H 0 1 N N N N N N 0.804  -11.012 24.615 3.465  -1.308 -2.312 HN3    TX2 25 
TX2 HN4    HN4    H 0 1 N N N N N N 5.386  -8.376  15.725 -4.567 -0.782 -1.324 HN4    TX2 26 
TX2 H6     H6     H 0 1 N N N N N N 1.982  -9.594  20.104 3.931  0.055  2.250  H6     TX2 27 
TX2 H7     H7     H 0 1 N N N N N N 1.897  -7.349  20.700 6.272  -2.580 1.030  H7     TX2 28 
TX2 H7A    H7A    H 0 1 N N N N N N 0.669  -6.962  21.952 6.396  -1.069 1.962  H7A    TX2 29 
TX2 H7B    H7B    H 0 1 N N N N N N 2.411  -7.017  22.389 5.237  -2.327 2.456  H7B    TX2 30 
TX2 "H1'"  "H1'"  H 0 1 N N N N N N 1.660  -13.268 20.855 2.163  1.445  2.018  "H1'"  TX2 31 
TX2 "H2'"  "H2'"  H 0 1 N N N N N N -0.074 -12.486 19.310 2.575  3.429  0.944  "H2'"  TX2 32 
TX2 "H2'A" "H2'A" H 0 0 N N N N N N 0.848  -11.049 18.862 3.014  2.542  -0.549 "H2'A" TX2 33 
TX2 "H3'"  "H3'"  H 0 1 N N N N N N 1.563  -12.486 17.068 0.851  2.743  -1.442 "H3'"  TX2 34 
TX2 "HO3'" "HO3'" H 0 0 N N N N N N 1.675  -14.759 17.363 1.279  5.007  -0.697 "HO3'" TX2 35 
TX2 "H4'"  "H4'"  H 0 1 N N N N N N 3.486  -13.969 18.779 -0.307 2.711  1.402  "H4'"  TX2 36 
TX2 "H5'"  "H5'"  H 0 1 N N N N N N 5.101  -12.264 17.977 -1.809 2.880  -0.651 "H5'"  TX2 37 
TX2 "H5'A" "H5'A" H 0 0 N N N N N N 4.163  -13.114 16.685 -1.162 1.308  -1.179 "H5'A" TX2 38 
TX2 "H7'"  "H7'"  H 0 1 N N N N N N 2.579  -8.199  15.428 -2.021 -1.779 -0.581 "H7'"  TX2 39 
TX2 "H7'A" "H7'A" H 0 0 N N N N N N 3.237  -7.725  17.031 -3.053 -1.450 0.831  "H7'A" TX2 40 
TX2 "H8'"  "H8'"  H 0 1 N N N N N N 3.813  -6.569  14.287 -3.837 -3.130 -1.594 "H8'"  TX2 41 
TX2 "H8'A" "H8'A" H 0 0 N N N N N N 5.041  -6.436  15.604 -4.869 -2.802 -0.181 "H8'A" TX2 42 
TX2 OP3    OP3    O 0 1 N Y N N N N 5.148  -9.332  18.587 -4.693 0.467  1.326  O7     TX2 43 
TX2 HOP3   HOP3   H 0 0 N Y N N N N 6.033  -9.582  18.826 -4.344 -0.255 1.865  H20    TX2 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 
TX2 P     N4     SING N N 1  
TX2 P     "O5'"  SING N N 2  
TX2 P     OP1    DOUB N N 3  
TX2 S     "C8'"  SING N N 4  
TX2 S     HS     SING N N 5  
TX2 N1    C2     SING N N 6  
TX2 N1    C6     SING N N 7  
TX2 N1    "C1'"  SING N N 8  
TX2 C2    O2     DOUB N N 9  
TX2 C2    N3     SING N N 10 
TX2 N3    C4     SING N N 11 
TX2 N3    HN3    SING N N 12 
TX2 C4    O4     DOUB N N 13 
TX2 C4    C5     SING N N 14 
TX2 N4    "C7'"  SING N N 15 
TX2 N4    HN4    SING N N 16 
TX2 C5    C6     DOUB N N 17 
TX2 C5    C7     SING N N 18 
TX2 C6    H6     SING N N 19 
TX2 C7    H7     SING N N 20 
TX2 C7    H7A    SING N N 21 
TX2 C7    H7B    SING N N 22 
TX2 "C1'" "C2'"  SING N N 23 
TX2 "C1'" "O4'"  SING N N 24 
TX2 "C1'" "H1'"  SING N N 25 
TX2 "C2'" "C3'"  SING N N 26 
TX2 "C2'" "H2'"  SING N N 27 
TX2 "C2'" "H2'A" SING N N 28 
TX2 "C3'" "O3'"  SING N N 29 
TX2 "C3'" "C4'"  SING N N 30 
TX2 "C3'" "H3'"  SING N N 31 
TX2 "O3'" "HO3'" SING N N 32 
TX2 "C4'" "O4'"  SING N N 33 
TX2 "C4'" "C5'"  SING N N 34 
TX2 "C4'" "H4'"  SING N N 35 
TX2 "C5'" "O5'"  SING N N 36 
TX2 "C5'" "H5'"  SING N N 37 
TX2 "C5'" "H5'A" SING N N 38 
TX2 "C7'" "C8'"  SING N N 39 
TX2 "C7'" "H7'"  SING N N 40 
TX2 "C7'" "H7'A" SING N N 41 
TX2 "C8'" "H8'"  SING N N 42 
TX2 "C8'" "H8'A" SING N N 43 
TX2 P     OP3    SING N N 44 
TX2 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 
TX2 SMILES           ACDLabs              11.02 "O=P(O)(OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O)NCCS"                                                                                                                     
TX2 SMILES_CANONICAL CACTVS               3.352 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O"                                                                                                      
TX2 SMILES           CACTVS               3.352 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O"                                                                                                          
TX2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(NCCS)O)O"                                                                                                    
TX2 SMILES           "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NCCS)O)O"                                                                                                                     
TX2 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" 
TX2 InChIKey         InChI                1.03  NNHLQGCWACQGSN-IVZWLZJFSA-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 
TX2 "SYSTEMATIC NAME" ACDLabs              11.02 "5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine"                                                         
TX2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)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 
TX2 "Create component"  2009-10-01 RCSB 
TX2 "Modify descriptor" 2011-06-04 RCSB 
TX2 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            TX2 
_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      ? 
# 
