data_CX2
# 
_chem_comp.id                                    CX2 
_chem_comp.name                                  "2'-deoxy-5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}cytidine" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H19 N4 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                     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                        366.331 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CX2 
_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        3JY2 
_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 
CX2 P      P      P 0 1 N N N N N N -4.876 57.787 16.749 -3.499 1.000  -0.066 P      CX2 1  
CX2 S      S      S 0 1 N N N N N N -2.868 53.060 16.065 -3.166 -4.167 0.460  S      CX2 2  
CX2 N1     N1     N 0 1 N N N N N N -1.468 58.384 19.818 3.100  0.031  0.597  N1     CX2 3  
CX2 C2     C2     C 0 1 N N N N N N -1.557 58.292 21.222 3.001  -0.400 -0.674 C2     CX2 4  
CX2 O2     O2     O 0 1 N N N N N N -1.690 59.311 21.905 2.212  0.140  -1.431 O2     CX2 5  
CX2 N3     N3     N 0 1 N N N N N N -1.493 57.033 21.844 3.752  -1.406 -1.119 N3     CX2 6  
CX2 C4     C4     C 0 1 N N N N N N -1.343 55.873 21.072 4.619  -2.011 -0.317 C4     CX2 7  
CX2 N4     N4     N 0 1 N N N N N N -1.283 54.687 21.672 5.389  -3.049 -0.788 N4     CX2 8  
CX2 C5     C5     C 0 1 N N N N N N -1.256 55.967 19.680 4.746  -1.584 1.020  C5     CX2 9  
CX2 C6     C6     C 0 1 N N N N N N -1.321 57.211 19.052 3.976  -0.559 1.458  C6     CX2 10 
CX2 "C1'"  "C1'"  C 0 1 N N R N N N -1.552 59.725 19.173 2.266  1.144  1.056  "C1'"  CX2 11 
CX2 "C2'"  "C2'"  C 0 1 N N N N N N -1.186 59.811 17.693 2.650  2.433  0.303  "C2'"  CX2 12 
CX2 "C3'"  "C3'"  C 0 1 N N S N N N -2.010 61.016 17.228 1.338  2.873  -0.390 "C3'"  CX2 13 
CX2 "O3'"  "O3'"  O 0 1 N N N N N N -1.432 62.253 17.636 1.169  4.290  -0.309 "O3'"  CX2 14 
CX2 "C4'"  "C4'"  C 0 1 N N R N N N -3.283 60.900 18.059 0.264  2.140  0.453  "C4'"  CX2 15 
CX2 "N4'"  "N4'"  N 0 1 N N N N N N -4.425 56.796 15.549 -3.433 -0.393 -1.008 "N4'"  CX2 16 
CX2 "O4'"  "O4'"  O 0 1 N N N N N N -2.964 60.050 19.212 0.885  0.874  0.762  "O4'"  CX2 17 
CX2 "C5'"  "C5'"  C 0 1 N N N N N N -4.395 60.286 17.224 -1.012 1.929  -0.365 "C5'"  CX2 18 
CX2 "O5'"  "O5'"  O 0 1 N N N N N N -3.967 59.074 16.608 -2.023 1.357  0.468  "O5'"  CX2 19 
CX2 "C7'"  "C7'"  C 0 1 N N N N N N -4.468 55.332 15.692 -2.925 -1.531 -0.231 "C7'"  CX2 20 
CX2 "C8'"  "C8'"  C 0 1 N N N N N N -3.053 54.790 15.487 -3.794 -2.761 -0.500 "C8'"  CX2 21 
CX2 OP1    OP1    O 0 1 N N N N N N -6.303 58.125 16.650 -4.015 2.123  -0.880 OP1    CX2 22 
CX2 HS     HS     H 0 1 N N N N N N -1.619 52.818 15.798 -4.011 -5.160 0.130  HS     CX2 23 
CX2 HN4    HN4    H 0 1 N N N N N N -1.345 54.627 22.668 5.299  -3.340 -1.709 HN4    CX2 24 
CX2 HN4A   HN4A   H 0 0 N N N N N N -1.176 53.856 21.127 6.022  -3.489 -0.199 HN4A   CX2 25 
CX2 H5     H5     H 0 1 N N N N N N -1.138 55.072 19.088 5.447  -2.066 1.686  H5     CX2 26 
CX2 H6     H6     H 0 1 N N N N N N -1.258 57.275 17.976 4.056  -0.213 2.478  H6     CX2 27 
CX2 "H1'"  "H1'"  H 0 1 N N N N N N -0.842 60.374 19.707 2.398  1.289  2.128  "H1'"  CX2 28 
CX2 "H2'"  "H2'"  H 0 1 N N N N N N -0.107 59.967 17.543 2.988  3.197  1.002  "H2'"  CX2 29 
CX2 "H2'A" "H2'A" H 0 0 N N N N N N -1.454 58.894 17.148 3.422  2.225  -0.439 "H2'A" CX2 30 
CX2 "H3'"  "H3'"  H 0 1 N N N N N N -2.115 61.011 16.133 1.314  2.539  -1.427 "H3'"  CX2 31 
CX2 "HO3'" "HO3'" H 0 0 N N N N N N -1.972 62.972 17.329 1.869  4.795  -0.746 "HO3'" CX2 32 
CX2 "H4'"  "H4'"  H 0 1 N N N N N N -3.632 61.887 18.395 0.048  2.694  1.366  "H4'"  CX2 33 
CX2 "HN4'" "HN4'" H 0 0 N N N N N N -5.033 57.008 14.784 -4.336 -0.602 -1.408 "HN4'" CX2 34 
CX2 "H5'"  "H5'"  H 0 1 N N N N N N -5.253 60.070 17.877 -1.358 2.887  -0.752 "H5'"  CX2 35 
CX2 "H5'A" "H5'A" H 0 0 N N N N N N -4.688 61.000 16.440 -0.803 1.255  -1.197 "H5'A" CX2 36 
CX2 "H7'"  "H7'"  H 0 1 N N N N N N -4.829 55.064 16.696 -1.896 -1.741 -0.525 "H7'"  CX2 37 
CX2 "H7'A" "H7'A" H 0 0 N N N N N N -5.146 54.902 14.940 -2.957 -1.289 0.831  "H7'A" CX2 38 
CX2 "H8'"  "H8'"  H 0 1 N N N N N N -2.353 55.422 16.053 -3.761 -3.004 -1.562 "H8'"  CX2 39 
CX2 "H8'A" "H8'A" H 0 0 N N N N N N -2.820 54.824 14.412 -4.822 -2.551 -0.206 "H8'A" CX2 40 
CX2 OP3    OP3    O 0 1 N Y N N N N -5.167 57.118 18.307 -4.478 0.753  1.189  O6     CX2 41 
CX2 HOP3   HOP3   H 0 0 N Y N N N N -6.088 57.205 18.523 -4.201 0.030  1.768  H19    CX2 42 
# 
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 
CX2 P     "N4'"  SING N N 1  
CX2 P     "O5'"  SING N N 2  
CX2 P     OP1    DOUB N N 3  
CX2 S     "C8'"  SING N N 4  
CX2 S     HS     SING N N 5  
CX2 N1    C2     SING N N 6  
CX2 N1    C6     SING N N 7  
CX2 N1    "C1'"  SING N N 8  
CX2 C2    O2     DOUB N N 9  
CX2 C2    N3     SING N N 10 
CX2 N3    C4     DOUB N N 11 
CX2 C4    N4     SING N N 12 
CX2 C4    C5     SING N N 13 
CX2 N4    HN4    SING N N 14 
CX2 N4    HN4A   SING N N 15 
CX2 C5    C6     DOUB N N 16 
CX2 C5    H5     SING N N 17 
CX2 C6    H6     SING N N 18 
CX2 "C1'" "C2'"  SING N N 19 
CX2 "C1'" "O4'"  SING N N 20 
CX2 "C1'" "H1'"  SING N N 21 
CX2 "C2'" "C3'"  SING N N 22 
CX2 "C2'" "H2'"  SING N N 23 
CX2 "C2'" "H2'A" SING N N 24 
CX2 "C3'" "O3'"  SING N N 25 
CX2 "C3'" "C4'"  SING N N 26 
CX2 "C3'" "H3'"  SING N N 27 
CX2 "O3'" "HO3'" SING N N 28 
CX2 "C4'" "O4'"  SING N N 29 
CX2 "C4'" "C5'"  SING N N 30 
CX2 "C4'" "H4'"  SING N N 31 
CX2 "N4'" "C7'"  SING N N 32 
CX2 "N4'" "HN4'" SING N N 33 
CX2 "C5'" "O5'"  SING N N 34 
CX2 "C5'" "H5'"  SING N N 35 
CX2 "C5'" "H5'A" SING N N 36 
CX2 "C7'" "C8'"  SING N N 37 
CX2 "C7'" "H7'"  SING N N 38 
CX2 "C7'" "H7'A" SING N N 39 
CX2 "C8'" "H8'"  SING N N 40 
CX2 "C8'" "H8'A" SING N N 41 
CX2 P     OP3    SING N N 42 
CX2 OP3   HOP3   SING N N 43 
# 
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 
CX2 SMILES           ACDLabs              11.02 "O=P(O)(OCC2OC(N1C(=O)N=C(N)C=C1)CC2O)NCCS"                                                                                                                      
CX2 SMILES_CANONICAL CACTVS               3.352 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O2"                                                                                                     
CX2 SMILES           CACTVS               3.352 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)NCCS)O2"                                                                                                         
CX2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(NCCS)O)O"                                                                                                     
CX2 SMILES           "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(NCCS)O)O"                                                                                                                      
CX2 InChI            InChI                1.03  "InChI=1S/C11H19N4O6PS/c12-9-1-3-15(11(17)14-9)10-5-7(16)8(21-10)6-20-22(18,19)13-2-4-23/h1,3,7-8,10,16,23H,2,4-6H2,(H2,12,14,17)(H2,13,18,19)/t7-,8+,10+/m0/s1" 
CX2 InChIKey         InChI                1.03  UBFVQIIQWMOGNR-QXFUBDJGSA-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 
CX2 "SYSTEMATIC NAME" ACDLabs              11.02 "2'-deoxy-5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}cytidine"                                              
CX2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 
CX2 "Create component"  2009-10-01 RCSB 
CX2 "Modify descriptor" 2011-06-04 RCSB 
CX2 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            CX2 
_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      ? 
# 
