data_C2S
# 
_chem_comp.id                                    C2S 
_chem_comp.name                                  "CYTIDINE-5'-DITHIOPHOSPHORATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H14 N3 O5 P S2" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2001-11-02 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        339.328 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     C2S 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        "OpenEye/OEToolkits V1.4.2" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_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 
C2S OP3    O3P  O 0 1 N Y N ?      ?      ?       -3.988 -2.586 4.525  OP3    C2S 1  
C2S P      P    P 0 1 N N S 10.760 1.198  -11.374 -3.975 -1.694 3.157  P      C2S 2  
C2S S1P    S1P  S 0 1 N N N 10.681 2.397  -12.945 -4.140 -2.844 1.583  S1P    C2S 3  
C2S S2P    S2P  S 0 1 N N N 12.180 -0.142 -11.691 -5.409 -0.167 3.469  S2P    C2S 4  
C2S "O5'"  O5*  O 0 1 N N N 11.062 2.037  -10.032 -2.493 -1.028 3.315  "O5'"  C2S 5  
C2S "C5'"  C5*  C 0 1 N N N 10.310 3.199  -9.722  -2.005 -0.136 2.327  "C5'"  C2S 6  
C2S "C4'"  C4*  C 0 1 N N R 10.632 3.743  -8.327  -0.611 0.328  2.728  "C4'"  C2S 7  
C2S "O4'"  O4*  O 0 1 N N N 10.195 2.834  -7.326  0.247  -0.829 2.764  "O4'"  C2S 8  
C2S "C3'"  C3*  C 0 1 N N S 12.125 4.020  -8.078  0.008  1.286  1.720  "C3'"  C2S 9  
C2S "O3'"  O3*  O 0 1 N N N 12.273 5.374  -7.671  0.965  2.121  2.368  "O3'"  C2S 10 
C2S "C2'"  C2*  C 0 1 N N N 12.446 3.044  -6.948  0.710  0.360  0.754  "C2'"  C2S 11 
C2S "C1'"  C1*  C 0 1 N N R 11.094 2.965  -6.247  1.157  -0.778 1.657  "C1'"  C2S 12 
C2S N1     N1   N 0 1 N N N 10.979 1.825  -5.298  1.164  -2.047 0.989  N1     C2S 13 
C2S C2     C2   C 0 1 N N N 10.759 2.094  -3.943  2.328  -2.561 0.367  C2     C2S 14 
C2S O2     O2   O 0 1 N N N 10.617 3.240  -3.522  3.386  -1.929 0.379  O2     C2S 15 
C2S N3     N3   N 0 1 N N N 10.712 1.076  -3.049  2.260  -3.794 -0.259 N3     C2S 16 
C2S C4     C4   C 0 1 N N N 10.850 -0.168 -3.470  1.147  -4.479 -0.282 C4     C2S 17 
C2S N4     N4   N 0 1 N N N 10.774 -1.098 -2.553  1.101  -5.702 -0.910 N4     C2S 18 
C2S C5     C5   C 0 1 N N N 11.062 -0.501 -4.842  -0.094 -3.972 0.359  C5     C2S 19 
C2S C6     C6   C 0 1 N N N 11.118 0.527  -5.728  -0.008 -2.785 0.956  C6     C2S 20 
C2S HOP3   3HOP H 0 0 N N N 0.038  -0.576 0.755   -4.102 -2.123 5.382  HOP3   C2S 21 
C2S HOP2   2HOP H 0 0 N N N 12.831 -0.069 -12.379 -6.500 -0.946 3.500  HOP2   C2S 22 
C2S "H5'"  1H5* H 0 1 N N N 10.527 3.973  -10.460 -1.971 -0.654 1.366  "H5'"  C2S 23 
C2S "H5''" 2H5* H 0 0 N N N 9.245  2.966  -9.763  -2.683 0.718  2.254  "H5''" C2S 24 
C2S "H4'"  H4*  H 0 1 N N N 10.090 4.681  -8.196  -0.644 0.753  3.736  "H4'"  C2S 25 
C2S "H3'"  H3*  H 0 1 N N N 12.730 3.812  -8.963  -0.722 1.941  1.236  "H3'"  C2S 26 
C2S "HO3'" H3T  H 0 0 N Y N 13.195 5.545  -7.517  0.743  3.042  2.146  "HO3'" C2S 27 
C2S "H2'1" 1H2* H 0 0 N N N 13.535 2.833  -7.058  -0.003 -0.001 0.003  "H2'1" C2S 28 
C2S "H1'"  H1*  H 0 1 N N N 10.909 3.915  -5.732  2.163  -0.604 2.054  "H1'"  C2S 29 
C2S H41    1H4  H 0 1 N N N 10.570 -0.771 -1.603  0.349  -6.310 -0.691 H41    C2S 30 
C2S H42    2H4  H 0 1 N N N 10.780 -2.070 -2.785  1.822  -5.923 -1.553 H42    C2S 31 
C2S H5     H5   H 0 1 N N N 11.170 -1.519 -5.181  -1.005 -4.554 0.330  H5     C2S 32 
C2S H6     H6   H 0 1 N N N 11.268 0.346  -6.784  -0.867 -2.341 1.449  H6     C2S 33 
C2S "H2'2" 2H2* H 0 0 N N N 12.680 2.266  -6.207  1.556  0.818  0.232  "H2'2" C2S 34 
# 
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 
C2S OP3   P      SING N N 1  
C2S OP3   HOP3   SING N N 2  
C2S P     S1P    DOUB N N 3  
C2S P     S2P    SING N N 4  
C2S P     "O5'"  SING N N 5  
C2S S2P   HOP2   SING N N 6  
C2S "O5'" "C5'"  SING N N 7  
C2S "C5'" "C4'"  SING N N 8  
C2S "C5'" "H5'"  SING N N 9  
C2S "C5'" "H5''" SING N N 10 
C2S "C4'" "O4'"  SING N N 11 
C2S "C4'" "C3'"  SING N N 12 
C2S "C4'" "H4'"  SING N N 13 
C2S "O4'" "C1'"  SING N N 14 
C2S "C3'" "O3'"  SING N N 15 
C2S "C3'" "C2'"  SING N N 16 
C2S "C3'" "H3'"  SING N N 17 
C2S "O3'" "HO3'" SING N N 18 
C2S "C2'" "C1'"  SING N N 19 
C2S "C2'" "H2'1" SING N N 20 
C2S "C1'" N1     SING N N 21 
C2S "C1'" "H1'"  SING N N 22 
C2S N1    C2     SING N N 23 
C2S N1    C6     SING N N 24 
C2S C2    O2     DOUB N N 25 
C2S C2    N3     SING N N 26 
C2S N3    C4     DOUB N N 27 
C2S C4    N4     SING N N 28 
C2S C4    C5     SING N N 29 
C2S N4    H41    SING N N 30 
C2S N4    H42    SING N N 31 
C2S C5    C6     DOUB N N 32 
C2S C5    H5     SING N N 33 
C2S C6    H6     SING N N 34 
C2S "C2'" "H2'2" SING N N 35 
# 
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 
C2S SMILES           ACDLabs              10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=S)(O)S"                                                                                                        
C2S SMILES_CANONICAL CACTVS               3.341 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(S)=S)O2"                                                                                      
C2S SMILES           CACTVS               3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=S)O2"                                                                                           
C2S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=S)(O)S)O"                                                                                           
C2S SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=S)(O)S)O"                                                                                                        
C2S InChI            InChI                1.03  "InChI=1S/C9H14N3O5PS2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(17-8)4-16-18(15,19)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,19,20)/t5-,6+,8+/m0/s1" 
C2S InChIKey         InChI                1.03  YPTNEFVBJOMHCI-SHYZEUOFSA-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 
C2S "SYSTEMATIC NAME" ACDLabs              10.04 "2'-deoxy-5'-O-[(dithiophosphono)]cytidine"                                                                  
C2S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(2R,4S,5R)-4-hydroxy-5-[(hydroxy-sulfanyl-phosphinothioyl)oxymethyl]oxolan-2-yl]pyrimidin-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
C2S "Create component"  2001-11-02 RCSB 
C2S "Modify descriptor" 2011-06-04 RCSB 
# 
