data_2GT
# 
_chem_comp.id                                    2GT 
_chem_comp.name                                  
;2'-O-PROPARGYL THYMIDINE-5'-MONOPHOSPHATE
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H17 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-12-17 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        376.256 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     2GT 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1Y9S 
_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 
2GT P      P      P 0 1 N N N 10.749 4.067  5.377  2.787  0.324  -4.407 P      2GT 1  
2GT OP1    O1P    O 0 1 N N N 11.961 4.604  4.673  3.659  1.172  -5.286 OP1    2GT 2  
2GT OP2    O2P    O 0 1 N N N 10.921 3.350  6.620  1.198  0.588  -4.548 OP2    2GT 3  
2GT "O5'"  O5*    O 0 1 N N N 9.747  5.281  5.596  3.063  0.476  -2.819 "O5'"  2GT 4  
2GT "C5'"  C5*    C 0 1 N N N 9.479  6.145  4.523  2.282  -0.292 -1.921 "C5'"  2GT 5  
2GT "C4'"  C4*    C 0 1 N N R 8.428  7.143  4.925  2.725  0.023  -0.498 "C4'"  2GT 6  
2GT "O4'"  O4*    O 0 1 N N N 7.160  6.460  5.106  2.470  1.422  -0.246 "O4'"  2GT 7  
2GT "C1'"  C1*    C 0 1 N N R 6.438  7.082  6.161  1.373  1.543  0.675  "C1'"  2GT 8  
2GT N1     N1     N 0 1 N N N 6.258  6.107  7.266  0.452  2.524  0.177  N1     2GT 9  
2GT C6     C6     C 0 1 N N N 7.110  5.029  7.466  0.309  2.663  -1.199 C6     2GT 10 
2GT C2     C2     C 0 1 N N N 5.200  6.336  8.099  -0.300 3.336  1.055  C2     2GT 11 
2GT O2     O2     O 0 1 N N N 4.485  7.315  7.980  -0.225 3.269  2.283  O2     2GT 12 
2GT N3     N3     N 0 1 N N N 5.027  5.398  9.095  -1.159 4.248  0.431  N3     2GT 13 
2GT C4     C4     C 0 1 N N N 5.827  4.304  9.354  -1.338 4.427  -0.932 C4     2GT 14 
2GT O4     O4     O 0 1 N N N 5.576  3.577  10.291 -2.112 5.251  -1.413 O4     2GT 15 
2GT C5     C5     C 0 1 N N N 6.949  4.135  8.461  -0.514 3.537  -1.792 C5     2GT 16 
2GT C5M    C5M    C 0 1 N N N 7.884  2.988  8.690  -0.651 3.669  -3.275 C5M    2GT 17 
2GT "C2'"  C2*    C 0 1 N N R 7.268  8.288  6.624  0.748  0.163  0.786  "C2'"  2GT 18 
2GT "O2'"  O2*    O 0 1 N N N 6.939  9.362  5.745  0.137  -0.058 2.041  "O2'"  2GT 19 
2GT "CB'"  "CB'"  C 0 1 N N N 5.693  9.974  6.052  -0.332 -1.396 2.174  "CB'"  2GT 20 
2GT "CC'"  "CC'"  C 0 1 N N N 5.418  11.002 5.044  -0.958 -1.592 3.481  "CC'"  2GT 21 
2GT "CD'"  "CD'"  C 0 1 N N N 5.193  11.831 4.192  -1.472 -1.755 4.554  "CD'"  2GT 22 
2GT "C3'"  C3*    C 0 1 N N R 8.666  7.817  6.267  1.940  -0.742 0.560  "C3'"  2GT 23 
2GT "O3'"  O3*    O 0 1 N N N 9.613  8.876  6.221  2.742  -0.809 1.739  "O3'"  2GT 24 
2GT OP3    O3P    O 0 1 N Y N ?      ?      ?      2.921  -1.270 -4.647 OP3    2GT 25 
2GT HOP2   2HOP   H 0 0 N N N 10.154 3.010  7.066  0.799  0.616  -5.443 HOP2   2GT 26 
2GT "H5'"  1H5*   H 0 1 N N N 9.199  5.590  3.597  1.229  -0.035 -2.051 "H5'"  2GT 27 
2GT "H5''" 2H5*   H 0 0 N N N 10.403 6.639  4.141  2.428  -1.352 -2.133 "H5''" 2GT 28 
2GT "H4'"  H4*    H 0 1 N N N 8.448  7.904  4.110  3.804  -0.139 -0.410 "H4'"  2GT 29 
2GT "H1'"  H1*    H 0 1 N N N 5.428  7.419  5.830  1.754  1.910  1.633  "H1'"  2GT 30 
2GT H6     H6     H 0 1 N N N 7.969  4.873  6.792  0.928  1.995  -1.790 H6     2GT 31 
2GT HN3    HN3    H 0 1 N N N 4.221  5.527  9.706  -1.709 4.843  1.045  HN3    2GT 32 
2GT H71    1H5M   H 0 1 N N N 8.912  3.410  8.785  -1.057 2.748  -3.690 H71    2GT 33 
2GT H72    2H5M   H 0 1 N N N 7.751  2.248  9.514  0.324  3.866  -3.719 H72    2GT 34 
2GT H73    3H5M   H 0 1 N N N 7.948  2.415  7.735  -1.320 4.497  -3.510 H73    2GT 35 
2GT "H2'"  H2*    H 0 1 N N N 7.130  8.603  7.685  -0.000 0.004  -0.000 "H2'"  2GT 36 
2GT "HB'1" "1HB'" H 0 0 N N N 5.658  10.375 7.092  -1.036 -1.599 1.361  "HB'1" 2GT 37 
2GT "HB'2" "2HB'" H 0 0 N N N 4.864  9.234  6.145  0.525  -2.065 2.052  "HB'2" 2GT 38 
2GT "HD'"  "HD'"  H 0 1 N N N 4.990  12.578 3.424  -1.928 -1.900 5.505  "HD'"  2GT 39 
2GT "H3'"  H3*    H 0 1 N N N 9.123  7.137  7.023  1.675  -1.764 0.277  "H3'"  2GT 40 
2GT "HO3'" H3T    H 0 0 N Y N 9.762  9.297  7.060  3.447  -0.153 1.628  "HO3'" 2GT 41 
2GT HOP3   3HOP   H 0 0 N N N -0.767 -0.340 0.446  2.886  -1.617 -5.563 HOP3   2GT 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 
2GT P     OP1    DOUB N N 1  
2GT P     OP2    SING N N 2  
2GT P     "O5'"  SING N N 3  
2GT P     OP3    SING N N 4  
2GT OP2   HOP2   SING N N 5  
2GT "O5'" "C5'"  SING N N 6  
2GT "C5'" "C4'"  SING N N 7  
2GT "C5'" "H5'"  SING N N 8  
2GT "C5'" "H5''" SING N N 9  
2GT "C4'" "O4'"  SING N N 10 
2GT "C4'" "C3'"  SING N N 11 
2GT "C4'" "H4'"  SING N N 12 
2GT "O4'" "C1'"  SING N N 13 
2GT "C1'" N1     SING N N 14 
2GT "C1'" "C2'"  SING N N 15 
2GT "C1'" "H1'"  SING N N 16 
2GT N1    C6     SING N N 17 
2GT N1    C2     SING N N 18 
2GT C6    C5     DOUB N N 19 
2GT C6    H6     SING N N 20 
2GT C2    O2     DOUB N N 21 
2GT C2    N3     SING N N 22 
2GT N3    C4     SING N N 23 
2GT N3    HN3    SING N N 24 
2GT C4    O4     DOUB N N 25 
2GT C4    C5     SING N N 26 
2GT C5    C5M    SING N N 27 
2GT C5M   H71    SING N N 28 
2GT C5M   H72    SING N N 29 
2GT C5M   H73    SING N N 30 
2GT "C2'" "O2'"  SING N N 31 
2GT "C2'" "C3'"  SING N N 32 
2GT "C2'" "H2'"  SING N N 33 
2GT "O2'" "CB'"  SING N N 34 
2GT "CB'" "CC'"  SING N N 35 
2GT "CB'" "HB'1" SING N N 36 
2GT "CB'" "HB'2" SING N N 37 
2GT "CC'" "CD'"  TRIP N N 38 
2GT "CD'" "HD'"  SING N N 39 
2GT "C3'" "O3'"  SING N N 40 
2GT "C3'" "H3'"  SING N N 41 
2GT "O3'" "HO3'" SING N N 42 
2GT 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 
2GT SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCC#C)COP(=O)(O)O"                                                                                                                                      
2GT InChI            InChI                1.02b "InChI=1/C13H17N2O9P/c1-3-4-22-10-9(16)8(6-23-25(19,20)21)24-12(10)15-5-7(2)11(17)14-13(15)18/h1,5,8-10,12,16H,4,6H2,2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1/f/h14,19-20H" 
2GT InChIKey         InChI                1.02b HARKMJGNXJUASR-IHXBBRRKDT                                                                                                                                                             
2GT SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2OCC#C)C(=O)NC1=O"                                                                                                                  
2GT SMILES           CACTVS               3.341 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2OCC#C)C(=O)NC1=O"                                                                                                                        
2GT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCC#C"                                                                                                                  
2GT SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCC#C"                                                                                                                                    
# 
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 
2GT "SYSTEMATIC NAME" ACDLabs              10.04 
;5-methyl-2'-O-prop-2-yn-1-yluridine 5'-(dihydrogen phosphate)
;
2GT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-prop-2-ynoxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
