data_D4D
# 
_chem_comp.id                                    D4D 
_chem_comp.name                                  
;2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H14 N2 O10 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2000-08-23 
_chem_comp.pdbx_modified_date                    2008-10-14 
_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                        384.173 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D4D 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1F3F 
_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 
D4D PA     PA     P 0 1 N N S -13.113 45.306 33.353 -2.869 0.575  0.008  PA     D4D 1  
D4D O1A    O1A    O 0 1 N N N -14.247 46.212 33.053 -2.505 -0.335 -1.101 O1A    D4D 2  
D4D O2A    O2A    O 0 1 N N N -12.504 44.504 32.260 -3.697 1.827  -0.574 O2A    D4D 3  
D4D O3A    O3A    O 0 1 N N N -11.972 46.148 34.084 -3.775 -0.218 1.077  O3A    D4D 4  
D4D PB     PB     P 0 1 N N N -11.430 47.635 33.877 -4.781 -1.150 0.234  PB     D4D 5  
D4D O1B    O1B    O 0 1 N N N -12.592 48.400 33.354 -4.009 -2.479 -0.243 O1B    D4D 6  
D4D O2B    O2B    O 0 1 N N N -10.236 47.492 33.002 -5.264 -0.408 -0.952 O2B    D4D 7  
D4D O3B    O3B    O 0 1 N N N -11.229 48.128 35.267 -6.035 -1.560 1.157  O3B    D4D 8  
D4D "O5'"  "O5'"  O 0 1 N N N -13.582 44.314 34.510 -1.530 1.105  0.728  "O5'"  D4D 9  
D4D "C5'"  "C5'"  C 0 1 N N N -14.433 44.768 35.562 -0.718 1.692  -0.291 "C5'"  D4D 10 
D4D "C4'"  "C4'"  C 0 1 N N S -13.936 44.255 36.894 0.578  2.218  0.330  "C4'"  D4D 11 
D4D "O4'"  "O4'"  O 0 1 N N N -14.012 42.807 36.902 1.377  1.123  0.818  "O4'"  D4D 12 
D4D "C3'"  "C3'"  C 0 1 N N N -12.493 44.568 37.217 1.421  2.904  -0.720 "C3'"  D4D 13 
D4D "C2'"  "C2'"  C 0 1 N N N -11.875 43.435 37.592 2.669  2.528  -0.561 "C2'"  D4D 14 
D4D "C1'"  "C1'"  C 0 1 N N R -12.863 42.290 37.537 2.730  1.566  0.603  "C1'"  D4D 15 
D4D N1     N1     N 0 1 Y N N -12.361 41.166 36.726 3.589  0.426  0.274  N1     D4D 16 
D4D C2     C2     C 0 1 Y N N -12.011 39.993 37.363 3.238  -0.406 -0.723 C2     D4D 17 
D4D O2     O2     O 0 1 N N N -12.112 39.829 38.570 2.211  -0.203 -1.340 O2     D4D 18 
D4D N3     N3     N 0 1 Y N N -11.535 39.011 36.527 4.009  -1.461 -1.047 N3     D4D 19 
D4D C4     C4     C 0 1 Y N N -11.377 39.086 35.155 5.154  -1.698 -0.376 C4     D4D 20 
D4D O4     O4     O 0 1 N N N -10.923 38.125 34.539 5.852  -2.652 -0.669 O4     D4D 21 
D4D C5     C5     C 0 1 Y N N -11.774 40.341 34.555 5.533  -0.833 0.679  C5     D4D 22 
D4D C5M    C5M    C 0 1 N N N -11.648 40.513 33.073 6.805  -1.078 1.448  C5M    D4D 23 
D4D C6     C6     C 0 1 Y N N -12.239 41.303 35.360 4.741  0.218  0.983  C6     D4D 24 
D4D H2AO   OH2A   H 0 0 N N N -11.777 43.923 32.452 -3.913 2.393  0.179  H2AO   D4D 25 
D4D H1BO   OH1B   H 0 0 N N N -12.269 49.285 33.230 -3.711 -2.932 0.558  H1BO   D4D 26 
D4D H3BO   OH3B   H 0 0 N N N -10.906 49.013 35.143 -6.611 -2.116 0.615  H3BO   D4D 27 
D4D "H5'1" "1H5'" H 0 0 N N N -14.544 45.877 35.558 -1.258 2.515  -0.757 "H5'1" D4D 28 
D4D "H5'2" "2H5'" H 0 0 N N N -15.499 44.495 35.382 -0.480 0.941  -1.044 "H5'2" D4D 29 
D4D "H4'C" "CH4'" H 0 0 N N N -14.584 44.766 37.642 0.352  2.910  1.142  "H4'C" D4D 30 
D4D "H3'C" "CH3'" H 0 0 N N N -11.946 45.525 37.182 1.059  3.589  -1.473 "H3'C" D4D 31 
D4D "H2'C" "CH2'" H 0 0 N N N -10.809 43.443 37.877 3.508  2.849  -1.162 "H2'C" D4D 32 
D4D "H1'C" "CH1'" H 0 0 N N N -13.054 41.905 38.565 3.105  2.074  1.492  "H1'C" D4D 33 
D4D HN3    HN3    H 0 1 N N N -11.270 38.132 36.972 3.741  -2.051 -1.769 HN3    D4D 34 
D4D H5M1   1H5M   H 0 0 N N N -11.954 41.480 32.610 6.595  -1.720 2.303  H5M1   D4D 35 
D4D H5M2   2H5M   H 0 0 N N N -10.597 40.290 32.774 7.534  -1.563 0.799  H5M2   D4D 36 
D4D H5M3   3H5M   H 0 0 N N N -12.198 39.685 32.568 7.207  -0.127 1.798  H5M3   D4D 37 
D4D H66    6H6    H 0 1 N N N -12.534 42.250 34.877 5.016  0.891  1.782  H66    D4D 38 
# 
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 
D4D PA    O1A    DOUB N N 1  
D4D PA    O2A    SING N N 2  
D4D PA    O3A    SING N N 3  
D4D PA    "O5'"  SING N N 4  
D4D O2A   H2AO   SING N N 5  
D4D O3A   PB     SING N N 6  
D4D PB    O1B    SING N N 7  
D4D PB    O2B    DOUB N N 8  
D4D PB    O3B    SING N N 9  
D4D O1B   H1BO   SING N N 10 
D4D O3B   H3BO   SING N N 11 
D4D "O5'" "C5'"  SING N N 12 
D4D "C5'" "C4'"  SING N N 13 
D4D "C5'" "H5'1" SING N N 14 
D4D "C5'" "H5'2" SING N N 15 
D4D "C4'" "O4'"  SING N N 16 
D4D "C4'" "C3'"  SING N N 17 
D4D "C4'" "H4'C" SING N N 18 
D4D "O4'" "C1'"  SING N N 19 
D4D "C3'" "C2'"  DOUB N N 20 
D4D "C3'" "H3'C" SING N N 21 
D4D "C2'" "C1'"  SING N N 22 
D4D "C2'" "H2'C" SING N N 23 
D4D "C1'" N1     SING N N 24 
D4D "C1'" "H1'C" SING N N 25 
D4D N1    C2     SING Y N 26 
D4D N1    C6     SING Y N 27 
D4D C2    O2     DOUB N N 28 
D4D C2    N3     SING Y N 29 
D4D N3    C4     SING Y N 30 
D4D N3    HN3    SING N N 31 
D4D C4    O4     DOUB N N 32 
D4D C4    C5     SING Y N 33 
D4D C5    C5M    SING N N 34 
D4D C5    C6     DOUB Y N 35 
D4D C5M   H5M1   SING N N 36 
D4D C5M   H5M2   SING N N 37 
D4D C5M   H5M3   SING N N 38 
D4D C6    H66    SING N N 39 
# 
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 
D4D SMILES           ACDLabs              10.04 O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)C=C2                                                                                                                          
D4D InChI            InChI                1.02b InChI=1/C10H14N2O10P2/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(21-8)5-20-24(18,19)22-23(15,16)17/h2-4,7-8H,5H2,1H3,(H,18,19)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1/f/h11,15-16,18H 
D4D InChIKey         InChI                1.02b LXCAIISEDMYORY-BFRVXCLEDY                                                                                                                                                   
D4D SMILES_CANONICAL CACTVS               3.341 CC1=CN([C@@H]2O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)C=C2)C(=O)NC1=O                                                                                                             
D4D SMILES           CACTVS               3.341 CC1=CN([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)C=C2)C(=O)NC1=O                                                                                                                  
D4D SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2C=C[C@H](O2)CO[P@](=O)(O)OP(=O)(O)O                                                                                                                 
D4D SMILES           "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2C=CC(O2)COP(=O)(O)OP(=O)(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 
D4D "SYSTEMATIC NAME" ACDLabs              10.04 "[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,5-dihydrofuran-2-yl]methyl trihydrogen diphosphate" 
D4D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2,5-dihydrofuran-2-yl]methyl phosphono hydrogen phosphate"           
# 
