data_139
# 
_chem_comp.id                                    139 
_chem_comp.name                                  
;ADENOSINE-5'-[TRIHYDROGEN DIPHOSPHATE] P'-3'-ESTER WITH 2'-DEOXYURIDINE
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H25 N7 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2001-07-30 
_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                        637.388 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     139 
_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        ? 
_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 
139 PA   PA   P 0 1 N N R 21.304 38.292 -4.569 0.329   -0.491 0.514  PA   139 1  
139 O1A  O1A  O 0 1 N N N 21.605 39.518 -5.432 -0.162  -1.833 0.901  O1A  139 2  
139 O2A  O2A  O 0 1 N N N 20.830 38.631 -3.184 0.540   0.404  1.836  O2A  139 3  
139 O5D  O5*A O 0 1 N N N 20.229 37.317 -5.244 1.730   -0.636 -0.265 O5D  139 4  
139 PB   PB   P 0 1 N N S 23.340 36.671 -3.178 -2.196  -0.024 0.216  PB   139 5  
139 O1B  O1B  O 0 1 N N N 22.329 35.704 -2.635 -2.268  -1.400 0.755  O1B  139 6  
139 O2B  O2B  O 0 1 N N N 24.628 36.152 -3.713 -2.422  1.033  1.410  O2B  139 7  
139 O3A  O3A  O 0 1 N N N 22.644 37.446 -4.387 -0.750  0.218  -0.448 O3A  139 8  
139 N9A  N9A  N 0 1 Y N N 15.832 36.208 -6.037 6.846   0.583  -0.085 N9A  139 9  
139 C4A  C4A  C 0 1 Y N N 15.650 36.704 -4.759 8.127   0.817  -0.517 C4A  139 10 
139 N3A  N3A  N 0 1 Y N N 16.347 37.688 -4.134 8.989   0.167  -1.291 N3A  139 11 
139 C2A  C2A  C 0 1 Y N N 15.874 37.897 -2.886 10.185  0.664  -1.527 C2A  139 12 
139 N1A  N1A  N 0 1 Y N N 14.857 37.273 -2.250 10.588  1.814  -1.020 N1A  139 13 
139 C6A  C6A  C 0 1 Y N N 14.170 36.303 -2.917 9.794   2.535  -0.234 C6A  139 14 
139 N6A  N6A  N 0 1 N N N 13.143 35.703 -2.314 10.225  3.740  0.293  N6A  139 15 
139 C5A  C5A  C 0 1 Y N N 14.578 35.984 -4.233 8.510   2.043  0.053  C5A  139 16 
139 N7A  N7A  N 0 1 Y N N 14.108 35.054 -5.148 7.459   2.490  0.781  N7A  139 17 
139 C8A  C8A  C 0 1 Y N N 14.888 35.217 -6.188 6.483   1.633  0.705  C8A  139 18 
139 C5D  C5*A C 0 1 N N N 20.356 36.923 -6.614 2.604   -1.374 0.592  C5D  139 19 
139 C4D  C4*A C 0 1 N N R 19.034 37.074 -7.342 3.962   -1.548 -0.093 C4D  139 20 
139 O4D  O4*A O 0 1 N N N 18.074 36.136 -6.802 4.620   -0.270 -0.237 O4D  139 21 
139 C1D  C1*A C 0 1 N N R 16.774 36.609 -7.094 6.019   -0.581 -0.413 C1D  139 22 
139 C2D  C2*A C 0 1 N N R 16.865 38.086 -7.509 6.298   -1.734 0.577  C2D  139 23 
139 O2D  O2*A O 0 1 N N N 16.528 38.247 -8.882 7.210   -2.678 0.012  O2D  139 24 
139 C3D  C3*A C 0 1 N N S 18.329 38.421 -7.204 4.911   -2.383 0.794  C3D  139 25 
139 O3D  O3*A O 0 1 N N N 18.826 39.473 -8.063 4.923   -3.747 0.368  O3D  139 26 
139 O5B  O5*U O 0 1 N N N 21.919 39.547 1.613  -5.631  -3.697 -1.143 O5B  139 27 
139 C5B  C5*U C 0 1 N N N 22.643 40.174 0.540  -5.017  -2.655 -0.382 C5B  139 28 
139 C4B  C4*U C 0 1 N N R 23.609 39.194 -0.086 -5.276  -1.308 -1.059 C4B  139 29 
139 O4B  O4*U O 0 1 N N N 24.321 38.501 0.977  -6.684  -0.983 -1.011 O4B  139 30 
139 C1B  C1*U C 0 1 N N R 24.178 37.097 0.816  -6.754  0.447  -1.203 C1B  139 31 
139 C2B  C2*U C 0 1 N N N 22.925 36.905 -0.022 -5.576  1.014  -0.379 C2B  139 32 
139 C3B  C3*U C 0 1 N N S 22.957 38.107 -0.951 -4.583  -0.166 -0.284 C3B  139 33 
139 O3B  O3*U O 0 1 N N N 23.749 37.855 -2.131 -3.339  0.176  -0.900 O3B  139 34 
139 N1U  N1U  N 0 1 Y N N 24.096 36.463 2.146  -8.026  0.970  -0.700 N1U  139 35 
139 C6U  C6U  C 0 1 Y N N 23.286 36.977 3.157  -8.787  1.783  -1.496 C6U  139 36 
139 C2U  C2U  C 0 1 Y N N 24.840 35.293 2.349  -8.438  0.643  0.538  C2U  139 37 
139 O2U  O2U  O 0 1 N N N 25.572 34.810 1.503  -7.747  -0.080 1.229  O2U  139 38 
139 N3U  N3U  N 0 1 Y N N 24.672 34.706 3.583  -9.601  1.114  1.027  N3U  139 39 
139 C4U  C4U  C 0 1 Y N N 23.843 35.133 4.611  -10.380 1.917  0.274  C4U  139 40 
139 O4U  O4U  O 0 1 N N N 23.634 34.372 5.560  -11.434 2.339  0.714  O4U  139 41 
139 C5U  C5U  C 0 1 Y N N 23.135 36.368 4.345  -9.960  2.264  -1.033 C5U  139 42 
139 HOA2 2HOA H 0 0 N N N 21.577 38.703 -2.602 0.859   1.268  1.540  HOA2 139 43 
139 HOB2 2HOB H 0 0 N N N 24.559 36.041 -4.654 -2.368  1.914  1.017  HOB2 139 44 
139 H2A  H2A  H 0 1 N N N 16.376 38.667 -2.319 10.862  0.110  -2.161 H2A  139 45 
139 H6A1 1H6A H 0 0 N N N 12.331 36.282 -2.384 11.115  4.067  0.091  H6A1 139 46 
139 H6A2 2H6A H 0 0 N N N 13.363 35.553 -1.350 9.635   4.259  0.862  H6A2 139 47 
139 H8A  H8A  H 0 1 N N N 14.798 34.625 -7.087 5.526   1.739  1.194  H8A  139 48 
139 HA51 1HA5 H 0 0 N N N 20.661 35.867 -6.651 2.172   -2.353 0.796  HA51 139 49 
139 HA52 2HA5 H 0 0 N N N 21.109 37.559 -7.102 2.737   -0.832 1.528  HA52 139 50 
139 H4D  H4*A H 0 1 N N N 19.317 36.924 -8.394 3.836   -2.022 -1.067 H4D  139 51 
139 H1D  H1*A H 0 1 N N N 16.319 36.133 -7.975 6.210   -0.905 -1.436 H1D  139 52 
139 H2D  H2*A H 0 1 N N N 16.166 38.753 -6.983 6.688   -1.343 1.517  H2D  139 53 
139 HD2  2H*A H 0 1 N N N 15.583 38.283 -8.975 7.295   -3.400 0.650  HD2  139 54 
139 H3D  H3*A H 0 1 N N N 18.499 38.844 -6.203 4.615   -2.314 1.841  H3D  139 55 
139 HD3  3H*A H 0 1 N N N 18.125 40.086 -8.251 5.530   -4.218 0.955  HD3  139 56 
139 HB5  5H*U H 0 1 N N N 22.502 39.409 2.350  -5.445  -4.527 -0.683 HB5  139 57 
139 HU51 1HU5 H 0 0 N N N 23.209 41.027 0.941  -3.943  -2.833 -0.325 HU51 139 58 
139 HU52 2HU5 H 0 0 N N N 21.930 40.517 -0.224 -5.437  -2.643 0.624  HU52 139 59 
139 H4B  H4*U H 0 1 N N N 24.256 39.798 -0.740 -4.927  -1.330 -2.092 H4B  139 60 
139 H1B  H1*U H 0 1 N N N 25.032 36.623 0.309  -6.632  0.695  -2.257 H1B  139 61 
139 HU21 1HU2 H 0 0 N N N 22.006 36.846 0.579  -5.913  1.310  0.615  HU21 139 62 
139 HU22 2HU2 H 0 0 N N N 22.948 35.957 -0.580 -5.119  1.857  -0.896 HU22 139 63 
139 H3B  H3*U H 0 1 N N N 21.959 38.377 -1.326 -4.426  -0.451 0.757  H3B  139 64 
139 H6U  H6U  H 0 1 N N N 22.758 37.902 2.978  -8.451  2.037  -2.490 H6U  139 65 
139 HN3U HN3U H 0 0 N N N 25.221 33.864 3.754  -9.881  0.871  1.924  HN3U 139 66 
139 H5U  H5U  H 0 1 N N N 22.489 36.797 5.097  -10.570 2.907  -1.650 H5U  139 67 
# 
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 
139 PA  O1A  DOUB N N 1  
139 PA  O2A  SING N N 2  
139 PA  O5D  SING N N 3  
139 PA  O3A  SING N N 4  
139 O2A HOA2 SING N N 5  
139 O5D C5D  SING N N 6  
139 PB  O1B  DOUB N N 7  
139 PB  O2B  SING N N 8  
139 PB  O3A  SING N N 9  
139 PB  O3B  SING N N 10 
139 O2B HOB2 SING N N 11 
139 N9A C4A  SING Y N 12 
139 N9A C8A  SING Y N 13 
139 N9A C1D  SING N N 14 
139 C4A N3A  SING Y N 15 
139 C4A C5A  DOUB Y N 16 
139 N3A C2A  DOUB Y N 17 
139 C2A N1A  SING Y N 18 
139 C2A H2A  SING N N 19 
139 N1A C6A  DOUB Y N 20 
139 C6A N6A  SING N N 21 
139 C6A C5A  SING Y N 22 
139 N6A H6A1 SING N N 23 
139 N6A H6A2 SING N N 24 
139 C5A N7A  SING Y N 25 
139 N7A C8A  DOUB Y N 26 
139 C8A H8A  SING N N 27 
139 C5D C4D  SING N N 28 
139 C5D HA51 SING N N 29 
139 C5D HA52 SING N N 30 
139 C4D O4D  SING N N 31 
139 C4D C3D  SING N N 32 
139 C4D H4D  SING N N 33 
139 O4D C1D  SING N N 34 
139 C1D C2D  SING N N 35 
139 C1D H1D  SING N N 36 
139 C2D O2D  SING N N 37 
139 C2D C3D  SING N N 38 
139 C2D H2D  SING N N 39 
139 O2D HD2  SING N N 40 
139 C3D O3D  SING N N 41 
139 C3D H3D  SING N N 42 
139 O3D HD3  SING N N 43 
139 O5B C5B  SING N N 44 
139 O5B HB5  SING N N 45 
139 C5B C4B  SING N N 46 
139 C5B HU51 SING N N 47 
139 C5B HU52 SING N N 48 
139 C4B O4B  SING N N 49 
139 C4B C3B  SING N N 50 
139 C4B H4B  SING N N 51 
139 O4B C1B  SING N N 52 
139 C1B C2B  SING N N 53 
139 C1B N1U  SING N N 54 
139 C1B H1B  SING N N 55 
139 C2B C3B  SING N N 56 
139 C2B HU21 SING N N 57 
139 C2B HU22 SING N N 58 
139 C3B O3B  SING N N 59 
139 C3B H3B  SING N N 60 
139 N1U C6U  SING Y N 61 
139 N1U C2U  SING Y N 62 
139 C6U C5U  DOUB Y N 63 
139 C6U H6U  SING N N 64 
139 C2U O2U  DOUB N N 65 
139 C2U N3U  SING Y N 66 
139 N3U C4U  SING Y N 67 
139 N3U HN3U SING N N 68 
139 C4U O4U  DOUB N N 69 
139 C4U C5U  SING Y N 70 
139 C5U H5U  SING N N 71 
# 
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 
139 SMILES           ACDLabs              10.04 O=C1C=CN(C(=O)N1)C5OC(CO)C(OP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O)C5 
139 InChI            InChI                1.02b 
;InChI=1/C19H25N7O14P2/c20-16-13-17(22-6-21-16)26(7-23-13)18-15(30)14(29)10(38-18)5-36-41(32,33)40-42(34,35)39-8-3-12(37-9(8)4-27)25-2-1-11(28)24-19(25)31/h1-2,6-10,12,14-15,18,27,29-30H,3-5H2,(H,32,33)(H,34,35)(H2,20,21,22)(H,24,28,31)/t8-,9+,10+,12+,14+,15+,18+/m0/s1/f/h24,32,34H,20H2
;
139 InChIKey         InChI                1.02b NGHFJGUDQJTSRY-YFFRKVGFDN 
139 SMILES_CANONICAL CACTVS               3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[C@H]4C[C@@H](O[C@@H]4CO)N5C=CC(=O)NC5=O)[C@@H](O)[C@H]3O 
139 SMILES           CACTVS               3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4C[CH](O[CH]4CO)N5C=CC(=O)NC5=O)[CH](O)[CH]3O 
139 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@H]4C[C@@H](O[C@@H]4CO)N5C=CC(=O)NC5=O)O)O)N 
139 SMILES           "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4CC(OC4CO)N5C=CC(=O)NC5=O)O)O)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 
139 "SYSTEMATIC NAME" ACDLabs              10.04 
"[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-(hydroxymethyl)tetrahydrofuran-3-yl dihydrogen diphosphate (non-preferred name)" 
139 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy-hydroxy-phosphoryl] hydrogen phosphate" 
# 
