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 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 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 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" 139 InChI InChI 1.03 ;InChI=1S/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 ; 139 InChIKey InChI 1.03 NGHFJGUDQJTSRY-LNAOLWRRSA-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" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 139 "Create component" 2001-07-30 RCSB 139 "Modify descriptor" 2011-06-04 RCSB #