data_UPC # _chem_comp.id UPC _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H17 N2 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-07-11 _chem_comp.pdbx_modified_date 2011-10-07 _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 466.169 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UPC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3SPY _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 UPC N1 N1 N 0 1 N N N -0.290 6.055 19.427 5.184 -0.648 0.717 N1 UPC 1 UPC C2 C2 C 0 1 N N N -0.671 5.321 20.570 5.215 -0.822 -0.617 C2 UPC 2 UPC O2 O2 O 0 1 N N N -1.040 4.017 20.448 4.586 -0.070 -1.335 O2 UPC 3 UPC N3 N3 N 0 1 N N N -0.671 5.909 21.781 5.934 -1.818 -1.168 N3 UPC 4 UPC C4 C4 C 0 1 N N N -0.316 7.208 21.907 6.637 -2.662 -0.386 C4 UPC 5 UPC O4 O4 O 0 1 N N N -0.341 7.767 23.139 7.288 -3.563 -0.883 O4 UPC 6 UPC C5 C5 C 0 1 N N N 0.068 7.964 20.796 6.613 -2.490 1.019 C5 UPC 7 UPC C6 C6 C 0 1 N N N 0.073 7.354 19.548 5.884 -1.482 1.545 C6 UPC 8 UPC PA PA P 0 1 N N N 0.051 10.409 16.154 -1.173 1.129 -0.450 PA UPC 9 UPC PB PB P 0 1 N N N -2.786 9.989 15.316 -3.947 0.063 -0.266 PB UPC 10 UPC PG PG P 0 1 N N N -3.258 12.543 14.175 -6.510 -1.228 0.473 PG UPC 11 UPC "C1'" "C1'" C 0 1 N N R -0.332 5.364 18.133 4.398 0.449 1.287 "C1'" UPC 12 UPC O1A O1A O 0 1 N N N 0.922 11.094 17.157 -1.758 2.611 -0.682 O1A UPC 13 UPC O1B O1B O 0 1 N N N -3.608 8.985 16.087 -3.760 -0.669 -1.688 O1B UPC 14 UPC O1G O1G O 0 1 N N N -1.888 12.275 13.599 -7.468 0.040 0.732 O1G UPC 15 UPC "C2'" "C2'" C 0 1 N N N -1.787 5.462 17.659 4.983 1.802 0.837 "C2'" UPC 16 UPC O2A O2A O 0 1 N N N 0.385 10.659 14.701 -1.001 0.456 -1.757 O2A UPC 17 UPC O2B O2B O 0 1 N N N -2.140 9.478 14.060 -4.484 1.425 -0.479 O2B UPC 18 UPC O2G O2G O 0 1 N N N -4.358 12.840 13.183 -6.728 -1.738 -0.900 O2G UPC 19 UPC "C3'" "C3'" C 0 1 N N S -1.764 6.651 16.723 3.810 2.498 0.105 "C3'" UPC 20 UPC "O3'" "O3'" O 0 1 N N N -2.862 6.616 15.803 3.756 3.887 0.434 "O3'" UPC 21 UPC C3A C3A C 0 1 N N N -1.625 10.730 16.372 -2.335 0.171 0.578 C3A UPC 22 UPC O3B O3B O 0 1 N N N -3.772 11.180 14.888 -4.973 -0.783 0.642 O3B UPC 23 UPC O3G O3G O 0 1 N N N -3.234 13.911 15.379 -6.854 -2.386 1.537 O3G UPC 24 UPC "C4'" "C4'" C 0 1 N N R -0.390 6.505 16.083 2.580 1.746 0.674 "C4'" UPC 25 UPC "O4'" "O4'" O 0 1 N N N 0.457 6.004 17.130 3.045 0.383 0.804 "O4'" UPC 26 UPC "C5'" "C5'" C 0 1 N N N 0.196 7.798 15.528 1.403 1.822 -0.301 "C5'" UPC 27 UPC "O5'" "O5'" O 0 1 N N N 0.155 8.825 16.505 0.250 1.224 0.296 "O5'" UPC 28 UPC H5 H5 H 0 1 N N N 0.355 9.000 20.905 7.170 -3.156 1.662 H5 UPC 29 UPC H6 H6 H 0 1 N N N 0.367 7.916 18.674 5.854 -1.335 2.615 H6 UPC 30 UPC "H1'" "H1'" H 0 1 N N N 0.050 4.341 18.268 4.407 0.384 2.375 "H1'" UPC 31 UPC HO1A HO1A H 0 0 N N N 1.583 11.606 16.706 -1.896 3.111 0.134 HO1A UPC 32 UPC HO1B HO1B H 0 0 N N N -3.589 8.148 15.638 -3.410 -1.568 -1.625 HO1B UPC 33 UPC HO1G HO1G H 0 0 N N N -1.925 12.336 12.652 -7.378 0.427 1.614 HO1G UPC 34 UPC "H2'" "H2'" H 0 1 N N N -2.108 4.545 17.143 5.295 2.388 1.701 "H2'" UPC 35 UPC "H2'A" "H2'A" H 0 0 N N N -2.478 5.621 18.500 5.822 1.648 0.158 "H2'A" UPC 36 UPC "H3'" "H3'" H 0 1 N N N -1.895 7.632 17.204 3.887 2.358 -0.974 "H3'" UPC 37 UPC "HO3'" "HO3'" H 0 0 N N N -2.820 7.373 15.230 4.545 4.383 0.177 "HO3'" UPC 38 UPC H3A H3A H 0 1 N N N -1.873 10.390 17.388 -1.939 -0.832 0.735 H3A UPC 39 UPC H3AA H3AA H 0 0 N N N -1.748 11.816 16.250 -2.461 0.666 1.541 H3AA UPC 40 UPC HO3G HO3G H 0 0 N N N -3.909 14.541 15.156 -7.766 -2.704 1.492 HO3G UPC 41 UPC "H4'" "H4'" H 0 1 N N N -0.470 5.842 15.209 2.300 2.148 1.647 "H4'" UPC 42 UPC "H5'" "H5'" H 0 1 N N N 1.241 7.622 15.235 1.191 2.866 -0.534 "H5'" UPC 43 UPC "H5'A" "H5'A" H 0 0 N N N -0.390 8.112 14.652 1.655 1.290 -1.218 "H5'A" UPC 44 UPC HN3 HN3 H 0 1 N N N -0.934 5.384 22.590 5.945 -1.930 -2.131 HN3 UPC 45 # 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 UPC "C1'" N1 SING N N 1 UPC N1 C6 SING N N 2 UPC N1 C2 SING N N 3 UPC O2 C2 DOUB N N 4 UPC C2 N3 SING N N 5 UPC N3 C4 SING N N 6 UPC C5 C4 SING N N 7 UPC C4 O4 DOUB N N 8 UPC C6 C5 DOUB N N 9 UPC C5 H5 SING N N 10 UPC C6 H6 SING N N 11 UPC O2A PA DOUB N N 12 UPC PA C3A SING N N 13 UPC PA "O5'" SING N N 14 UPC PA O1A SING N N 15 UPC O2B PB DOUB N N 16 UPC O3B PB SING N N 17 UPC PB O1B SING N N 18 UPC PB C3A SING N N 19 UPC O2G PG DOUB N N 20 UPC O1G PG SING N N 21 UPC PG O3B SING N N 22 UPC PG O3G SING N N 23 UPC "O4'" "C1'" SING N N 24 UPC "C2'" "C1'" SING N N 25 UPC "C1'" "H1'" SING N N 26 UPC O1A HO1A SING N N 27 UPC O1B HO1B SING N N 28 UPC O1G HO1G SING N N 29 UPC "C3'" "C2'" SING N N 30 UPC "C2'" "H2'" SING N N 31 UPC "C2'" "H2'A" SING N N 32 UPC "O3'" "C3'" SING N N 33 UPC "C4'" "C3'" SING N N 34 UPC "C3'" "H3'" SING N N 35 UPC "O3'" "HO3'" SING N N 36 UPC C3A H3A SING N N 37 UPC C3A H3AA SING N N 38 UPC O3G HO3G SING N N 39 UPC "C5'" "C4'" SING N N 40 UPC "C4'" "O4'" SING N N 41 UPC "C4'" "H4'" SING N N 42 UPC "C5'" "O5'" SING N N 43 UPC "C5'" "H5'" SING N N 44 UPC "C5'" "H5'A" SING N N 45 UPC N3 HN3 SING N N 46 # 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 UPC SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O" UPC InChI InChI 1.03 "InChI=1S/C10H17N2O13P3/c13-6-3-9(12-2-1-8(14)11-10(12)15)24-7(6)4-23-26(16,17)5-27(18,19)25-28(20,21)22/h1-2,6-7,9,13H,3-5H2,(H,16,17)(H,18,19)(H,11,14,15)(H2,20,21,22)/t6-,7+,9+/m0/s1" UPC InChIKey InChI 1.03 CLYYXAGDTAZMBH-LKEWCRSYSA-N UPC SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" UPC SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" UPC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=O)(C[P@@](=O)(O)OP(=O)(O)O)O)O" UPC SMILES "OpenEye OEToolkits" 1.7.2 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(CP(=O)(O)OP(=O)(O)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 UPC "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine" UPC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UPC "Create component" 2011-07-11 RCSB #