data_UPV # _chem_comp.id UPV _chem_comp.name ;2'-O-{[(2,2-dimethylpropanoyl)oxy]methyl}uridine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H23 N2 O11 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-07-30 _chem_comp.pdbx_modified_date 2013-04-05 _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 438.324 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UPV _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 2LVY _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 UPV P P P 0 1 N N N 41.927 25.595 31.924 -4.466 -2.524 0.095 P UPV 1 UPV N1 N1 N 0 1 N N N 41.458 29.589 28.573 -0.380 2.786 -0.508 N1 UPV 2 UPV C2 C2 C 0 1 N N N 40.833 30.293 27.560 -0.668 3.036 0.783 C2 UPV 3 UPV O2 O2 O 0 1 N N N 40.969 31.506 27.410 -0.817 2.109 1.554 O2 UPV 4 UPV N3 N3 N 0 1 N N N 40.023 29.547 26.715 -0.792 4.299 1.231 N3 UPV 5 UPV C4 C4 C 0 1 N N N 39.795 28.181 26.795 -0.629 5.339 0.388 C4 UPV 6 UPV O4 O4 O 0 1 N N N 39.058 27.620 25.988 -0.741 6.482 0.793 O4 UPV 7 UPV C5 C5 C 0 1 N N N 40.493 27.536 27.883 -0.327 5.089 -0.972 C5 UPV 8 UPV C6 C6 C 0 1 N N N 41.278 28.244 28.722 -0.208 3.813 -1.395 C6 UPV 9 UPV CA CA C 0 1 N N N 42.027 33.355 29.946 3.298 0.948 -0.297 CA UPV 10 UPV CB CB C 0 1 N N N 43.469 34.678 28.645 4.177 -1.265 -0.200 CB UPV 11 UPV CG CG C 0 1 N N N 43.467 34.872 27.126 4.579 -2.518 0.535 CG UPV 12 UPV "C1'" "C1'" C 0 1 N N R 42.332 30.345 29.491 -0.245 1.401 -0.965 "C1'" UPV 13 UPV "C2'" "C2'" C 0 1 N N R 41.503 31.047 30.562 0.915 0.700 -0.224 "C2'" UPV 14 UPV "O2'" "O2'" O 0 1 N N N 42.137 32.251 31.001 2.096 0.700 -1.028 "O2'" UPV 15 UPV "C3'" "C3'" C 0 1 N N R 41.482 29.981 31.653 0.407 -0.743 -0.008 "C3'" UPV 16 UPV "O3'" "O3'" O 0 1 N N N 41.234 30.523 32.951 1.258 -1.678 -0.674 "O3'" UPV 17 UPV "C4'" "C4'" C 0 1 N N R 42.899 29.429 31.535 -1.001 -0.743 -0.645 "C4'" UPV 18 UPV "O4'" "O4'" O 0 1 N N N 43.256 29.477 30.151 -1.420 0.638 -0.615 "O4'" UPV 19 UPV "C5'" "C5'" C 0 1 N N N 42.975 28.013 32.097 -1.957 -1.609 0.178 "C5'" UPV 20 UPV "O5'" "O5'" O 0 1 N N N 42.075 27.122 31.433 -3.218 -1.691 -0.489 "O5'" UPV 21 UPV OB1 OB1 O 0 1 N N N 43.334 33.471 29.160 3.648 -0.232 0.474 OB1 UPV 22 UPV OB2 OB2 O 0 1 N N N 43.595 35.650 29.386 4.332 -1.191 -1.396 OB2 UPV 23 UPV CD1 CD1 C 0 1 N N N 43.550 33.515 26.426 5.007 -3.586 -0.473 CD1 UPV 24 UPV CD2 CD2 C 0 1 N N N 44.633 35.760 26.691 5.746 -2.206 1.475 CD2 UPV 25 UPV CD3 CD3 C 0 1 N N N 42.152 35.534 26.711 3.391 -3.033 1.351 CD3 UPV 26 UPV OP3 OP3 O 0 1 N Y N 41.769 25.591 33.396 -5.754 -2.289 -0.843 OP3 UPV 27 UPV OP2 OP2 O 0 1 N N N 40.902 24.940 31.082 -4.100 -4.091 0.121 OP2 UPV 28 UPV HN3 HN3 H 0 1 N N N 39.560 30.041 25.979 -0.999 4.462 2.165 HN3 UPV 29 UPV H5 H5 H 0 1 N N N 40.385 26.471 28.027 -0.193 5.909 -1.662 H5 UPV 30 UPV H6 H6 H 0 1 N N N 41.777 27.733 29.532 0.027 3.603 -2.428 H6 UPV 31 UPV "H5'" "H5'" H 0 1 N N N 42.721 28.042 33.167 -1.539 -2.609 0.287 "H5'" UPV 32 UPV "H1'" "H1'" H 0 1 N N N 42.881 31.108 28.919 -0.081 1.372 -2.043 "H1'" UPV 33 UPV HD1 HD1 H 0 1 N N N 42.684 32.901 26.714 5.297 -4.492 0.059 HD1 UPV 34 UPV HD1A HD1A H 0 0 N N N 44.477 33.005 26.725 4.175 -3.808 -1.142 HD1A UPV 35 UPV HD1B HD1B H 0 0 N N N 43.548 33.663 25.336 5.853 -3.219 -1.054 HD1B UPV 36 UPV "H2'" "H2'" H 0 1 N N N 40.484 31.235 30.193 1.106 1.187 0.733 "H2'" UPV 37 UPV HD2 HD2 H 0 1 N N N 44.545 36.744 27.175 6.036 -3.112 2.006 HD2 UPV 38 UPV HD2A HD2A H 0 0 N N N 45.582 35.290 26.987 6.592 -1.839 0.894 HD2A UPV 39 UPV HD2B HD2B H 0 0 N N N 44.611 35.885 25.598 5.441 -1.445 2.193 HD2B UPV 40 UPV "H3'" "H3'" H 0 1 N N N 40.752 29.198 31.399 0.347 -0.972 1.056 "H3'" UPV 41 UPV HD3 HD3 H 0 1 N N N 42.141 35.678 25.620 2.559 -3.252 0.682 HD3 UPV 42 UPV HD3A HD3A H 0 0 N N N 42.059 36.510 27.210 3.681 -3.941 1.881 HD3A UPV 43 UPV HD3B HD3B H 0 0 N N N 41.309 34.891 27.004 3.088 -2.273 2.071 HD3B UPV 44 UPV "H4'" "H4'" H 0 1 N N N 43.575 30.073 32.117 -0.952 -1.104 -1.673 "H4'" UPV 45 UPV "H5'A" "H5'A" H 0 0 N N N 44.001 27.637 31.974 -2.095 -1.162 1.162 "H5'A" UPV 46 UPV HA HA H 0 1 N N N 41.817 34.313 30.444 4.105 1.180 -0.992 HA UPV 47 UPV HAA HAA H 0 1 N N N 41.207 33.114 29.253 3.146 1.791 0.378 HAA UPV 48 UPV "HO3'" "HO3'" H 0 0 N N N 41.231 29.822 33.592 0.969 -2.598 -0.595 "HO3'" UPV 49 UPV HOP3 HOP3 H 0 0 N Y N 42.617 25.466 33.806 -6.545 -2.762 -0.550 HOP3 UPV 50 UPV HOP2 HOP2 H 0 0 N N N 41.221 24.093 30.795 -3.892 -4.461 -0.748 HOP2 UPV 51 UPV OP1 OP1 O 0 1 N N N 43.274 25.398 32.478 -4.766 -2.064 1.469 OP1 UPV 52 # 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 UPV P OP3 SING N N 1 UPV N1 C6 SING N N 2 UPV N1 "C1'" SING N N 3 UPV C2 N1 SING N N 4 UPV O2 C2 DOUB N N 5 UPV N3 C2 SING N N 6 UPV N3 C4 SING N N 7 UPV C4 C5 SING N N 8 UPV O4 C4 DOUB N N 9 UPV C5 H5 SING N N 10 UPV C5 C6 DOUB N N 11 UPV C6 H6 SING N N 12 UPV CA HAA SING N N 13 UPV CA "O2'" SING N N 14 UPV CB OB1 SING N N 15 UPV CB OB2 DOUB N N 16 UPV CG CB SING N N 17 UPV "C1'" "O4'" SING N N 18 UPV "C1'" "C2'" SING N N 19 UPV "C2'" "O2'" SING N N 20 UPV "C2'" "C3'" SING N N 21 UPV "C3'" "O3'" SING N N 22 UPV "O3'" "HO3'" SING N N 23 UPV "C4'" "C3'" SING N N 24 UPV "C4'" "C5'" SING N N 25 UPV "C4'" "H4'" SING N N 26 UPV "O4'" "C4'" SING N N 27 UPV "C5'" "H5'A" SING N N 28 UPV "O5'" P SING N N 29 UPV "O5'" "C5'" SING N N 30 UPV OB1 CA SING N N 31 UPV CD1 CG SING N N 32 UPV CD1 HD1B SING N N 33 UPV CD1 HD1A SING N N 34 UPV CD2 CG SING N N 35 UPV CD2 HD2B SING N N 36 UPV CD2 HD2 SING N N 37 UPV CD3 CG SING N N 38 UPV CD3 HD3 SING N N 39 UPV CD3 HD3B SING N N 40 UPV OP3 HOP3 SING N N 41 UPV OP2 P SING N N 42 UPV OP2 HOP2 SING N N 43 UPV HN3 N3 SING N N 44 UPV "H5'" "C5'" SING N N 45 UPV "H1'" "C1'" SING N N 46 UPV HD1 CD1 SING N N 47 UPV "H2'" "C2'" SING N N 48 UPV HD2A CD2 SING N N 49 UPV "H3'" "C3'" SING N N 50 UPV HD3A CD3 SING N N 51 UPV HA CA SING N N 52 UPV P OP1 DOUB N N 53 # 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 UPV SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(OCOC(=O)C(C)(C)C)C2O" UPV InChI InChI 1.03 "InChI=1S/C15H23N2O11P/c1-15(2,3)13(20)26-7-25-11-10(19)8(6-27-29(22,23)24)28-12(11)17-5-4-9(18)16-14(17)21/h4-5,8,10-12,19H,6-7H2,1-3H3,(H,16,18,21)(H2,22,23,24)/t8-,10-,11-,12-/m1/s1" UPV InChIKey InChI 1.03 AVEWAPSZWXGLGF-HJQYOEGKSA-N UPV SMILES_CANONICAL CACTVS 3.370 "CC(C)(C)C(=O)OCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" UPV SMILES CACTVS 3.370 "CC(C)(C)C(=O)OCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" UPV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(C)(C)C(=O)OCO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" UPV SMILES "OpenEye OEToolkits" 1.7.6 "CC(C)(C)C(=O)OCOC1C(C(OC1N2C=CC(=O)NC2=O)COP(=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 UPV "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-O-{[(2,2-dimethylpropanoyl)oxy]methyl}uridine 5'-(dihydrogen phosphate) ; UPV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-5-(phosphonooxymethyl)oxolan-3-yl]oxymethyl 2,2-dimethylpropanoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UPV "Create component" 2012-07-30 RCSB UPV "Initial release" 2013-04-10 RCSB #