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 
# 
