data_UBI
# 
_chem_comp.id                                    UBI 
_chem_comp.name                                  
;2'-deoxy-5-[(2-methylpropyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H22 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               DU 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-11-07 
_chem_comp.pdbx_modified_date                    2012-11-16 
_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                        407.313 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UBI 
_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        4HQX 
_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 
UBI P      P      P 0 1 N N N 20.963 -2.702  6.980  5.662  1.677  0.204  P      UBI 1  
UBI N1     N1     N 0 1 N N N 18.925 -7.912  7.794  -0.504 -0.949 0.099  N1     UBI 2  
UBI C2     C2     C 0 1 N N N 19.294 -9.254  8.004  -0.426 -0.652 -1.208 C2     UBI 3  
UBI O2     O2     O 0 1 N N N 19.592 -9.939  7.007  0.643  -0.765 -1.774 O2     UBI 4  
UBI N3     N3     N 0 1 N N N 19.322 -9.793  9.243  -1.493 -0.233 -1.910 N3     UBI 5  
UBI C4     C4     C 0 1 N N N 18.994 -9.046  10.315 -2.695 -0.096 -1.312 C4     UBI 6  
UBI O4     O4     O 0 1 N N N 19.017 -9.543  11.459 -3.664 0.282  -1.943 O4     UBI 7  
UBI C5     C5     C 0 1 N N N 18.603 -7.623  10.106 -2.808 -0.415 0.120  C5     UBI 8  
UBI C6     C6     C 0 1 N N N 18.599 -7.122  8.815  -1.673 -0.840 0.783  C6     UBI 9  
UBI "C1'"  "C1'"  C 0 1 N N R 18.927 -7.391  6.429  0.697  -1.406 0.802  "C1'"  UBI 10 
UBI "C2'"  "C2'"  C 0 1 N N N 17.642 -6.660  6.032  1.156  -2.761 0.229  "C2'"  UBI 11 
UBI C21    C21    C 0 1 N N N 18.209 -6.690  11.211 -4.091 -0.285 0.826  C21    UBI 12 
UBI O22    O22    O 0 1 N N N 17.784 -5.593  10.886 -4.190 -0.650 1.982  O22    UBI 13 
UBI N23    N23    N 0 1 N N N 18.298 -7.048  12.491 -5.159 0.240  0.191  N23    UBI 14 
UBI C24    C24    C 0 1 N N N 17.950 -6.227  13.647 -6.405 0.473  0.925  C24    UBI 15 
UBI C25    C25    C 0 1 N N N 16.942 -6.949  14.544 -7.450 1.070  -0.021 C25    UBI 16 
UBI C26    C26    C 0 1 N N N 16.634 -8.395  14.181 -8.787 1.198  0.711  C26    UBI 17 
UBI C27    C27    C 0 1 N N N 15.650 -6.159  14.582 -6.987 2.453  -0.484 C27    UBI 18 
UBI "C3'"  "C3'"  C 0 1 N N S 18.128 -5.674  4.990  2.599  -2.496 -0.262 "C3'"  UBI 19 
UBI "O3'"  "O3'"  O 0 1 N N N 17.817 -6.240  3.717  3.456  -3.595 0.056  "O3'"  UBI 20 
UBI "C4'"  "C4'"  C 0 1 N N R 19.644 -5.711  5.089  2.993  -1.235 0.549  "C4'"  UBI 21 
UBI "O4'"  "O4'"  O 0 1 N N N 19.960 -6.420  6.284  1.768  -0.469 0.600  "O4'"  UBI 22 
UBI "C5'"  "C5'"  C 0 1 N N N 20.304 -4.344  5.026  4.090  -0.451 -0.172 "C5'"  UBI 23 
UBI "O5'"  "O5'"  O 0 1 N N N 19.916 -3.612  6.163  4.515  0.639  0.649  "O5'"  UBI 24 
UBI OP1    OP1    O 0 1 N N N 22.351 -2.843  6.399  6.892  0.934  -0.146 OP1    UBI 25 
UBI OP2    OP2    O 0 1 N N N 20.312 -1.349  7.148  5.159  2.516  -1.075 OP2    UBI 26 
UBI OP3    OP3    O 0 1 N Y N 20.909 -3.481  8.382  5.972  2.687  1.419  OP3    UBI 27 
UBI HN3    HN3    H 0 1 N N N 19.587 -10.750 9.364  -1.398 -0.028 -2.854 HN3    UBI 28 
UBI H6     H6     H 0 1 N N N 18.332 -6.091  8.636  -1.714 -1.084 1.834  H6     UBI 29 
UBI "H1'"  "H1'"  H 0 1 N N N 19.089 -8.219  5.723  0.488  -1.505 1.867  "H1'"  UBI 30 
UBI "H2'"  "H2'"  H 0 1 N N N 16.905 -7.357  5.606  1.151  -3.525 1.006  "H2'"  UBI 31 
UBI "H2'A" "H2'A" H 0 0 N N N 17.199 -6.140  6.894  0.516  -3.060 -0.602 "H2'A" UBI 32 
UBI HN23   HN23   H 0 0 N N N 18.637 -7.970  12.679 -5.102 0.462  -0.751 HN23   UBI 33 
UBI H24    H24    H 0 1 N N N 18.861 -6.015  14.226 -6.774 -0.472 1.324  H24    UBI 34 
UBI H24A   H24A   H 0 0 N N N 17.509 -5.281  13.298 -6.220 1.167  1.745  H24A   UBI 35 
UBI H25    H25    H 0 1 N N N 17.356 -6.949  15.563 -7.570 0.418  -0.886 H25    UBI 36 
UBI H26    H26    H 0 1 N N N 15.902 -8.804  14.893 -8.666 1.849  1.577  H26    UBI 37 
UBI H26A   H26A   H 0 0 N N N 16.219 -8.437  13.163 -9.531 1.622  0.038  H26A   UBI 38 
UBI H26B   H26B   H 0 0 N N N 17.559 -8.989  14.225 -9.116 0.212  1.042  H26B   UBI 39 
UBI H27    H27    H 0 1 N N N 14.923 -6.675  15.226 -6.035 2.361  -1.006 H27    UBI 40 
UBI H27A   H27A   H 0 0 N N N 15.847 -5.154  14.983 -7.732 2.878  -1.158 H27A   UBI 41 
UBI H27B   H27B   H 0 0 N N N 15.242 -6.074  13.564 -6.867 3.104  0.381  H27B   UBI 42 
UBI "H3'"  "H3'"  H 0 1 N N N 17.721 -4.664  5.143  2.615  -2.290 -1.333 "H3'"  UBI 43 
UBI "HO3'" "HO3'" H 0 0 N N N 18.106 -5.652  3.029  3.196  -4.429 -0.359 "HO3'" UBI 44 
UBI "H4'"  "H4'"  H 0 1 N N N 20.013 -6.292  4.231  3.313  -1.510 1.554  "H4'"  UBI 45 
UBI "H5'"  "H5'"  H 0 1 N N N 21.398 -4.460  5.014  4.937  -1.109 -0.369 "H5'"  UBI 46 
UBI "H5'A" "H5'A" H 0 0 N N N 19.981 -3.817  4.116  3.702  -0.065 -1.115 "H5'A" UBI 47 
UBI HOP2   HOP2   H 0 0 N N N 20.903 -0.672  6.841  4.355  3.029  -0.918 HOP2   UBI 48 
UBI HOP3   HOP3   H 0 0 N Y N 21.757 -3.871  8.561  6.655  3.343  1.221  HOP3   UBI 49 
# 
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 
UBI "O5'" P      SING N N 1  
UBI OP1   P      DOUB N N 2  
UBI P     OP2    SING N N 3  
UBI P     OP3    SING N N 4  
UBI "C1'" N1     SING N N 5  
UBI N1    C2     SING N N 6  
UBI N1    C6     SING N N 7  
UBI O2    C2     DOUB N N 8  
UBI C2    N3     SING N N 9  
UBI N3    C4     SING N N 10 
UBI N3    HN3    SING N N 11 
UBI C5    C4     SING N N 12 
UBI C4    O4     DOUB N N 13 
UBI C6    C5     DOUB N N 14 
UBI C5    C21    SING N N 15 
UBI C6    H6     SING N N 16 
UBI "C2'" "C1'"  SING N N 17 
UBI "O4'" "C1'"  SING N N 18 
UBI "C1'" "H1'"  SING N N 19 
UBI "C3'" "C2'"  SING N N 20 
UBI "C2'" "H2'"  SING N N 21 
UBI "C2'" "H2'A" SING N N 22 
UBI O22   C21    DOUB N N 23 
UBI C21   N23    SING N N 24 
UBI N23   C24    SING N N 25 
UBI N23   HN23   SING N N 26 
UBI C24   C25    SING N N 27 
UBI C24   H24    SING N N 28 
UBI C24   H24A   SING N N 29 
UBI C26   C25    SING N N 30 
UBI C25   C27    SING N N 31 
UBI C25   H25    SING N N 32 
UBI C26   H26    SING N N 33 
UBI C26   H26A   SING N N 34 
UBI C26   H26B   SING N N 35 
UBI C27   H27    SING N N 36 
UBI C27   H27A   SING N N 37 
UBI C27   H27B   SING N N 38 
UBI "O3'" "C3'"  SING N N 39 
UBI "C3'" "C4'"  SING N N 40 
UBI "C3'" "H3'"  SING N N 41 
UBI "O3'" "HO3'" SING N N 42 
UBI "C5'" "C4'"  SING N N 43 
UBI "C4'" "O4'"  SING N N 44 
UBI "C4'" "H4'"  SING N N 45 
UBI "C5'" "O5'"  SING N N 46 
UBI "C5'" "H5'"  SING N N 47 
UBI "C5'" "H5'A" SING N N 48 
UBI OP2   HOP2   SING N N 49 
UBI OP3   HOP3   SING N N 50 
# 
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 
UBI SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(C(=O)NCC(C)C)=C1)CC2O"                                                                                                                                
UBI InChI            InChI                1.03  "InChI=1S/C14H22N3O9P/c1-7(2)4-15-12(19)8-5-17(14(21)16-13(8)20)11-3-9(18)10(26-11)6-25-27(22,23)24/h5,7,9-11,18H,3-4,6H2,1-2H3,(H,15,19)(H,16,20,21)(H2,22,23,24)/t9-,10+,11+/m0/s1" 
UBI InChIKey         InChI                1.03  MVIGTWKPLCSGIV-HBNTYKKESA-N                                                                                                                                                           
UBI SMILES_CANONICAL CACTVS               3.370 "CC(C)CNC(=O)C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                 
UBI SMILES           CACTVS               3.370 "CC(C)CNC(=O)C1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                     
UBI SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(C)CNC(=O)C1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                                                   
UBI SMILES           "OpenEye OEToolkits" 1.7.6 "CC(C)CNC(=O)C1=CN(C(=O)NC1=O)C2CC(C(O2)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 
UBI "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-deoxy-5-[(2-methylpropyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
;
UBI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[5-(2-methylpropylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 
UBI "Create component" 2012-11-07 RCSB 
UBI "Initial release"  2012-11-16 RCSB 
# 
