data_UPM
# 
_chem_comp.id                                    UPM 
_chem_comp.name                                  
;URIDINE-5'-DIPHOSPHATE-N-1-HYDROOXY-ETHANOYL MURAMAIC ACID
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H31 N3 O20 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_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                        695.416 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UPM 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1CC9 
_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 
UPM N1     N1   N 0 1 Y N N 2.829  21.357 -19.266 7.732   -0.741 -0.301 N1     UPM 1  
UPM C2     C2   C 0 1 Y N N 2.955  21.636 -20.628 8.988   -0.542 -0.742 C2     UPM 2  
UPM N3     N3   N 0 1 Y N N 4.166  21.583 -21.242 9.896   -1.535 -0.714 N3     UPM 3  
UPM C4     C4   C 0 1 Y N N 5.322  21.274 -20.615 9.556   -2.755 -0.251 C4     UPM 4  
UPM C5     C5   C 0 1 Y N N 5.249  20.969 -19.100 8.237   -2.980 0.211  C5     UPM 5  
UPM C6     C6   C 0 1 Y N N 4.047  21.004 -18.484 7.347   -1.965 0.176  C6     UPM 6  
UPM O2     O2   O 0 1 N N N 1.981  21.919 -21.327 9.309   0.553  -1.162 O2     UPM 7  
UPM O4     O4   O 0 1 N N N 6.375  21.249 -21.244 10.376  -3.655 -0.230 O4     UPM 8  
UPM PA     PA   P 0 1 N N S 2.716  17.033 -16.885 1.274   0.802  -0.275 PA     UPM 9  
UPM O1A    O1A  O 0 1 N N N 3.575  16.563 -18.158 0.837   2.083  0.323  O1A    UPM 10 
UPM O2A    O2A  O 0 1 N N N 3.711  17.516 -15.720 1.520   1.004  -1.854 O2A    UPM 11 
UPM O3A    O3A  O 0 1 N N N 1.840  15.821 -16.359 0.136   -0.313 -0.048 O3A    UPM 12 
UPM PB     PB   P 0 1 N N S 2.622  14.743 -15.507 -1.273  0.380  -0.404 PB     UPM 13 
UPM O1B    O1B  O 0 1 N N N 2.885  15.309 -14.030 -1.284  1.768  0.111  O1B    UPM 14 
UPM O2B    O2B  O 0 1 N N N 4.043  14.379 -16.179 -1.473  0.399  -2.001 O2B    UPM 15 
UPM "C1'"  C1*  C 0 1 N N R 1.488  21.443 -18.602 6.767   0.360  -0.339 "C1'"  UPM 16 
UPM "C2'"  C2*  C 0 1 N N R 0.444  20.469 -19.183 7.233   1.515  0.582  "C2'"  UPM 17 
UPM "O2'"  O2*  O 0 1 N N N -0.199 21.002 -20.343 8.111   2.404  -0.111 "O2'"  UPM 18 
UPM "C3'"  C3*  C 0 1 N N S -0.525 20.233 -18.038 5.878   2.203  0.901  "C3'"  UPM 19 
UPM "O3'"  O3*  O 0 1 N N N -1.478 21.292 -18.033 5.517   3.121  -0.133 "O3'"  UPM 20 
UPM "C4'"  C4*  C 0 1 N N R 0.400  20.304 -16.813 4.903   1.006  0.938  "C4'"  UPM 21 
UPM "O4'"  O4*  O 0 1 N N N 1.521  21.142 -17.183 5.505   -0.065 0.201  "O4'"  UPM 22 
UPM "C5'"  C5*  C 0 1 N N N 0.914  18.939 -16.298 3.574   1.399  0.291  "C5'"  UPM 23 
UPM "O5'"  O5*  O 0 1 N N N 1.742  18.261 -17.273 2.643   0.323  0.424  "O5'"  UPM 24 
UPM C18    C18  C 0 1 N N R -2.277 10.507 -16.579 -8.242  -0.268 -1.194 C18    UPM 25 
UPM C19    C19  C 0 1 N N N -2.327 9.504  -17.762 -8.051  -0.852 -2.570 C19    UPM 26 
UPM O18    O18  O 0 1 N N N -3.059 9.754  -18.747 -7.219  -1.709 -2.753 O18    UPM 27 
UPM C20    C20  C 0 1 N N N -3.588 10.565 -15.783 -9.637  -0.628 -0.677 C20    UPM 28 
UPM C1D    C1D  C 0 1 N N R 2.116  12.102 -15.704 -3.674  0.271  0.026  C1D    UPM 29 
UPM O1D    O1D  O 0 1 N N N 1.688  13.453 -15.432 -2.469  -0.454 0.277  O1D    UPM 30 
UPM C2D    C2D  C 0 1 N N R 0.944  11.260 -16.286 -4.847  -0.707 -0.067 C2D    UPM 31 
UPM N2D    N2D  N 0 1 N N N 0.493  11.839 -17.578 -4.996  -1.416 1.207  N2D    UPM 32 
UPM C7D    C7D  C 0 1 N N N 0.606  11.203 -18.742 -4.264  -2.521 1.452  C7D    UPM 33 
UPM O7D    O7D  O 0 1 N N N 1.269  10.180 -18.921 -3.481  -2.927 0.620  O7D    UPM 34 
UPM C8D    C8D  C 0 1 N N N -0.154 11.857 -19.872 -4.417  -3.250 2.762  C8D    UPM 35 
UPM C3D    C3D  C 0 1 N N R -0.227 11.180 -15.251 -6.129  0.077  -0.370 C3D    UPM 36 
UPM O3D    O3D  O 0 1 N N N -1.215 10.178 -15.636 -7.254  -0.801 -0.309 O3D    UPM 37 
UPM C4D    C4D  C 0 1 N N S 0.271  10.757 -13.838 -6.285  1.186  0.678  C4D    UPM 38 
UPM O4D    O4D  O 0 1 N N N -0.727 11.092 -12.875 -6.512  0.602  1.962  O4D    UPM 39 
UPM C5D    C5D  C 0 1 N N R 1.617  11.399 -13.390 -5.003  2.021  0.714  C5D    UPM 40 
UPM O5D    O5D  O 0 1 N N N 2.584  11.503 -14.475 -3.900  1.197  1.088  O5D    UPM 41 
UPM C6D    C6D  C 0 1 N N N 2.281  10.606 -12.252 -5.161  3.151  1.733  C6D    UPM 42 
UPM O6D    O6D  O 0 1 N N N 2.819  9.350  -12.687 -4.013  4.000  1.686  O6D    UPM 43 
UPM O1     O1   O 0 1 N N N -1.622 8.469  -17.739 -8.804  -0.419 -3.593 O1     UPM 44 
UPM OXT    OXT  O 0 1 N N N ?      ?      ?       -3.541  -4.379 2.784  OXT    UPM 45 
UPM HN3    HN3  H 0 1 N N N 4.204  21.786 -22.221 10.798  -1.373 -1.032 HN3    UPM 46 
UPM H5     H5   H 0 1 N N N 6.144  20.732 -18.544 7.946   -3.950 0.585  H5     UPM 47 
UPM H6     H6   H 0 1 N N N 3.970  20.777 -17.431 6.336   -2.117 0.525  H6     UPM 48 
UPM HOA2   2HOA H 0 0 N N N 4.588  17.611 -16.072 1.803   0.148  -2.204 HOA2   UPM 49 
UPM HOB2   2HOB H 0 0 N N N 3.939  14.307 -17.121 -1.460  -0.522 -2.295 HOB2   UPM 50 
UPM "H1'"  H1*  H 0 1 N N N 1.207  22.490 -18.787 6.640   0.718  -1.360 "H1'"  UPM 51 
UPM "H2'"  H2*  H 0 1 N N N 0.898  19.531 -19.536 7.702   1.131  1.488  "H2'"  UPM 52 
UPM "HO'2" 2HO* H 0 0 N N N -1.125 21.120 -20.166 8.362   3.096  0.517  "HO'2" UPM 53 
UPM "H3'"  H3*  H 0 1 N N N -1.094 19.292 -18.084 5.915   2.703  1.869  "H3'"  UPM 54 
UPM "HO'3" 3HO* H 0 0 N N N -1.690 21.523 -17.136 6.211   3.793  -0.165 "HO'3" UPM 55 
UPM "H4'"  H4*  H 0 1 N N N -0.187 20.711 -15.976 4.735   0.697  1.970  "H4'"  UPM 56 
UPM "H5'1" 1H5* H 0 0 N N N 1.511  19.110 -15.390 3.734   1.612  -0.766 "H5'1" UPM 57 
UPM "H5'2" 2H5* H 0 0 N N N 0.040  18.303 -16.096 3.177   2.286  0.784  "H5'2" UPM 58 
UPM H18    H18  H 0 1 N N N -2.092 11.483 -17.051 -8.141  0.816  -1.241 H18    UPM 59 
UPM H201   1H20 H 0 0 N N N -3.363 10.579 -14.706 -9.746  -0.276 0.348  H201   UPM 60 
UPM H202   2H20 H 0 0 N N N -4.141 11.476 -16.054 -10.390 -0.155 -1.306 H202   UPM 61 
UPM H203   3H20 H 0 0 N N N -4.199 9.681  -16.018 -9.767  -1.710 -0.706 H203   UPM 62 
UPM H1D    H1D  H 0 1 N N N 2.927  12.124 -16.447 -3.581  0.814  -0.914 H1D    UPM 63 
UPM H2D    H2D  H 0 1 N N N 1.292  10.235 -16.479 -4.661  -1.425 -0.866 H2D    UPM 64 
UPM HND2   2HND H 0 0 N N N 0.084  12.752 -17.573 -5.622  -1.091 1.873  HND2   UPM 65 
UPM H8D1   1H8D H 0 0 N N N -0.429 12.733 -20.478 -4.165  -2.579 3.583  H8D1   UPM 66 
UPM H8D2   2H8D H 0 0 N N N -0.414 12.006 -20.930 -5.447  -3.588 2.872  H8D2   UPM 67 
UPM H3D    H3D  H 0 1 N N N -0.662 12.190 -15.231 -6.063  0.520  -1.364 H3D    UPM 68 
UPM H4D    H4D  H 0 1 N N N 0.454  9.674  -13.903 -7.129  1.822  0.412  H4D    UPM 69 
UPM HOD4   4HOD H 0 0 N N N -0.327 11.166 -12.017 -6.604  1.332  2.589  HOD4   UPM 70 
UPM H5D    H5D  H 0 1 N N N 1.345  12.408 -13.046 -4.819  2.446  -0.272 H5D    UPM 71 
UPM H6D1   1H6D H 0 0 N N N 3.103  11.211 -11.842 -6.052  3.732  1.496  H6D1   UPM 72 
UPM H6D2   2H6D H 0 0 N N N 1.507  10.393 -11.500 -5.259  2.728  2.733  H6D2   UPM 73 
UPM HOD6   6HOD H 0 0 N N N 2.938  9.365  -13.629 -4.153  4.697  2.341  HOD6   UPM 74 
UPM HO1    HO1  H 0 1 N N N -1.754 7.978  -18.541 -8.681  -0.793 -4.477 HO1    UPM 75 
UPM HXT    HXT  H 0 1 N N N ?      ?      ?       -3.670  -4.817 3.636  HXT    UPM 76 
# 
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 
UPM N1    C2     SING Y N 1  
UPM N1    C6     SING Y N 2  
UPM N1    "C1'"  SING N N 3  
UPM C2    N3     SING Y N 4  
UPM C2    O2     DOUB N N 5  
UPM N3    C4     SING Y N 6  
UPM N3    HN3    SING N N 7  
UPM C4    C5     SING Y N 8  
UPM C4    O4     DOUB N N 9  
UPM C5    C6     DOUB Y N 10 
UPM C5    H5     SING N N 11 
UPM C6    H6     SING N N 12 
UPM PA    O1A    DOUB N N 13 
UPM PA    O2A    SING N N 14 
UPM PA    O3A    SING N N 15 
UPM PA    "O5'"  SING N N 16 
UPM O2A   HOA2   SING N N 17 
UPM O3A   PB     SING N N 18 
UPM PB    O1B    DOUB N N 19 
UPM PB    O2B    SING N N 20 
UPM PB    O1D    SING N N 21 
UPM O2B   HOB2   SING N N 22 
UPM "C1'" "C2'"  SING N N 23 
UPM "C1'" "O4'"  SING N N 24 
UPM "C1'" "H1'"  SING N N 25 
UPM "C2'" "O2'"  SING N N 26 
UPM "C2'" "C3'"  SING N N 27 
UPM "C2'" "H2'"  SING N N 28 
UPM "O2'" "HO'2" SING N N 29 
UPM "C3'" "O3'"  SING N N 30 
UPM "C3'" "C4'"  SING N N 31 
UPM "C3'" "H3'"  SING N N 32 
UPM "O3'" "HO'3" SING N N 33 
UPM "C4'" "O4'"  SING N N 34 
UPM "C4'" "C5'"  SING N N 35 
UPM "C4'" "H4'"  SING N N 36 
UPM "C5'" "O5'"  SING N N 37 
UPM "C5'" "H5'1" SING N N 38 
UPM "C5'" "H5'2" SING N N 39 
UPM C18   C19    SING N N 40 
UPM C18   C20    SING N N 41 
UPM C18   O3D    SING N N 42 
UPM C18   H18    SING N N 43 
UPM C19   O18    DOUB N N 44 
UPM C19   O1     SING N N 45 
UPM C20   H201   SING N N 46 
UPM C20   H202   SING N N 47 
UPM C20   H203   SING N N 48 
UPM C1D   O1D    SING N N 49 
UPM C1D   C2D    SING N N 50 
UPM C1D   O5D    SING N N 51 
UPM C1D   H1D    SING N N 52 
UPM C2D   N2D    SING N N 53 
UPM C2D   C3D    SING N N 54 
UPM C2D   H2D    SING N N 55 
UPM N2D   C7D    SING N N 56 
UPM N2D   HND2   SING N N 57 
UPM C7D   O7D    DOUB N N 58 
UPM C7D   C8D    SING N N 59 
UPM C8D   OXT    SING N N 60 
UPM C8D   H8D1   SING N N 61 
UPM C8D   H8D2   SING N N 62 
UPM C3D   O3D    SING N N 63 
UPM C3D   C4D    SING N N 64 
UPM C3D   H3D    SING N N 65 
UPM C4D   O4D    SING N N 66 
UPM C4D   C5D    SING N N 67 
UPM C4D   H4D    SING N N 68 
UPM O4D   HOD4   SING N N 69 
UPM C5D   O5D    SING N N 70 
UPM C5D   C6D    SING N N 71 
UPM C5D   H5D    SING N N 72 
UPM C6D   O6D    SING N N 73 
UPM C6D   H6D1   SING N N 74 
UPM C6D   H6D2   SING N N 75 
UPM O6D   HOD6   SING N N 76 
UPM O1    HO1    SING N N 77 
UPM OXT   HXT    SING N N 78 
# 
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 
UPM SMILES           ACDLabs              10.04 "O=P(OC1OC(C(O)C(OC(C(=O)O)C)C1NC(=O)CO)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" 
UPM SMILES_CANONICAL CACTVS               3.341 "C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(=O)CO)C(O)=O" 
UPM SMILES           CACTVS               3.341 "C[CH](O[CH]1[CH](O)[CH](CO)O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(=O)CO)C(O)=O" 
UPM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H](C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)CO" 
UPM SMILES           "OpenEye OEToolkits" 1.5.0 "CC(C(=O)O)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)CO" 
UPM InChI            InChI                1.03  
;InChI=1S/C20H31N3O20P2/c1-7(18(31)32)39-16-12(21-11(27)5-25)19(41-8(4-24)14(16)29)42-45(36,37)43-44(34,35)38-6-9-13(28)15(30)17(40-9)23-3-2-10(26)22-20(23)33/h2-3,7-9,12-17,19,24-25,28-30H,4-6H2,1H3,(H,21,27)(H,31,32)(H,34,35)(H,36,37)(H,22,26,33)/t7-,8-,9-,12-,13-,14-,15-,16-,17-,19-/m1/s1
;
UPM InChIKey         InChI                1.03  NZYFYXRHIWOMRL-LRVZQNRTSA-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 
UPM "SYSTEMATIC NAME" ACDLabs              10.04 
;(2R)-2-{[(2R,3R,4R,5S,6R)-2-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-3-[(hydroxyacetyl)amino]-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid (non-preferred name)
;
UPM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 
"(2R)-2-[(2R,3R,4R,5S,6R)-2-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-5-hydroxy-3-(2-hydroxyethanoylamino)-6-(hydroxymethyl)oxan-4-yl]oxypropanoic 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 
UPM "Create component"  1999-07-08 RCSB 
UPM "Modify descriptor" 2011-06-04 RCSB 
# 
