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 #