data_UP5 # _chem_comp.id UP5 _chem_comp.name "P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H28 N7 O24 P5" _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 893.327 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UP5 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1UKE _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 UP5 N9A AN9 N 0 1 Y N N 35.001 60.668 -7.101 0.522 -0.676 10.722 N9A UP5 1 UP5 C8A AC8 C 0 1 Y N N 36.340 60.685 -7.460 1.703 -0.191 10.244 C8A UP5 2 UP5 N7A AN7 N 0 1 Y N N 36.833 59.534 -7.718 2.673 -0.513 11.050 N7A UP5 3 UP5 C5A AC5 C 0 1 Y N N 35.750 58.688 -7.471 2.177 -1.218 12.095 C5A UP5 4 UP5 C6A AC6 C 0 1 Y N N 35.624 57.297 -7.561 2.736 -1.818 13.235 C6A UP5 5 UP5 N6A AN6 N 0 1 N N N 36.629 56.481 -7.833 4.095 -1.740 13.483 N6A UP5 6 UP5 N1A AN1 N 0 1 Y N N 34.383 56.770 -7.383 1.928 -2.459 14.074 N1A UP5 7 UP5 C2A AC2 C 0 1 Y N N 33.375 57.600 -7.089 0.630 -2.538 13.846 C2A UP5 8 UP5 N3A AN3 N 0 1 Y N N 33.448 58.900 -6.830 0.063 -1.996 12.788 N3A UP5 9 UP5 C4A AC4 C 0 1 Y N N 34.670 59.381 -7.081 0.792 -1.336 11.894 C4A UP5 10 UP5 O5F AO5* O 0 1 N N N 35.871 64.068 -8.497 -1.329 -0.045 5.903 O5F UP5 11 UP5 C5F AC5* C 0 1 N N N 34.528 64.370 -8.930 -1.689 0.936 6.877 C5F UP5 12 UP5 C4F AC4* C 0 1 N N R 33.581 63.723 -7.982 -1.886 0.259 8.235 C4F UP5 13 UP5 O4F AO4* O 0 1 N N N 33.827 62.329 -8.154 -0.657 -0.364 8.668 O4F UP5 14 UP5 C3F AC3* C 0 1 N N S 33.866 64.087 -6.541 -2.200 1.310 9.322 C3F UP5 15 UP5 O3F AO3* O 0 1 N N N 32.681 64.267 -5.830 -3.608 1.382 9.557 O3F UP5 16 UP5 C2F AC2* C 0 1 N N R 34.639 62.897 -6.055 -1.466 0.783 10.578 C2F UP5 17 UP5 O2F AO2* O 0 1 N N N 34.438 62.659 -4.705 -2.399 0.517 11.628 O2F UP5 18 UP5 C1F AC1* C 0 1 N N R 34.072 61.770 -6.907 -0.794 -0.521 10.098 C1F UP5 19 UP5 PA PA P 0 1 N N S 37.167 64.910 -8.789 -1.139 0.732 4.506 PA UP5 20 UP5 O1A O1A O 0 1 N N N 38.276 64.200 -8.202 -0.072 1.747 4.648 O1A UP5 21 UP5 O2A O2A O 0 1 N N N 36.988 66.257 -8.376 -2.519 1.457 4.104 O2A UP5 22 UP5 O3A O3A O 0 1 N N N 37.352 64.868 -10.385 -0.730 -0.318 3.358 O3A UP5 23 UP5 PB PB P 0 1 N N S 38.099 65.681 -11.536 -0.558 0.523 1.996 PB UP5 24 UP5 O1B O1B O 0 1 N N N 38.557 64.783 -12.568 0.500 1.541 2.177 O1B UP5 25 UP5 O2B O2B O 0 1 N N N 39.130 66.525 -10.938 -1.948 1.251 1.636 O2B UP5 26 UP5 O3B O3B O 0 1 N N N 36.986 66.614 -12.123 -0.147 -0.471 0.799 O3B UP5 27 UP5 PG PG P 0 1 N N N 36.576 68.145 -12.094 0.007 0.432 -0.524 PG UP5 28 UP5 O1G O1G O 0 1 N N N 35.332 68.285 -11.401 -1.278 1.103 -0.816 O1G UP5 29 UP5 O2G O2G O 0 1 N N N 37.687 68.950 -11.600 1.149 1.542 -0.285 O2G UP5 30 UP5 O3G O3G O 0 1 N N N 36.342 68.490 -13.620 0.420 -0.502 -1.767 O3G UP5 31 UP5 PD PD P 0 1 N N S 37.121 69.067 -14.824 0.557 0.461 -3.049 PD UP5 32 UP5 O1D O1D O 0 1 N N N 38.304 68.232 -15.106 -0.737 1.132 -3.303 O1D UP5 33 UP5 O2D O2D O 0 1 N N N 36.163 69.245 -15.893 1.689 1.571 -2.768 O2D UP5 34 UP5 O3D O3D O 0 1 N N N 37.568 70.531 -14.323 0.970 -0.412 -4.337 O3D UP5 35 UP5 PE PE P 0 1 N N S 38.852 71.428 -14.150 1.088 0.610 -5.575 PE UP5 36 UP5 O1E O1E O 0 1 N N N 38.801 72.079 -12.859 -0.214 1.278 -5.790 O1E UP5 37 UP5 O2E O2E O 0 1 N N N 40.031 70.645 -14.424 2.212 1.716 -5.251 O2E UP5 38 UP5 O5J UO5* O 0 1 N N N 38.693 72.563 -15.279 1.500 -0.201 -6.903 O5J UP5 39 UP5 C5J UC5* C 0 1 N N N 37.484 73.342 -15.459 1.589 0.755 -7.961 C5J UP5 40 UP5 C4J UC4* C 0 1 N N R 37.603 74.180 -16.697 1.980 0.046 -9.259 C4J UP5 41 UP5 O4J UO4* O 0 1 N N N 38.804 74.880 -16.549 0.970 -0.912 -9.615 O4J UP5 42 UP5 C3J UC3* C 0 1 N N S 37.750 73.399 -17.985 2.071 1.069 -10.408 C3J UP5 43 UP5 O3J UO3* O 0 1 N N N 36.537 72.892 -18.441 3.387 1.090 -10.964 O3J UP5 44 UP5 C2J UC2* C 0 1 N N R 38.298 74.481 -18.867 1.048 0.552 -11.453 C2J UP5 45 UP5 O2J UO2* O 0 1 N N N 37.308 75.346 -19.346 1.566 0.680 -12.779 O2J UP5 46 UP5 C1J UC1* C 0 1 N N R 39.247 75.199 -17.883 0.904 -0.939 -11.057 C1J UP5 47 UP5 N1U UN1 N 0 1 N N N 40.607 74.782 -17.965 -0.384 -1.473 -11.505 N1U UP5 48 UP5 C2U UC2 C 0 1 N N N 41.419 75.367 -18.858 -1.524 -0.869 -11.123 C2U UP5 49 UP5 O2X "UO2'" O 0 1 N N N 40.865 76.278 -19.686 -1.472 0.116 -10.413 O2X UP5 50 UP5 N3U UN3 N 0 1 N N N 42.704 75.093 -19.083 -2.722 -1.336 -11.523 N3U UP5 51 UP5 C4U UC4 C 0 1 N N N 43.360 74.220 -18.286 -2.797 -2.428 -12.310 C4U UP5 52 UP5 O4U UO4 O 0 1 N N N 44.652 73.943 -18.605 -3.880 -2.854 -12.669 O4U UP5 53 UP5 C5U UC5 C 0 1 N N N 42.619 73.655 -17.299 -1.605 -3.076 -12.715 C5U UP5 54 UP5 C6U UC6 C 0 1 N N N 41.301 73.861 -17.097 -0.417 -2.584 -12.303 C6U UP5 55 UP5 H8A AH8 H 0 1 N N N 36.985 61.576 -7.537 1.817 0.375 9.333 H8A UP5 56 UP5 H61A AH61 H 0 0 N N N 36.537 55.467 -7.898 4.468 -2.156 14.276 H61A UP5 57 UP5 H62A AH62 H 0 0 N N N 37.363 56.672 -7.151 4.676 -1.274 12.861 H62A UP5 58 UP5 H2A AH2 H 0 1 N N N 32.363 57.160 -7.056 0.009 -3.068 14.554 H2A UP5 59 UP5 H51A AH51 H 0 0 N N N 34.346 65.464 -9.040 -2.617 1.423 6.576 H51A UP5 60 UP5 H52A AH52 H 0 0 N N N 34.341 64.079 -9.990 -0.896 1.680 6.953 H52A UP5 61 UP5 H4F AH4* H 0 1 N N N 32.532 64.040 -8.186 -2.686 -0.478 8.178 H4F UP5 62 UP5 H3F AH3* H 0 1 N N N 34.420 65.046 -6.415 -1.811 2.286 9.033 H3F UP5 63 UP5 HO3A AHO3 H 0 0 N N N 32.859 64.495 -4.925 -3.743 2.051 10.242 HO3A UP5 64 UP5 H2F AH2* H 0 1 N N N 35.742 63.023 -6.151 -0.714 1.499 10.909 H2F UP5 65 UP5 HO2A AHO2 H 0 0 N N N 34.927 61.905 -4.397 -2.827 1.357 11.841 HO2A UP5 66 UP5 H1F AH1* H 0 1 N N N 33.171 61.354 -6.397 -1.425 -1.379 10.326 H1F UP5 67 UP5 HOA2 2HOA H 0 0 N N N 37.770 66.765 -8.552 -3.186 0.762 4.022 HOA2 UP5 68 UP5 HOB2 2HOB H 0 0 N N N 39.574 67.009 -11.623 -2.608 0.554 1.527 HOB2 UP5 69 UP5 HOG2 2HOG H 0 0 N N N 37.441 69.867 -11.582 1.969 1.064 -0.098 HOG2 UP5 70 UP5 HOD2 2HOD H 0 0 N N N 36.641 69.599 -16.633 2.515 1.093 -2.608 HOD2 UP5 71 UP5 HOE2 2HOE H 0 0 N N N 40.805 71.185 -14.319 3.043 1.240 -5.119 HOE2 UP5 72 UP5 H51U UH51 H 0 0 N N N 36.570 72.703 -15.470 0.624 1.244 -8.090 H51U UP5 73 UP5 H52U UH52 H 0 0 N N N 37.240 73.954 -14.559 2.344 1.501 -7.713 H52U UP5 74 UP5 H4J UH4* H 0 1 N N N 36.672 74.789 -16.782 2.939 -0.455 -9.133 H4J UP5 75 UP5 H3J UH3* H 0 1 N N N 38.382 72.483 -17.917 1.789 2.062 -10.057 H3J UP5 76 UP5 "HO3'" *HO3 H 0 0 N N N 36.629 72.401 -19.249 3.364 1.701 -11.713 "HO3'" UP5 77 UP5 H2J UH2* H 0 1 N N N 38.780 74.100 -19.797 0.095 1.073 -11.358 H2J UP5 78 UP5 "HO2'" *HO2 H 0 0 N N N 37.655 76.031 -19.904 1.631 1.627 -12.964 "HO2'" UP5 79 UP5 H1J UH1* H 0 1 N N N 39.210 76.283 -18.138 1.725 -1.526 -11.468 H1J UP5 80 UP5 H3U UH3 H 0 1 N N N 43.182 75.548 -19.860 -3.534 -0.886 -11.242 H3U UP5 81 UP5 H5U UH5 H 0 1 N N N 43.131 72.970 -16.602 -1.645 -3.952 -13.345 H5U UP5 82 UP5 H6U UH6 H 0 1 N N N 40.819 73.309 -16.271 0.502 -3.064 -12.602 H6U UP5 83 # 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 UP5 N9A C8A SING Y N 1 UP5 N9A C4A SING Y N 2 UP5 N9A C1F SING N N 3 UP5 C8A N7A DOUB Y N 4 UP5 C8A H8A SING N N 5 UP5 N7A C5A SING Y N 6 UP5 C5A C6A SING Y N 7 UP5 C5A C4A DOUB Y N 8 UP5 C6A N6A SING N N 9 UP5 C6A N1A DOUB Y N 10 UP5 N6A H61A SING N N 11 UP5 N6A H62A SING N N 12 UP5 N1A C2A SING Y N 13 UP5 C2A N3A DOUB Y N 14 UP5 C2A H2A SING N N 15 UP5 N3A C4A SING Y N 16 UP5 O5F C5F SING N N 17 UP5 O5F PA SING N N 18 UP5 C5F C4F SING N N 19 UP5 C5F H51A SING N N 20 UP5 C5F H52A SING N N 21 UP5 C4F O4F SING N N 22 UP5 C4F C3F SING N N 23 UP5 C4F H4F SING N N 24 UP5 O4F C1F SING N N 25 UP5 C3F O3F SING N N 26 UP5 C3F C2F SING N N 27 UP5 C3F H3F SING N N 28 UP5 O3F HO3A SING N N 29 UP5 C2F O2F SING N N 30 UP5 C2F C1F SING N N 31 UP5 C2F H2F SING N N 32 UP5 O2F HO2A SING N N 33 UP5 C1F H1F SING N N 34 UP5 PA O1A DOUB N N 35 UP5 PA O2A SING N N 36 UP5 PA O3A SING N N 37 UP5 O2A HOA2 SING N N 38 UP5 O3A PB SING N N 39 UP5 PB O1B DOUB N N 40 UP5 PB O2B SING N N 41 UP5 PB O3B SING N N 42 UP5 O2B HOB2 SING N N 43 UP5 O3B PG SING N N 44 UP5 PG O1G DOUB N N 45 UP5 PG O2G SING N N 46 UP5 PG O3G SING N N 47 UP5 O2G HOG2 SING N N 48 UP5 O3G PD SING N N 49 UP5 PD O1D DOUB N N 50 UP5 PD O2D SING N N 51 UP5 PD O3D SING N N 52 UP5 O2D HOD2 SING N N 53 UP5 O3D PE SING N N 54 UP5 PE O1E DOUB N N 55 UP5 PE O2E SING N N 56 UP5 PE O5J SING N N 57 UP5 O2E HOE2 SING N N 58 UP5 O5J C5J SING N N 59 UP5 C5J C4J SING N N 60 UP5 C5J H51U SING N N 61 UP5 C5J H52U SING N N 62 UP5 C4J O4J SING N N 63 UP5 C4J C3J SING N N 64 UP5 C4J H4J SING N N 65 UP5 O4J C1J SING N N 66 UP5 C3J O3J SING N N 67 UP5 C3J C2J SING N N 68 UP5 C3J H3J SING N N 69 UP5 O3J "HO3'" SING N N 70 UP5 C2J O2J SING N N 71 UP5 C2J C1J SING N N 72 UP5 C2J H2J SING N N 73 UP5 O2J "HO2'" SING N N 74 UP5 C1J N1U SING N N 75 UP5 C1J H1J SING N N 76 UP5 N1U C2U SING N N 77 UP5 N1U C6U SING N N 78 UP5 C2U O2X DOUB N N 79 UP5 C2U N3U SING N N 80 UP5 N3U C4U SING N N 81 UP5 N3U H3U SING N N 82 UP5 C4U O4U DOUB N N 83 UP5 C4U C5U SING N N 84 UP5 C5U C6U DOUB N N 85 UP5 C5U H5U SING N N 86 UP5 C6U H6U SING N N 87 # 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 UP5 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)N5C=CC(=O)NC5=O)[C@@H](O)[C@H]3O" UP5 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)N5C=CC(=O)NC5=O)[CH](O)[CH]3O" UP5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CC(=O)NC5=O)O)O)O)O)N" UP5 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CC(=O)NC5=O)O)O)O)O)N" UP5 InChI InChI 1.03 ;InChI=1S/C19H28N7O24P5/c20-15-10-16(22-5-21-15)26(6-23-10)18-14(31)12(29)8(46-18)4-44-52(35,36)48-54(39,40)50-55(41,42)49-53(37,38)47-51(33,34)43-3-7-11(28)13(30)17(45-7)25-2-1-9(27)24-19(25)32/h1-2,5-8,11-14,17-18,28-31H,3-4H2,(H,33,34)(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,20,21,22)(H,24,27,32)/t7-,8-,11-,12-,13-,14-,17-,18-/m1/s1 ; UP5 InChIKey InChI 1.03 CPTLFMDLEWCNMJ-KPKSGTNCSA-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 UP5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 ;[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] hydrogen 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 UP5 "Create component" 1999-07-08 RCSB UP5 "Modify descriptor" 2011-06-04 RCSB #