data_UKU # _chem_comp.id UKU _chem_comp.name "[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H34 N6 O16 P2" _chem_comp.mon_nstd_parent_comp_id C84 _chem_comp.pdbx_synonyms "Agrocin 84 (alpha-D-glucopyranose form)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-07 _chem_comp.pdbx_modified_date 2024-01-19 _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 688.473 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UKU _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 8CAW _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 UKU CAA C1 C 0 1 N N N N N N 18.571 -15.669 21.017 -3.694 5.043 -0.662 CAA UKU 1 UKU CBF C2 C 0 1 N N N N N N 19.163 -16.344 19.760 -4.821 4.977 0.371 CBF UKU 2 UKU CAB C3 C 0 1 N N N N N N 20.045 -17.506 20.272 -5.836 6.086 0.089 CAB UKU 3 UKU CBK C4 C 0 1 N N S N N N 18.063 -16.879 18.779 -5.514 3.616 0.283 CBK UKU 4 UKU OAJ O1 O 0 1 N N N N N N 18.723 -17.475 17.638 -6.567 3.555 1.248 OAJ UKU 5 UKU CBJ C5 C 0 1 N N R N N N 17.076 -15.819 18.202 -4.499 2.507 0.565 CBJ UKU 6 UKU OAI O2 O 0 1 N N N N N N 16.242 -15.207 19.208 -3.870 2.746 1.826 OAI UKU 7 UKU CBB C6 C 0 1 N N N N N N 17.824 -14.767 17.352 -5.205 1.176 0.599 CBB UKU 8 UKU OAC O3 O 0 1 N N N N N N 17.893 -14.943 16.137 -5.251 0.540 1.631 OAC UKU 9 UKU NAV N1 N 0 1 N N N N N N 18.332 -13.683 17.983 -5.786 0.692 -0.516 NAV UKU 10 UKU PBR P1 P 0 1 N N N N N N 19.162 -12.529 17.030 -6.555 -0.756 -0.479 PBR UKU 11 UKU OAD O4 O 0 1 N N N N N N 19.834 -13.078 15.824 -7.103 -1.058 -1.820 OAD UKU 12 UKU OAM O5 O 0 1 N N N N N N 19.949 -11.525 17.800 -7.756 -0.698 0.592 OAM UKU 13 UKU OAZ O6 O 0 1 N N N N N N 17.958 -11.593 16.490 -5.512 -1.906 -0.054 OAZ UKU 14 UKU CBI C7 C 0 1 N N R N N N 17.239 -11.834 15.268 -4.451 -2.347 -0.903 CBI UKU 15 UKU OAY O7 O 0 1 N N N N N N 15.936 -11.178 15.401 -3.248 -1.590 -0.649 OAY UKU 16 UKU CAR C8 C 0 1 N N N N N N 17.956 -11.267 14.042 -4.043 -3.802 -0.556 CAR UKU 17 UKU CBG C9 C 0 1 N N S N N N 17.190 -10.015 13.678 -2.581 -3.858 -1.062 CBG UKU 18 UKU OAG O8 O 0 1 N N N N N N 18.016 -8.821 13.754 -1.760 -4.582 -0.143 OAG UKU 19 UKU CBP C10 C 0 1 N N R N N N 15.927 -10.006 14.602 -2.146 -2.381 -1.126 CBP UKU 20 UKU N9 N2 N 0 1 Y N N N N N 15.710 -8.724 15.466 -0.975 -2.169 -0.271 N9 UKU 21 UKU C8 C11 C 0 1 Y N N N N N 16.649 -8.127 16.207 -0.987 -1.736 1.021 C8 UKU 22 UKU N7 N3 N 0 1 Y N N N N N 16.072 -7.128 16.868 0.230 -1.661 1.476 N7 UKU 23 UKU C5 C12 C 0 1 Y N N N N N 14.732 -7.279 16.809 1.098 -2.040 0.507 C5 UKU 24 UKU C4 C13 C 0 1 Y N N N N N 14.512 -8.274 15.922 0.335 -2.377 -0.624 C4 UKU 25 UKU N3 N4 N 0 1 Y N N N N N 13.256 -8.555 15.521 0.957 -2.791 -1.723 N3 UKU 26 UKU C2 C14 C 0 1 Y N N N N N 12.069 -7.830 16.055 2.269 -2.889 -1.754 C2 UKU 27 UKU N1 N5 N 0 1 Y N N N N N 12.471 -6.616 16.852 3.028 -2.588 -0.716 N1 UKU 28 UKU C6 C15 C 0 1 Y N N N N N 13.762 -6.377 17.101 2.496 -2.157 0.423 C6 UKU 29 UKU N6 N6 N 0 1 N N N N N N 14.128 -5.426 17.984 3.299 -1.845 1.506 N6 UKU 30 UKU PBS P2 P 0 1 N N N N N N 13.112 -4.206 18.500 4.929 -1.989 1.387 PBS UKU 31 UKU OAN O9 O 0 1 N N N N N N 13.015 -3.232 17.367 5.553 -1.598 2.670 OAN UKU 32 UKU OAE O10 O 0 1 N N N N N N 11.853 -4.623 19.162 5.310 -3.515 1.046 OAE UKU 33 UKU OBA O11 O 0 1 N N N N N N 13.980 -3.559 19.675 5.467 -1.027 0.213 OBA UKU 34 UKU CBO C16 C 0 1 N N R N N N 15.035 -2.586 19.519 5.569 0.392 0.355 CBO UKU 35 UKU CBH C17 C 0 1 N N S N N N 14.771 -1.441 20.438 7.025 0.822 0.156 CBH UKU 36 UKU OAH O12 O 0 1 N N N N N N 14.245 -1.854 21.662 7.478 0.392 -1.129 OAH UKU 37 UKU OAX O13 O 0 1 N N N N N N 15.813 -0.509 20.520 7.115 2.246 0.241 OAX UKU 38 UKU CBN C18 C 0 1 N N R N N N 17.009 -1.145 21.016 6.354 2.938 -0.752 CBN UKU 39 UKU CAQ C19 C 0 1 N N N N N N 17.973 0.022 21.186 6.548 4.447 -0.582 CAQ UKU 40 UKU OAF O14 O 0 1 N N N N N N 18.270 0.532 19.948 7.910 4.785 -0.847 OAF UKU 41 UKU CBL C20 C 0 1 N N S N N N 17.467 -2.185 20.038 4.871 2.593 -0.589 CBL UKU 42 UKU OAK O15 O 0 1 N N N N N N 18.621 -2.836 20.544 4.115 3.238 -1.616 OAK UKU 43 UKU CBM C21 C 0 1 N N S N N N 16.359 -3.259 19.892 4.694 1.075 -0.700 CBM UKU 44 UKU OAL O16 O 0 1 N N N N N N 16.672 -4.256 18.905 3.324 0.737 -0.477 OAL UKU 45 UKU H10 H1 H 0 1 N N N N N N 19.388 -15.316 21.663 -4.109 4.911 -1.661 H10 UKU 46 UKU H11 H2 H 0 1 N N N N N N 17.947 -14.815 20.715 -3.200 6.012 -0.599 H11 UKU 47 UKU H12 H3 H 0 1 N N N N N N 17.956 -16.396 21.568 -2.970 4.253 -0.461 H12 UKU 48 UKU H13 H4 H 0 1 N N N N N N 19.795 -15.620 19.225 -4.406 5.109 1.370 H13 UKU 49 UKU H16 H5 H 0 1 N N N N N N 20.810 -17.112 20.958 -6.251 5.954 -0.910 H16 UKU 50 UKU H14 H6 H 0 1 N N N N N N 19.417 -18.236 20.804 -6.639 6.039 0.825 H14 UKU 51 UKU H15 H7 H 0 1 N N N N N N 20.536 -17.997 19.419 -5.342 7.056 0.152 H15 UKU 52 UKU H17 H8 H 0 1 N N N N N N 17.475 -17.644 19.308 -5.929 3.484 -0.716 H17 UKU 53 UKU H18 H9 H 0 1 N N N N N N 19.340 -18.133 17.936 -6.270 3.665 2.161 H18 UKU 54 UKU H19 H10 H 0 1 N N N N N N 16.415 -16.361 17.510 -3.744 2.497 -0.221 H19 UKU 55 UKU H20 H11 H 0 1 N N N N N N 15.800 -15.883 19.708 -4.484 2.767 2.573 H20 UKU 56 UKU H21 H12 H 0 1 N N N N N N 18.226 -13.561 18.970 -5.750 1.201 -1.342 H21 UKU 57 UKU H22 H13 H 0 1 N N N N N N 20.790 -11.391 17.379 -7.469 -0.504 1.495 H22 UKU 58 UKU H1 H14 H 0 1 N N N N N N 17.095 -12.915 15.124 -4.741 -2.267 -1.951 H1 UKU 59 UKU H2 H15 H 0 1 N N N N N N 17.931 -11.989 13.213 -4.089 -3.973 0.520 H2 UKU 60 UKU H3 H16 H 0 1 N N N N N N 19.001 -11.023 14.285 -4.667 -4.519 -1.089 H3 UKU 61 UKU H4 H17 H 0 1 N N N N N N 16.834 -10.128 12.643 -2.537 -4.314 -2.051 H4 UKU 62 UKU H5 H18 H 0 1 N N N N N N 17.497 -8.061 13.518 -2.026 -5.503 -0.020 H5 UKU 63 UKU H6 H19 H 0 1 N N N N N N 15.059 -10.068 13.929 -1.911 -2.108 -2.154 H6 UKU 64 UKU H7 H20 H 0 1 N N N N N N 17.691 -8.406 16.259 -1.875 -1.491 1.584 H7 UKU 65 UKU H33 H25 H 0 1 N N N N N N 11.047 -8.137 15.891 2.743 -3.230 -2.663 H33 UKU 66 UKU H9 H27 H 0 1 N N N N N N 14.410 -5.914 18.810 2.898 -1.542 2.336 H9 UKU 67 UKU H23 H28 H 0 1 N N N N N N 11.118 -4.186 18.748 4.933 -3.839 0.217 H23 UKU 68 UKU H24 H29 H 0 1 N N N N N N 15.085 -2.230 18.479 5.235 0.683 1.350 H24 UKU 69 UKU H35 H30 H 0 1 N N N N N N 13.949 -0.898 19.949 7.646 0.372 0.930 H35 UKU 70 UKU H34 H31 H 0 1 N N N N N N 14.093 -1.096 22.214 8.394 0.631 -1.323 H34 UKU 71 UKU H29 H32 H 0 1 N N N N N N 16.822 -1.611 21.995 6.691 2.638 -1.743 H29 UKU 72 UKU H31 H33 H 0 1 N N N N N N 18.895 -0.328 21.673 5.899 4.977 -1.280 H31 UKU 73 UKU H30 H34 H 0 1 N N N N N N 17.505 0.802 21.805 6.294 4.733 0.438 H30 UKU 74 UKU H32 H35 H 0 1 N N N N N N 18.871 1.261 20.041 8.106 5.727 -0.758 H32 UKU 75 UKU H27 H36 H 0 1 N N N N N N 17.663 -1.725 19.058 4.523 2.931 0.387 H27 UKU 76 UKU H28 H37 H 0 1 N N N N N N 19.323 -2.204 20.646 4.185 4.203 -1.608 H28 UKU 77 UKU H25 H38 H 0 1 N N N N N N 16.230 -3.745 20.870 4.995 0.745 -1.694 H25 UKU 78 UKU H26 H39 H 0 1 N N N N N N 17.493 -4.678 19.130 2.711 1.136 -1.110 H26 UKU 79 # 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 UKU CBG OAG SING N N 1 UKU CBG CAR SING N N 2 UKU CBG CBP SING N N 3 UKU CAR CBI SING N N 4 UKU CBP OAY SING N N 5 UKU CBP N9 SING N N 6 UKU CBI OAY SING N N 7 UKU CBI OAZ SING N N 8 UKU N9 C4 SING Y N 9 UKU N9 C8 SING Y N 10 UKU N3 C4 SING Y N 11 UKU N3 C2 DOUB Y N 12 UKU OAD PBR DOUB N N 13 UKU C4 C5 DOUB Y N 14 UKU C2 N1 SING Y N 15 UKU OAC CBB DOUB N N 16 UKU C8 N7 DOUB Y N 17 UKU OAZ PBR SING N N 18 UKU C5 N7 SING Y N 19 UKU C5 C6 SING Y N 20 UKU N1 C6 DOUB Y N 21 UKU PBR OAM SING N N 22 UKU PBR NAV SING N N 23 UKU C6 N6 SING N N 24 UKU CBB NAV SING N N 25 UKU CBB CBJ SING N N 26 UKU OAN PBS DOUB N N 27 UKU OAJ CBK SING N N 28 UKU N6 PBS SING N N 29 UKU CBJ CBK SING N N 30 UKU CBJ OAI SING N N 31 UKU PBS OAE SING N N 32 UKU PBS OBA SING N N 33 UKU CBK CBF SING N N 34 UKU OAL CBM SING N N 35 UKU CBO OBA SING N N 36 UKU CBO CBM SING N N 37 UKU CBO CBH SING N N 38 UKU CBF CAB SING N N 39 UKU CBF CAA SING N N 40 UKU CBM CBL SING N N 41 UKU OAF CAQ SING N N 42 UKU CBL OAK SING N N 43 UKU CBL CBN SING N N 44 UKU CBH OAX SING N N 45 UKU CBH OAH SING N N 46 UKU OAX CBN SING N N 47 UKU CBN CAQ SING N N 48 UKU CAA H10 SING N N 49 UKU CAA H11 SING N N 50 UKU CAA H12 SING N N 51 UKU CBF H13 SING N N 52 UKU CAB H16 SING N N 53 UKU CAB H14 SING N N 54 UKU CAB H15 SING N N 55 UKU CBK H17 SING N N 56 UKU OAJ H18 SING N N 57 UKU CBJ H19 SING N N 58 UKU OAI H20 SING N N 59 UKU NAV H21 SING N N 60 UKU OAM H22 SING N N 61 UKU CBI H1 SING N N 62 UKU CAR H2 SING N N 63 UKU CAR H3 SING N N 64 UKU CBG H4 SING N N 65 UKU OAG H5 SING N N 66 UKU CBP H6 SING N N 67 UKU C8 H7 SING N N 68 UKU C2 H33 SING N N 69 UKU N6 H9 SING N N 70 UKU OAE H23 SING N N 71 UKU CBO H24 SING N N 72 UKU CBH H35 SING N N 73 UKU OAH H34 SING N N 74 UKU CBN H29 SING N N 75 UKU CAQ H31 SING N N 76 UKU CAQ H30 SING N N 77 UKU OAF H32 SING N N 78 UKU CBL H27 SING N N 79 UKU OAK H28 SING N N 80 UKU CBM H25 SING N N 81 UKU OAL H26 SING N N 82 # 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 UKU InChI InChI 1.06 "InChI=1S/C21H34N6O16P2/c1-7(2)12(30)15(33)19(34)26-45(38,39)42-10-3-8(29)20(41-10)27-6-24-11-17(22-5-23-18(11)27)25-44(36,37)43-16-14(32)13(31)9(4-28)40-21(16)35/h5-10,12-16,20-21,28-33,35H,3-4H2,1-2H3,(H2,26,34,38,39)(H2,22,23,25,36,37)/t8-,9+,10+,12-,13+,14-,15+,16+,20+,21-/m0/s1" UKU InChIKey InChI 1.06 KOMSNTWZRZGGEF-IPMHYPRDSA-N UKU SMILES_CANONICAL CACTVS 3.385 "CC(C)[C@H](O)[C@@H](O)C(=O)N[P](O)(=O)O[C@@H]1C[C@H](O)[C@@H](O1)n2cnc3c(N[P](O)(=O)O[C@H]4[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]4O)ncnc23" UKU SMILES CACTVS 3.385 "CC(C)[CH](O)[CH](O)C(=O)N[P](O)(=O)O[CH]1C[CH](O)[CH](O1)n2cnc3c(N[P](O)(=O)O[CH]4[CH](O)O[CH](CO)[CH](O)[CH]4O)ncnc23" UKU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)[C@@H]([C@H](C(=O)NP(=O)(O)O[C@@H]1C[C@@H]([C@@H](O1)n2cnc3c2ncnc3NP(=O)(O)O[C@@H]4[C@H]([C@@H]([C@H](O[C@@H]4O)CO)O)O)O)O)O" UKU SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)C(C(C(=O)NP(=O)(O)OC1CC(C(O1)n2cnc3c2ncnc3NP(=O)(O)OC4C(C(C(OC4O)CO)O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id UKU _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-~{N}-[9-[(2~{R},3~{S},5~{R})-5-[[[(2~{R},3~{S})-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UKU _pdbx_chem_comp_synonyms.name "Agrocin 84 (alpha-D-glucopyranose form)" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UKU "Create component" 2023-02-07 PDBE UKU "Modify synonyms" 2023-02-15 PDBE UKU "Initial release" 2024-01-24 RCSB #