data_C84 # _chem_comp.id C84 _chem_comp.name "[(2R,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 ? _chem_comp.pdbx_synonyms "Agrocin 84 (beta-D-glucopyranose form)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-04-02 _chem_comp.pdbx_modified_date 2023-02-15 _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 C84 _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 4ZEC _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.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 C84 OAZ O1 O 0 1 N N N -9.155 -27.182 26.470 4.566 -0.424 1.436 OAZ C84 1 C84 CBI C1 C 0 1 N N R -10.347 -27.491 27.228 3.805 0.041 0.319 CBI C84 2 C84 OAY O2 O 0 1 N N N -11.525 -26.917 26.508 2.421 -0.352 0.448 OAY C84 3 C84 CAR C2 C 0 1 N N N -10.519 -29.016 27.175 3.745 1.590 0.306 CAR C84 4 C84 CBG C3 C 0 1 N N S -11.984 -29.271 26.999 2.447 1.858 -0.494 CBG C84 5 C84 OAG O3 O 0 1 N N N -12.197 -30.438 26.187 1.715 2.938 0.088 OAG C84 6 C84 CBP C4 C 0 1 N N R -12.553 -27.952 26.423 1.654 0.538 -0.381 CBP C84 7 C84 N9 N1 N 0 1 Y N N -13.167 -28.033 24.995 0.349 0.789 0.235 N9 C84 8 C84 C8 C5 C 0 1 Y N N -12.543 -28.423 23.880 0.045 0.673 1.559 C8 C84 9 C84 N7 N2 N 0 1 Y N N -13.316 -28.109 22.843 -1.206 0.973 1.756 N7 C84 10 C84 C5 C6 C 0 1 Y N N -14.253 -27.257 23.262 -1.783 1.300 0.575 C5 C84 11 C84 C4 C7 C 0 1 Y N N -14.110 -27.166 24.592 -0.791 1.191 -0.415 C4 C84 12 C84 N3 N3 N 0 1 Y N N -15.021 -26.508 25.337 -1.106 1.463 -1.677 N3 C84 13 C84 C2 C8 C 0 1 Y N N -16.138 -25.736 24.752 -2.328 1.829 -2.000 C2 C84 14 C84 N1 N4 N 0 1 Y N N -16.214 -25.953 23.295 -3.293 1.945 -1.106 N1 C84 15 C84 C6 C9 C 0 1 Y N N -15.274 -26.647 22.627 -3.072 1.698 0.181 C6 C84 16 C84 N6 N5 N 0 1 N N N -15.453 -27.027 21.359 -4.088 1.827 1.112 N6 C84 17 C84 CAA C10 C 0 1 N N N -4.173 -23.671 26.749 10.483 -1.275 -2.435 CAA C84 18 C84 CBF C11 C 0 1 N N N -4.228 -24.220 28.183 9.799 0.076 -2.212 CBF C84 19 C84 CAB C12 C 0 1 N N N -2.823 -24.044 28.802 9.433 0.692 -3.563 CAB C84 20 C84 CBK C13 C 0 1 N N S -5.336 -23.526 29.049 8.528 -0.127 -1.383 CBK C84 21 C84 OAJ O4 O 0 1 N N N -5.289 -23.977 30.421 7.825 1.112 -1.278 OAJ C84 22 C84 CBJ C14 C 0 1 N N R -6.797 -23.687 28.523 8.905 -0.620 0.015 CBJ C84 23 C84 OAI O5 O 0 1 N N N -7.022 -22.911 27.328 9.789 0.320 0.630 OAI C84 24 C84 CBB C15 C 0 1 N N N -7.247 -25.175 28.415 7.659 -0.758 0.852 CBB C84 25 C84 OAC O6 O 0 1 N N N -7.826 -25.719 29.360 7.499 -0.050 1.823 OAC C84 26 C84 NAV N6 N 0 1 N N N -7.084 -25.755 27.208 6.723 -1.669 0.520 NAV C84 27 C84 PBR P1 P 0 1 N N N -7.589 -27.372 26.948 5.367 -1.820 1.430 PBR C84 28 C84 OAM O7 O 0 1 N N N -7.645 -28.225 28.165 5.773 -2.212 2.938 OAM C84 29 C84 OAD O8 O 0 1 N N N -7.002 -28.034 25.748 4.506 -2.881 0.861 OAD C84 30 C84 PBS P2 P 0 1 N N N -16.710 -26.398 20.303 -5.586 2.293 0.631 PBS C84 31 C84 OAN O9 O 0 1 N N N -17.792 -27.379 20.136 -6.484 2.354 1.806 OAN C84 32 C84 OAE O10 O 0 1 N N N -17.153 -25.002 20.497 -5.501 3.746 -0.056 OAE C84 33 C84 OBA O11 O 0 1 N N N -16.053 -26.264 18.854 -6.163 1.230 -0.431 OBA C84 34 C84 CBO C16 C 0 1 N N R -15.900 -27.416 18.007 -6.649 -0.060 -0.055 CBO C84 35 C84 CBM C17 C 0 1 N N S -14.346 -27.811 17.945 -5.828 -1.143 -0.762 CBM C84 36 C84 OAL O12 O 0 1 N N N -13.891 -28.349 19.198 -4.469 -1.072 -0.327 OAL C84 37 C84 CBL C18 C 0 1 N N S -14.063 -28.878 16.889 -6.407 -2.517 -0.413 CBL C84 38 C84 OAK O13 O 0 1 N N N -12.644 -29.154 16.813 -5.693 -3.531 -1.124 OAK C84 39 C84 CBN C19 C 0 1 N N R -14.646 -28.426 15.535 -7.884 -2.556 -0.811 CBN C84 40 C84 CAQ C20 C 0 1 N N N -14.481 -29.495 14.452 -8.486 -3.905 -0.412 CAQ C84 41 C84 OAF O14 O 0 1 N N N -15.046 -30.713 14.938 -9.832 -3.986 -0.886 OAF C84 42 C84 OAX O15 O 0 1 N N N -16.072 -28.237 15.751 -8.584 -1.505 -0.142 OAX C84 43 C84 CBH C21 C 0 1 N N R -16.396 -27.119 16.579 -8.118 -0.194 -0.465 CBH C84 44 C84 OAH O16 O 0 1 N N N -17.816 -27.236 16.488 -8.900 0.776 0.234 OAH C84 45 C84 H1 H1 H 0 1 N N N -10.290 -27.134 28.267 4.225 -0.334 -0.614 H1 C84 46 C84 H2 H2 H 0 1 N N N -10.163 -29.472 28.111 3.666 1.985 1.319 H2 C84 47 C84 H3 H3 H 0 1 N N N -9.956 -29.433 26.327 4.612 2.009 -0.205 H3 C84 48 C84 H4 H4 H 0 1 N N N -12.433 -29.429 27.990 2.680 2.074 -1.537 H4 C84 49 C84 H5 H5 H 0 1 N N N -11.817 -31.196 26.615 2.192 3.779 0.094 H5 C84 50 C84 H6 H6 H 0 1 N N N -13.373 -27.653 27.092 1.521 0.100 -1.370 H6 C84 51 C84 H7 H7 H 0 1 N N N -11.580 -28.908 23.829 0.740 0.375 2.330 H7 C84 52 C84 H8 H10 H 0 1 N N N -16.806 -25.101 25.314 -2.550 2.043 -3.035 H10 C84 53 C84 H9 H11 H 0 1 N N N -15.599 -28.016 21.392 -3.915 1.642 2.048 H11 C84 54 C84 H10 H12 H 0 1 N N N -5.160 -23.780 26.276 11.388 -1.130 -3.025 H12 C84 55 C84 H11 H13 H 0 1 N N N -3.895 -22.607 26.774 10.743 -1.713 -1.472 H13 C84 56 C84 H12 H14 H 0 1 N N N -3.425 -24.232 26.170 9.805 -1.942 -2.967 H14 C84 57 C84 H13 H15 H 0 1 N N N -4.454 -25.295 28.136 10.476 0.743 -1.680 H15 C84 58 C84 H14 H16 H 0 1 N N N -2.825 -24.428 29.833 8.823 -0.012 -4.130 H16 C84 59 C84 H15 H17 H 0 1 N N N -2.087 -24.602 28.205 8.871 1.612 -3.403 H17 C84 60 C84 H16 H18 H 0 1 N N N -2.557 -22.977 28.809 10.343 0.914 -4.120 H18 C84 61 C84 H17 H19 H 0 1 N N N -5.114 -22.449 29.037 7.892 -0.867 -1.869 H19 C84 62 C84 H18 H20 H 0 1 N N N -5.969 -23.542 30.921 8.332 1.818 -0.854 H20 C84 63 C84 H19 H21 H 0 1 N N N -7.435 -23.248 29.305 9.401 -1.588 -0.061 H21 C84 64 C84 H20 H22 H 0 1 N N N -6.725 -22.020 27.468 9.413 1.206 0.730 H22 C84 65 C84 H21 H23 H 0 1 N N N -6.666 -25.238 26.461 6.851 -2.236 -0.257 H23 C84 66 C84 H22 H24 H 0 1 N N N -7.284 -29.082 27.969 6.339 -1.560 3.375 H24 C84 67 C84 H23 H25 H 0 1 N N N -18.102 -24.965 20.481 -4.928 3.780 -0.835 H25 C84 68 C84 H24 H26 H 0 1 N N N -16.459 -28.272 18.413 -6.560 -0.183 1.025 H26 C84 69 C84 H25 H27 H 0 1 N N N -13.776 -26.904 17.695 -5.874 -0.989 -1.840 H27 C84 70 C84 H26 H28 H 0 1 N N N -14.047 -27.717 19.890 -3.890 -1.730 -0.736 H28 C84 71 C84 H27 H29 H 0 1 N N N -14.588 -29.797 17.189 -6.314 -2.690 0.659 H29 C84 72 C84 H28 H30 H 0 1 N N N -12.328 -29.428 17.666 -6.007 -4.429 -0.950 H30 C84 73 C84 H29 H31 H 0 1 N N N -14.166 -27.489 15.216 -7.973 -2.424 -1.890 H31 C84 74 C84 H30 H32 H 0 1 N N N -13.413 -29.641 14.233 -7.897 -4.710 -0.851 H32 C84 75 C84 H31 H33 H 0 1 N N N -15.004 -29.181 13.536 -8.477 -4.000 0.674 H33 C84 76 C84 H32 H34 H 0 1 N N N -14.953 -31.391 14.279 -10.276 -4.817 -0.668 H34 C84 77 C84 H33 H35 H 0 1 N N N -16.007 -26.162 16.201 -8.210 -0.030 -1.539 H35 C84 78 C84 H34 H36 H 0 1 N N N -18.224 -26.546 16.998 -9.843 0.748 0.022 H36 C84 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 C84 CAQ OAF SING N N 1 C84 CAQ CBN SING N N 2 C84 CBN OAX SING N N 3 C84 CBN CBL SING N N 4 C84 OAX CBH SING N N 5 C84 OAH CBH SING N N 6 C84 CBH CBO SING N N 7 C84 OAK CBL SING N N 8 C84 CBL CBM SING N N 9 C84 CBM CBO SING N N 10 C84 CBM OAL SING N N 11 C84 CBO OBA SING N N 12 C84 OBA PBS SING N N 13 C84 OAN PBS DOUB N N 14 C84 PBS OAE SING N N 15 C84 PBS N6 SING N N 16 C84 N6 C6 SING N N 17 C84 C6 C5 SING Y N 18 C84 C6 N1 DOUB Y N 19 C84 N7 C5 SING Y N 20 C84 N7 C8 DOUB Y N 21 C84 C5 C4 DOUB Y N 22 C84 N1 C2 SING Y N 23 C84 C8 N9 SING Y N 24 C84 C4 N9 SING Y N 25 C84 C4 N3 SING Y N 26 C84 C2 N3 DOUB Y N 27 C84 N9 CBP SING N N 28 C84 OAD PBR DOUB N N 29 C84 OAG CBG SING N N 30 C84 CBP OAY SING N N 31 C84 CBP CBG SING N N 32 C84 OAZ PBR SING N N 33 C84 OAZ CBI SING N N 34 C84 OAY CBI SING N N 35 C84 CAA CBF SING N N 36 C84 PBR NAV SING N N 37 C84 PBR OAM SING N N 38 C84 CBG CAR SING N N 39 C84 CAR CBI SING N N 40 C84 NAV CBB SING N N 41 C84 OAI CBJ SING N N 42 C84 CBF CAB SING N N 43 C84 CBF CBK SING N N 44 C84 CBB CBJ SING N N 45 C84 CBB OAC DOUB N N 46 C84 CBJ CBK SING N N 47 C84 CBK OAJ SING N N 48 C84 CBI H1 SING N N 49 C84 CAR H2 SING N N 50 C84 CAR H3 SING N N 51 C84 CBG H4 SING N N 52 C84 OAG H5 SING N N 53 C84 CBP H6 SING N N 54 C84 C8 H7 SING N N 55 C84 C2 H8 SING N N 56 C84 N6 H9 SING N N 57 C84 CAA H10 SING N N 58 C84 CAA H11 SING N N 59 C84 CAA H12 SING N N 60 C84 CBF H13 SING N N 61 C84 CAB H14 SING N N 62 C84 CAB H15 SING N N 63 C84 CAB H16 SING N N 64 C84 CBK H17 SING N N 65 C84 OAJ H18 SING N N 66 C84 CBJ H19 SING N N 67 C84 OAI H20 SING N N 68 C84 NAV H21 SING N N 69 C84 OAM H22 SING N N 70 C84 OAE H23 SING N N 71 C84 CBO H24 SING N N 72 C84 CBM H25 SING N N 73 C84 OAL H26 SING N N 74 C84 CBL H27 SING N N 75 C84 OAK H28 SING N N 76 C84 CBN H29 SING N N 77 C84 CAQ H30 SING N N 78 C84 CAQ H31 SING N N 79 C84 OAF H32 SING N N 80 C84 CBH H33 SING N N 81 C84 OAH H34 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 C84 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" C84 InChIKey InChI 1.06 KOMSNTWZRZGGEF-AIJJVVIGSA-N C84 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" C84 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" C84 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" C84 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 C84 _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~{R},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" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site C84 "Create component" 2014-04-02 PDBJ C84 "Initial release" 2015-08-19 RCSB C84 "Modify synonyms" 2021-03-01 PDBE C84 "Modify model coordinates code" 2023-02-07 PDBE C84 "Modify synonyms" 2023-02-15 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id C84 _pdbx_chem_comp_synonyms.name "Agrocin 84 (beta-D-glucopyranose form)" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? #