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         ? 
# 
