data_I0B
# 
_chem_comp.id                                    I0B 
_chem_comp.name                                  "5'-([2-(benzylcarbamamido)ethyl]{3-[N'-(3-bromophenyl)carbamimidamido]propyl}amino)-5'-deoxyadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H38 Br N11 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-01 
_chem_comp.pdbx_modified_date                    2024-02-16 
_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                        696.598 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     I0B 
_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        8G2I 
_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.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 
I0B N1  N1  N  0 1 Y N N N N N 6.935  19.904 -29.544 2.606   6.280  2.060  N1  I0B 1  
I0B C7  C1  C  0 1 N N N N N N 2.348  26.001 -28.338 -2.123  0.293  -2.026 C7  I0B 2  
I0B C8  C2  C  0 1 N N N N N N 2.322  28.260 -29.136 -3.290  -1.015 -0.355 C8  I0B 3  
I0B N2  N2  N  0 1 Y N N N N N 5.412  21.392 -30.677 0.541   5.516  1.357  N2  I0B 4  
I0B C9  C3  C  0 1 N N N N N N 1.939  28.416 -30.559 -4.550  -1.250 -1.191 C9  I0B 5  
I0B O1  O1  O  0 1 N N N N N N 1.267  30.722 -31.812 -7.073  -1.710 -2.025 O1  I0B 6  
I0B C1  C4  C  0 1 Y N N N N N 6.540  20.682 -30.558 1.302   6.431  1.919  C1  I0B 7  
I0B C5  C5  C  0 1 N N R N N N 2.852  23.006 -30.041 -0.831  3.016  -0.064 C5  I0B 8  
I0B C6  C6  C  0 1 N N R N N N 2.496  25.268 -29.656 -2.246  1.492  -1.083 C6  I0B 9  
I0B N3  N3  N  0 1 Y N N N N N 3.877  20.571 -27.556 2.721   2.960  0.492  N3  I0B 10 
I0B C4  C7  C  0 1 Y N N N N N 3.022  21.392 -28.121 1.619   2.424  0.055  C4  I0B 11 
I0B C3  C8  C  0 1 Y N N N N N 4.920  20.501 -28.467 2.451   4.174  1.028  C3  I0B 12 
I0B O3  O2  O  0 1 N N N N N N 0.745  22.379 -30.985 -1.556  5.020  -1.281 O3  I0B 13 
I0B C2  C9  C  0 1 Y N N N N N 4.648  21.279 -29.585 1.067   4.384  0.901  C2  I0B 14 
I0B N4  N4  N  0 1 Y N N N N N 3.432  21.880 -29.335 0.570   3.264  0.284  N4  I0B 15 
I0B BR  BR1 BR 0 0 N N N N N N -3.067 35.377 -26.000 8.106   -3.818 1.632  BR  I0B 16 
I0B C24 C10 C  0 1 Y N N N N N -2.644 33.897 -24.909 7.852   -2.701 0.127  C24 I0B 17 
I0B C23 C11 C  0 1 Y N N N N N -1.605 33.118 -25.320 6.577   -2.465 -0.350 C23 I0B 18 
I0B C25 C12 C  0 1 Y N N N N N -3.485 33.530 -23.856 8.943   -2.116 -0.492 C25 I0B 19 
I0B C26 C13 C  0 1 Y N N N N N -3.306 32.284 -23.256 8.761   -1.299 -1.592 C26 I0B 20 
I0B C27 C14 C  0 1 Y N N N N N -2.304 31.443 -23.713 7.489   -1.064 -2.077 C27 I0B 21 
I0B C22 C15 C  0 1 Y N N N N N -1.444 31.881 -24.738 6.391   -1.645 -1.455 C22 I0B 22 
I0B N9  N5  N  0 1 N N N N N N -0.262 31.352 -25.233 5.102   -1.404 -1.941 N9  I0B 23 
I0B C21 C16 C  0 1 N N N N N N -0.107 30.138 -24.850 4.032   -1.386 -1.075 C21 I0B 24 
I0B N10 N6  N  0 1 N N N N N N -1.227 29.569 -24.319 4.232   -1.483 0.209  N10 I0B 25 
I0B N8  N7  N  0 1 N N N N N N 1.014  29.601 -25.143 2.753   -1.266 -1.565 N8  I0B 26 
I0B C20 C17 C  0 1 N N N N N N 1.434  28.262 -24.805 1.615   -1.246 -0.643 C20 I0B 27 
I0B C19 C18 C  0 1 N N N N N N 1.941  27.659 -26.042 0.316   -1.105 -1.439 C19 I0B 28 
I0B C18 C19 C  0 1 N N N N N N 0.955  27.632 -27.212 -0.873  -1.084 -0.476 C18 I0B 29 
I0B N5  N8  N  0 1 N N N N N N 1.548  27.200 -28.488 -2.120  -0.948 -1.241 N5  I0B 30 
I0B O   O3  O  0 1 N N N N N N 3.367  24.153 -29.422 -1.059  1.607  -0.280 O   I0B 31 
I0B C28 C20 C  0 1 N N S N N N 1.205  24.683 -30.241 -2.372  2.792  -1.902 C28 I0B 32 
I0B O2  O4  O  0 1 N N N N N N 1.174  25.014 -31.617 -3.606  3.451  -1.608 O2  I0B 33 
I0B C29 C21 C  0 1 N N R N N N 1.330  23.182 -29.965 -1.173  3.652  -1.435 C29 I0B 34 
I0B C   C22 C  0 1 Y N N N N N 6.138  19.783 -28.467 3.221   5.181  1.635  C   I0B 35 
I0B N   N9  N  0 1 N N N N N N 6.560  19.005 -27.454 4.589   5.031  1.787  N   I0B 36 
I0B N6  N10 N  0 1 N N N N N N 2.901  29.233 -31.297 -5.697  -1.443 -0.302 N6  I0B 37 
I0B C10 C23 C  0 1 N N N N N N 2.458  30.346 -31.911 -6.921  -1.668 -0.820 C10 I0B 38 
I0B N7  N11 N  0 1 N N N N N N 3.398  31.016 -32.603 -7.977  -1.846 -0.001 N7  I0B 39 
I0B C11 C24 C  0 1 N N N N N N 3.072  32.207 -33.390 -9.307  -2.091 -0.564 C11 I0B 40 
I0B C12 C25 C  0 1 Y N N N N N 3.143  33.512 -32.637 -10.304 -2.255 0.554  C12 I0B 41 
I0B C17 C26 C  0 1 Y N N N N N 3.840  33.595 -31.438 -10.971 -1.151 1.053  C17 I0B 42 
I0B C16 C27 C  0 1 Y N N N N N 3.959  34.799 -30.781 -11.885 -1.302 2.079  C16 I0B 43 
I0B C15 C28 C  0 1 Y N N N N N 3.384  35.948 -31.309 -12.132 -2.555 2.606  C15 I0B 44 
I0B C14 C29 C  0 1 Y N N N N N 2.709  35.876 -32.504 -11.465 -3.659 2.108  C14 I0B 45 
I0B C13 C30 C  0 1 Y N N N N N 2.564  34.660 -33.152 -10.555 -3.509 1.078  C13 I0B 46 
I0B H1  H1  H  0 1 N N N N N N 1.862  25.335 -27.610 -2.968  0.285  -2.715 H1  I0B 47 
I0B H2  H2  H  0 1 N N N N N N 3.346  26.280 -27.969 -1.194  0.369  -2.590 H2  I0B 48 
I0B H3  H3  H  0 1 N N N N N N 3.391  28.009 -29.079 -3.386  -0.076 0.191  H3  I0B 49 
I0B H4  H4  H  0 1 N N N N N N 2.140  29.209 -28.610 -3.165  -1.835 0.352  H4  I0B 50 
I0B H5  H5  H  0 1 N N N N N N 0.951  28.897 -30.611 -4.728  -0.385 -1.831 H5  I0B 51 
I0B H6  H6  H  0 1 N N N N N N 1.887  27.421 -31.024 -4.415  -2.138 -1.809 H6  I0B 52 
I0B H7  H7  H  0 1 N N N N N N 7.223  20.746 -31.392 0.842   7.340  2.278  H7  I0B 53 
I0B H8  H8  H  0 1 N N N N N N 3.149  22.974 -31.100 -1.494  3.397  0.712  H8  I0B 54 
I0B H9  H9  H  0 1 N N N N N N 2.943  25.948 -30.396 -3.118  1.370  -0.441 H9  I0B 55 
I0B H10 H10 H  0 1 N N N N N N 2.078  21.659 -27.669 1.546   1.457  -0.420 H10 I0B 56 
I0B H11 H11 H  0 1 N N N N N N 0.850  21.461 -30.765 -1.780  5.462  -2.112 H11 I0B 57 
I0B H12 H12 H  0 1 N N N N N N -0.924 33.463 -26.084 5.725   -2.918 0.136  H12 I0B 58 
I0B H13 H13 H  0 1 N N N N N N -4.260 34.199 -23.513 9.938   -2.298 -0.115 H13 I0B 59 
I0B H14 H14 H  0 1 N N N N N N -3.944 31.977 -22.441 9.614   -0.844 -2.073 H14 I0B 60 
I0B H15 H15 H  0 1 N N N N N N -2.184 30.458 -23.286 7.348   -0.426 -2.937 H15 I0B 61 
I0B H16 H16 H  0 1 N N N N N N 0.384  31.851 -25.812 4.962   -1.250 -2.888 H16 I0B 62 
I0B H17 H17 H  0 1 N N N N N N -1.107 28.590 -24.152 3.478   -1.470 0.820  H17 I0B 63 
I0B H18 H18 H  0 1 N N N N N N 1.663  30.162 -25.656 2.604   -1.194 -2.520 H18 I0B 64 
I0B H19 H19 H  0 1 N N N N N N 0.582  27.682 -24.421 1.592   -2.175 -0.073 H19 I0B 65 
I0B H20 H20 H  0 1 N N N N N N 2.228  28.294 -24.045 1.715   -0.403 0.041  H20 I0B 66 
I0B H21 H21 H  0 1 N N N N N N 2.232  26.622 -25.819 0.338   -0.175 -2.008 H21 I0B 67 
I0B H22 H22 H  0 1 N N N N N N 2.827  28.228 -26.358 0.215   -1.947 -2.123 H22 I0B 68 
I0B H23 H23 H  0 1 N N N N N N 0.549  28.646 -27.345 -0.895  -2.013 0.093  H23 I0B 69 
I0B H24 H24 H  0 1 N N N N N N 0.138  26.940 -26.959 -0.772  -0.242 0.208  H24 I0B 70 
I0B H26 H26 H  0 1 N N N N N N 0.334  25.091 -29.707 -2.297  2.579  -2.969 H26 I0B 71 
I0B H27 H27 H  0 1 N N N N N N 1.096  25.956 -31.715 -3.712  4.303  -2.052 H27 I0B 72 
I0B H28 H28 H  0 1 N N N N N N 0.955  22.933 -28.962 -0.336  3.560  -2.127 H28 I0B 73 
I0B H29 H29 H  0 1 N N N N N N 7.454  18.618 -27.680 5.109   5.733  2.208  H29 I0B 74 
I0B H30 H30 H  0 1 N N N N N N 6.635  19.554 -26.621 5.026   4.224  1.473  H30 I0B 75 
I0B H31 H31 H  0 1 N N N N N N 3.865  28.971 -31.345 -5.577  -1.410 0.660  H31 I0B 76 
I0B H32 H32 H  0 1 N N N N N N 4.344  30.692 -32.579 -7.856  -1.813 0.961  H32 I0B 77 
I0B H33 H33 H  0 1 N N N N N N 2.048  32.091 -33.775 -9.598  -1.246 -1.189 H33 I0B 78 
I0B H34 H34 H  0 1 N N N N N N 3.777  32.261 -34.233 -9.285  -2.999 -1.167 H34 I0B 79 
I0B H35 H35 H  0 1 N N N N N N 4.292  32.708 -31.018 -10.778 -0.172 0.641  H35 I0B 80 
I0B H36 H36 H  0 1 N N N N N N 4.503  34.850 -29.849 -12.406 -0.440 2.468  H36 I0B 81 
I0B H37 H37 H  0 1 N N N N N N 3.467  36.889 -30.785 -12.846 -2.673 3.408  H37 I0B 82 
I0B H38 H38 H  0 1 N N N N N N 2.290  36.771 -32.940 -11.657 -4.638 2.520  H38 I0B 83 
I0B H39 H39 H  0 1 N N N N N N 1.994  34.607 -34.068 -10.037 -4.372 0.686  H39 I0B 84 
# 
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 
I0B C11 C12 SING N N 1  
I0B C11 N7  SING N N 2  
I0B C13 C12 DOUB Y N 3  
I0B C13 C14 SING Y N 4  
I0B C12 C17 SING Y N 5  
I0B N7  C10 SING N N 6  
I0B C14 C15 DOUB Y N 7  
I0B C10 O1  DOUB N N 8  
I0B C10 N6  SING N N 9  
I0B O2  C28 SING N N 10 
I0B C17 C16 DOUB Y N 11 
I0B C15 C16 SING Y N 12 
I0B N6  C9  SING N N 13 
I0B O3  C29 SING N N 14 
I0B N2  C1  DOUB Y N 15 
I0B N2  C2  SING Y N 16 
I0B C9  C8  SING N N 17 
I0B C1  N1  SING Y N 18 
I0B C28 C29 SING N N 19 
I0B C28 C6  SING N N 20 
I0B C5  C29 SING N N 21 
I0B C5  O   SING N N 22 
I0B C5  N4  SING N N 23 
I0B C6  O   SING N N 24 
I0B C6  C7  SING N N 25 
I0B C2  N4  SING Y N 26 
I0B C2  C3  DOUB Y N 27 
I0B N1  C   DOUB Y N 28 
I0B N4  C4  SING Y N 29 
I0B C8  N5  SING N N 30 
I0B N5  C7  SING N N 31 
I0B N5  C18 SING N N 32 
I0B C   C3  SING Y N 33 
I0B C   N   SING N N 34 
I0B C3  N3  SING Y N 35 
I0B C4  N3  DOUB Y N 36 
I0B C18 C19 SING N N 37 
I0B C19 C20 SING N N 38 
I0B BR  C24 SING N N 39 
I0B C23 C24 DOUB Y N 40 
I0B C23 C22 SING Y N 41 
I0B N9  C21 SING N N 42 
I0B N9  C22 SING N N 43 
I0B N8  C21 SING N N 44 
I0B N8  C20 SING N N 45 
I0B C24 C25 SING Y N 46 
I0B C21 N10 DOUB N N 47 
I0B C22 C27 DOUB Y N 48 
I0B C25 C26 DOUB Y N 49 
I0B C27 C26 SING Y N 50 
I0B C7  H1  SING N N 51 
I0B C7  H2  SING N N 52 
I0B C8  H3  SING N N 53 
I0B C8  H4  SING N N 54 
I0B C9  H5  SING N N 55 
I0B C9  H6  SING N N 56 
I0B C1  H7  SING N N 57 
I0B C5  H8  SING N N 58 
I0B C6  H9  SING N N 59 
I0B C4  H10 SING N N 60 
I0B O3  H11 SING N N 61 
I0B C23 H12 SING N N 62 
I0B C25 H13 SING N N 63 
I0B C26 H14 SING N N 64 
I0B C27 H15 SING N N 65 
I0B N9  H16 SING N N 66 
I0B N10 H17 SING N N 67 
I0B N8  H18 SING N N 68 
I0B C20 H19 SING N N 69 
I0B C20 H20 SING N N 70 
I0B C19 H21 SING N N 71 
I0B C19 H22 SING N N 72 
I0B C18 H23 SING N N 73 
I0B C18 H24 SING N N 74 
I0B C28 H26 SING N N 75 
I0B O2  H27 SING N N 76 
I0B C29 H28 SING N N 77 
I0B N   H29 SING N N 78 
I0B N   H30 SING N N 79 
I0B N6  H31 SING N N 80 
I0B N7  H32 SING N N 81 
I0B C11 H33 SING N N 82 
I0B C11 H34 SING N N 83 
I0B C17 H35 SING N N 84 
I0B C16 H36 SING N N 85 
I0B C15 H37 SING N N 86 
I0B C14 H38 SING N N 87 
I0B C13 H39 SING N N 88 
# 
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 
I0B SMILES           ACDLabs              12.01 "Brc1cccc(c1)NC(=N)NCCCN(CCNC(=O)NCc1ccccc1)CC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                                                                                                   
I0B InChI            InChI                1.06  "InChI=1S/C30H38BrN11O4/c31-20-8-4-9-21(14-20)40-29(33)34-10-5-12-41(13-11-35-30(45)36-15-19-6-2-1-3-7-19)16-22-24(43)25(44)28(46-22)42-18-39-23-26(32)37-17-38-27(23)42/h1-4,6-9,14,17-18,22,24-25,28,43-44H,5,10-13,15-16H2,(H2,32,37,38)(H3,33,34,40)(H2,35,36,45)/t22-,24-,25-,28-/m1/s1" 
I0B InChIKey         InChI                1.06  GYMQWYWYFKTHMW-ZYWWQZICSA-N                                                                                                                                                                                                                                                                   
I0B SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CN(CCCNC(=N)Nc4cccc(Br)c4)CCNC(=O)NCc5ccccc5)[C@@H](O)[C@H]3O"                                                                                                                                                                                                 
I0B SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CN(CCCNC(=N)Nc4cccc(Br)c4)CCNC(=O)NCc5ccccc5)[CH](O)[CH]3O"                                                                                                                                                                                                       
I0B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/NCCCN(CCNC(=O)NCc1ccccc1)C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)\Nc5cccc(c5)Br"                                                                                                                                                                                           
I0B SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)NCCN(CCCNC(=N)Nc2cccc(c2)Br)CC3C(C(C(O3)n4cnc5c4ncnc5N)O)O"                                                                                                                                                                                                                 
# 
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 
I0B "SYSTEMATIC NAME" ACDLabs              12.01 "5'-([2-(benzylcarbamamido)ethyl]{3-[N'-(3-bromophenyl)carbamimidamido]propyl}amino)-5'-deoxyadenosine"                                                                            
I0B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[~{N}-(3-bromophenyl)carbamimidoyl]amino]propyl]amino]ethyl]-3-(phenylmethyl)urea" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
I0B "Create component" 2023-05-01 RCSB 
I0B "Initial release"  2024-02-21 RCSB 
# 
