data_JVL
# 
_chem_comp.id                                    JVL 
_chem_comp.name                                  "1-[(8R,15S,18S)-15-(4-azanylbutyl)-18-(1H-indol-3-ylmethyl)-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C35 H48 N10 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-05-11 
_chem_comp.pdbx_modified_date                    2023-03-17 
_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                        688.820 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     JVL 
_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        7ZQ1 
_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 
JVL N1  N1  N 0 1 N N N 5.064  -10.745 2.518  7.902  4.364  -0.324 N1  JVL 1  
JVL C7  C1  C 0 1 N N N -1.484 -14.574 3.561  -1.367 2.773  -1.087 C7  JVL 2  
JVL C8  C2  C 0 1 N N S -2.291 -13.530 2.786  -2.632 2.010  -1.382 C8  JVL 3  
JVL N2  N2  N 0 1 N N N 6.483  -10.395 4.481  6.691  2.661  -1.332 N2  JVL 4  
JVL C9  C3  C 0 1 N N N -3.061 -14.168 1.620  -3.829 2.760  -0.794 C9  JVL 5  
JVL O1  O1  O 0 1 N N N 5.769  -16.000 0.137  6.236  -1.599 -0.357 O1  JVL 6  
JVL C1  C4  C 0 1 N N R 3.540  -12.631 4.040  4.508  3.178  0.336  C1  JVL 7  
JVL C5  C5  C 0 1 N N N 0.724  -14.448 6.069  0.953  3.594  0.256  C5  JVL 8  
JVL C6  C6  C 0 1 N N N -0.588 -15.176 5.766  -0.173 4.589  -0.032 C6  JVL 9  
JVL N3  N3  N 0 1 N N N -1.442 -14.394 4.881  -1.428 3.843  -0.246 N3  JVL 10 
JVL C4  C7  C 0 1 N N N 1.530  -14.037 4.836  2.284  4.164  -0.235 C4  JVL 11 
JVL O4  O2  O 0 1 N N N -0.869 -15.476 2.970  -0.312 2.437  -1.584 O4  JVL 12 
JVL C3  C8  C 0 1 N N N 2.771  -13.238 5.213  3.340  4.014  0.862  C3  JVL 13 
JVL O3  O3  O 0 1 N N N -2.142 -10.846 3.601  -2.323 -0.192 -2.831 O3  JVL 14 
JVL C2  C9  C 0 1 N N N 5.460  -10.964 3.853  6.800  3.672  -0.407 C2  JVL 15 
JVL N4  N4  N 0 1 N N N -7.000 -11.003 1.122  -8.764 2.814  -0.453 N4  JVL 16 
JVL N   N5  N 0 1 N N N 4.678  -11.888 4.556  5.746  3.955  0.430  N   JVL 17 
JVL C   C10 C 0 1 N N N 3.952  -13.753 3.080  4.639  1.922  1.161  C   JVL 18 
JVL O   O4  O 0 1 N N N 3.205  -14.104 2.175  4.242  1.886  2.306  O   JVL 19 
JVL C10 C11 C 0 1 N N N -3.806 -13.132 0.778  -5.124 2.052  -1.199 C10 JVL 20 
JVL C11 C12 C 0 1 N N N -5.034 -12.531 1.462  -6.321 2.802  -0.612 C11 JVL 21 
JVL C12 C13 C 0 1 N N N -5.696 -11.482 0.588  -7.615 2.094  -1.017 C12 JVL 22 
JVL C13 C14 C 0 1 N N N -1.347 -11.267 2.751  -2.404 -0.380 -1.635 C13 JVL 23 
JVL C14 C15 C 0 1 N N S -0.234 -10.377 2.197  -2.349 -1.776 -1.071 C14 JVL 24 
JVL C15 C16 C 0 1 N N N -0.627 -8.899  2.121  -1.860 -1.727 0.377  C15 JVL 25 
JVL C16 C17 C 0 1 Y N N -1.354 -8.600  0.846  -2.833 -0.933 1.210  C16 JVL 26 
JVL C17 C18 C 0 1 Y N N -2.695 -8.698  0.618  -2.551 0.144  1.959  C17 JVL 27 
JVL C18 C19 C 0 1 Y N N -1.808 -8.046  -1.325 -4.757 -0.195 2.220  C18 JVL 28 
JVL C19 C20 C 0 1 Y N N -0.763 -8.180  -0.389 -4.269 -1.187 1.350  C19 JVL 29 
JVL C20 C21 C 0 1 Y N N 0.534  -7.855  -0.789 -5.141 -2.144 0.826  C20 JVL 30 
JVL C21 C22 C 0 1 Y N N 0.760  -7.396  -2.081 -6.465 -2.111 1.162  C21 JVL 31 
JVL C22 C23 C 0 1 Y N N -0.285 -7.280  -2.992 -6.951 -1.134 2.020  C22 JVL 32 
JVL C23 C24 C 0 1 Y N N -1.583 -7.611  -2.627 -6.109 -0.181 2.548  C23 JVL 33 
JVL C24 C25 C 0 1 N N N 1.564  -10.975 0.690  -0.774 -3.590 -1.224 C24 JVL 34 
JVL C25 C26 C 0 1 N N N 1.960  -11.385 -0.716 0.199  -4.453 -1.989 C25 JVL 35 
JVL C26 C27 C 0 1 Y N N 3.438  -11.275 -0.996 1.305  -4.885 -1.060 C26 JVL 36 
JVL C27 C28 C 0 1 Y N N 4.296  -12.312 -0.644 2.495  -4.186 -1.025 C27 JVL 37 
JVL C28 C29 C 0 1 Y N N 5.649  -12.277 -0.962 3.503  -4.578 -0.162 C28 JVL 38 
JVL C29 C30 C 0 1 N N N 6.546  -13.429 -0.580 4.802  -3.816 -0.120 C29 JVL 39 
JVL C30 C31 C 0 1 N N N 5.869  -15.140 1.017  5.443  -1.589 0.560  C30 JVL 40 
JVL C31 C32 C 0 1 N N N 5.553  -15.460 2.468  5.317  -0.376 1.448  C31 JVL 41 
JVL C32 C33 C 0 1 Y N N 6.143  -11.173 -1.640 3.319  -5.675 0.660  C32 JVL 42 
JVL C33 C34 C 0 1 Y N N 5.305  -10.131 -1.993 2.131  -6.381 0.616  C33 JVL 43 
JVL C34 C35 C 0 1 Y N N 3.962  -10.176 -1.663 1.123  -5.984 -0.243 C34 JVL 44 
JVL N5  N6  N 0 1 N N N -1.358 -12.526 2.297  -2.545 0.668  -0.775 N5  JVL 45 
JVL N6  N7  N 0 1 Y N N -2.979 -8.371  -0.680 -3.687 0.597  2.572  N6  JVL 46 
JVL N7  N8  N 0 1 N N N 0.256  -10.868 0.913  -1.414 -2.582 -1.888 N7  JVL 47 
JVL N8  N9  N 0 1 N N N 6.280  -13.899 0.774  4.655  -2.672 0.802  N8  JVL 48 
JVL N9  N10 N 0 1 N N N 5.141  -14.326 3.279  5.216  0.824  0.585  N9  JVL 49 
JVL O2  O5  O 0 1 N N N 2.397  -10.731 1.565  -0.983 -3.786 -0.045 O2  JVL 50 
JVL H1  H1  H 0 1 N N N 4.267  -11.295 2.269  7.979  5.077  0.329  H1  JVL 51 
JVL H2  H2  H 0 1 N N N -3.014 -13.063 3.471  -2.757 1.914  -2.460 H2  JVL 52 
JVL H3  H3  H 0 1 N N N 6.679  -10.630 5.433  7.435  2.462  -1.922 H3  JVL 53 
JVL H4  H4  H 0 1 N N N 7.057  -9.732  4.002  5.871  2.146  -1.394 H4  JVL 54 
JVL H5  H5  H 0 1 N N N -3.791 -14.883 2.028  -3.749 2.776  0.293  H5  JVL 55 
JVL H6  H6  H 0 1 N N N -2.347 -14.701 0.975  -3.840 3.782  -1.173 H6  JVL 56 
JVL H7  H7  H 0 1 N N N 2.869  -11.945 3.503  4.324  2.911  -0.705 H7  JVL 57 
JVL H8  H8  H 0 1 N N N 1.351  -15.113 6.681  1.010  3.412  1.329  H8  JVL 58 
JVL H9  H9  H 0 1 N N N 0.487  -13.539 6.641  0.749  2.656  -0.261 H9  JVL 59 
JVL H10 H10 H 0 1 N N N -1.122 -15.357 6.710  -0.289 5.264  0.816  H10 JVL 60 
JVL H11 H11 H 0 1 N N N -0.360 -16.138 5.284  0.068  5.163  -0.927 H11 JVL 61 
JVL H12 H12 H 0 1 N N N -2.025 -13.688 5.284  -2.255 4.101  0.190  H12 JVL 62 
JVL H13 H13 H 0 1 N N N 0.894  -13.420 4.184  2.606  3.622  -1.125 H13 JVL 63 
JVL H14 H14 H 0 1 N N N 1.840  -14.943 4.295  2.160  5.220  -0.478 H14 JVL 64 
JVL H15 H15 H 0 1 N N N 3.454  -13.908 5.757  2.898  3.518  1.726  H15 JVL 65 
JVL H16 H16 H 0 1 N N N 2.458  -12.417 5.875  3.702  5.000  1.155  H16 JVL 66 
JVL H17 H17 H 0 1 N N N -7.382 -10.317 0.503  -8.760 3.782  -0.738 H17 JVL 67 
JVL H18 H18 H 0 1 N N N -7.633 -11.774 1.197  -9.632 2.366  -0.707 H18 JVL 68 
JVL H20 H20 H 0 1 N N N 4.928  -12.054 5.510  5.823  4.668  1.082  H20 JVL 69 
JVL H21 H21 H 0 1 N N N -4.133 -13.616 -0.154 -5.203 2.035  -2.286 H21 JVL 70 
JVL H22 H22 H 0 1 N N N -3.109 -12.315 0.541  -5.113 1.030  -0.820 H22 JVL 71 
JVL H23 H23 H 0 1 N N N -4.724 -12.064 2.409  -6.241 2.819  0.475  H23 JVL 72 
JVL H24 H24 H 0 1 N N N -5.757 -13.333 1.668  -6.331 3.824  -0.991 H24 JVL 73 
JVL H25 H25 H 0 1 N N N -5.866 -11.915 -0.409 -7.605 1.072  -0.638 H25 JVL 74 
JVL H26 H26 H 0 1 N N N -5.017 -10.621 0.502  -7.695 2.078  -2.104 H26 JVL 75 
JVL H27 H27 H 0 1 N N N 0.600  -10.441 2.911  -3.343 -2.224 -1.106 H27 JVL 76 
JVL H28 H28 H 0 1 N N N 0.283  -8.282  2.169  -1.786 -2.740 0.771  H28 JVL 77 
JVL H29 H29 H 0 1 N N N -1.280 -8.656  2.972  -0.879 -1.251 0.413  H29 JVL 78 
JVL H30 H30 H 0 1 N N N -3.427 -8.991  1.356  -1.571 0.587  2.064  H30 JVL 79 
JVL H31 H31 H 0 1 N N N 1.358  -7.960  -0.098 -4.770 -2.907 0.157  H31 JVL 80 
JVL H32 H32 H 0 1 N N N 1.761  -7.125  -2.382 -7.139 -2.852 0.756  H32 JVL 81 
JVL H33 H33 H 0 1 N N N -0.084 -6.929  -3.993 -8.000 -1.121 2.275  H33 JVL 82 
JVL H34 H34 H 0 1 N N N -2.395 -7.533  -3.334 -6.496 0.575  3.215  H34 JVL 83 
JVL H35 H35 H 0 1 N N N 1.425  -10.740 -1.428 -0.319 -5.331 -2.375 H35 JVL 84 
JVL H36 H36 H 0 1 N N N 1.656  -12.431 -0.869 0.618  -3.883 -2.818 H36 JVL 85 
JVL H37 H37 H 0 1 N N N 3.902  -13.165 -0.111 2.640  -3.332 -1.671 H37 JVL 86 
JVL H38 H38 H 0 1 N N N 6.379  -14.258 -1.283 5.598  -4.471 0.234  H38 JVL 87 
JVL H39 H39 H 0 1 N N N 7.594  -13.100 -0.643 5.044  -3.452 -1.118 H39 JVL 88 
JVL H40 H40 H 0 1 N N N 4.741  -16.202 2.483  4.422  -0.462 2.063  H40 JVL 89 
JVL H41 H41 H 0 1 N N N 6.455  -15.894 2.924  6.196  -0.295 2.087  H41 JVL 90 
JVL H42 H42 H 0 1 N N N 7.192  -11.126 -1.895 4.103  -5.980 1.336  H42 JVL 91 
JVL H43 H43 H 0 1 N N N 5.700  -9.280  -2.528 1.991  -7.242 1.253  H43 JVL 92 
JVL H44 H44 H 0 1 N N N 3.317  -9.351  -1.926 0.194  -6.533 -0.274 H44 JVL 93 
JVL H45 H45 H 0 1 N N N -0.698 -12.787 1.593  -2.586 0.538  0.185  H45 JVL 94 
JVL H46 H46 H 0 1 N N N -3.890 -8.369  -1.093 -3.733 1.363  3.166  H46 JVL 95 
JVL H47 H47 H 0 1 N N N -0.394 -11.125 0.198  -1.265 -2.405 -2.830 H47 JVL 96 
JVL H48 H48 H 0 1 N N N 6.410  -13.271 1.541  4.028  -2.692 1.542  H48 JVL 97 
JVL H49 H49 H 0 1 N N N 5.751  -13.974 3.989  5.539  0.831  -0.330 H49 JVL 98 
# 
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 
JVL C22 C23 DOUB Y N 1   
JVL C22 C21 SING Y N 2   
JVL C23 C18 SING Y N 3   
JVL C21 C20 DOUB Y N 4   
JVL C33 C34 DOUB Y N 5   
JVL C33 C32 SING Y N 6   
JVL C34 C26 SING Y N 7   
JVL C32 C28 DOUB Y N 8   
JVL C18 N6  SING Y N 9   
JVL C18 C19 DOUB Y N 10  
JVL C26 C25 SING N N 11  
JVL C26 C27 DOUB Y N 12  
JVL C28 C27 SING Y N 13  
JVL C28 C29 SING N N 14  
JVL C20 C19 SING Y N 15  
JVL C25 C24 SING N N 16  
JVL N6  C17 SING Y N 17  
JVL C29 N8  SING N N 18  
JVL C19 C16 SING Y N 19  
JVL O1  C30 DOUB N N 20  
JVL C12 N4  SING N N 21  
JVL C12 C11 SING N N 22  
JVL C17 C16 DOUB Y N 23  
JVL C24 N7  SING N N 24  
JVL C24 O2  DOUB N N 25  
JVL N8  C30 SING N N 26  
JVL C10 C11 SING N N 27  
JVL C10 C9  SING N N 28  
JVL C16 C15 SING N N 29  
JVL N7  C14 SING N N 30  
JVL C30 C31 SING N N 31  
JVL C9  C8  SING N N 32  
JVL C15 C14 SING N N 33  
JVL O   C   DOUB N N 34  
JVL C14 C13 SING N N 35  
JVL N5  C13 SING N N 36  
JVL N5  C8  SING N N 37  
JVL C31 N9  SING N N 38  
JVL N1  C2  DOUB N N 39  
JVL C13 O3  DOUB N N 40  
JVL C8  C7  SING N N 41  
JVL O4  C7  DOUB N N 42  
JVL C   N9  SING N N 43  
JVL C   C1  SING N N 44  
JVL C7  N3  SING N N 45  
JVL C2  N2  SING N N 46  
JVL C2  N   SING N N 47  
JVL C1  N   SING N N 48  
JVL C1  C3  SING N N 49  
JVL C4  C3  SING N N 50  
JVL C4  C5  SING N N 51  
JVL N3  C6  SING N N 52  
JVL C6  C5  SING N N 53  
JVL N1  H1  SING N N 54  
JVL C8  H2  SING N N 55  
JVL N2  H3  SING N N 56  
JVL N2  H4  SING N N 57  
JVL C9  H5  SING N N 58  
JVL C9  H6  SING N N 59  
JVL C1  H7  SING N N 60  
JVL C5  H8  SING N N 61  
JVL C5  H9  SING N N 62  
JVL C6  H10 SING N N 63  
JVL C6  H11 SING N N 64  
JVL N3  H12 SING N N 65  
JVL C4  H13 SING N N 66  
JVL C4  H14 SING N N 67  
JVL C3  H15 SING N N 68  
JVL C3  H16 SING N N 69  
JVL N4  H17 SING N N 70  
JVL N4  H18 SING N N 71  
JVL N   H20 SING N N 72  
JVL C10 H21 SING N N 73  
JVL C10 H22 SING N N 74  
JVL C11 H23 SING N N 75  
JVL C11 H24 SING N N 76  
JVL C12 H25 SING N N 77  
JVL C12 H26 SING N N 78  
JVL C14 H27 SING N N 79  
JVL C15 H28 SING N N 80  
JVL C15 H29 SING N N 81  
JVL C17 H30 SING N N 82  
JVL C20 H31 SING N N 83  
JVL C21 H32 SING N N 84  
JVL C22 H33 SING N N 85  
JVL C23 H34 SING N N 86  
JVL C25 H35 SING N N 87  
JVL C25 H36 SING N N 88  
JVL C27 H37 SING N N 89  
JVL C29 H38 SING N N 90  
JVL C29 H39 SING N N 91  
JVL C31 H40 SING N N 92  
JVL C31 H41 SING N N 93  
JVL C32 H42 SING N N 94  
JVL C33 H43 SING N N 95  
JVL C34 H44 SING N N 96  
JVL N5  H45 SING N N 97  
JVL N6  H46 SING N N 98  
JVL N7  H47 SING N N 99  
JVL N8  H48 SING N N 100 
JVL N9  H49 SING N N 101 
# 
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 
JVL InChI            InChI                1.06  "InChI=1S/C35H48N10O5/c36-14-5-3-12-27-32(48)39-15-6-4-13-28(45-35(37)38)33(49)42-21-31(47)41-19-23-9-7-8-22(16-23)17-30(46)43-29(34(50)44-27)18-24-20-40-26-11-2-1-10-25(24)26/h1-2,7-11,16,20,27-29,40H,3-6,12-15,17-19,21,36H2,(H,39,48)(H,41,47)(H,42,49)(H,43,46)(H,44,50)(H4,37,38,45)/t27-,28+,29-/m0/s1" 
JVL InChIKey         InChI                1.06  NAEFAWNAIOVILE-NHKHRBQYSA-N                                                                                                                                                                                                                                                                                      
JVL SMILES_CANONICAL CACTVS               3.385 "NCCCC[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)Cc4cccc(CNC(=O)CNC(=O)[C@@H](CCCCNC1=O)NC(N)=N)c4"                                                                                                                                                                                                              
JVL SMILES           CACTVS               3.385 "NCCCC[CH]1NC(=O)[CH](Cc2c[nH]c3ccccc23)NC(=O)Cc4cccc(CNC(=O)CNC(=O)[CH](CCCCNC1=O)NC(N)=N)c4"                                                                                                                                                                                                                   
JVL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\N[C@@H]1CCCCNC(=O)[C@@H](NC(=O)[C@@H](NC(=O)Cc2cccc(c2)CNC(=O)CNC1=O)Cc3c[nH]c4c3cccc4)CCCCN"                                                                                                                                                                                                       
JVL SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)c(c[nH]2)CC3C(=O)NC(C(=O)NCCCCC(C(=O)NCC(=O)NCc4cccc(c4)CC(=O)N3)NC(=N)N)CCCCN"                                                                                                                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           JVL 
_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        "1-[(8~{R},15~{S},18~{S})-15-(4-azanylbutyl)-18-(1~{H}-indol-3-ylmethyl)-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
JVL "Create component"  2022-05-11 PDBE 
JVL "Modify descriptor" 2022-08-22 RCSB 
JVL "Initial release"   2023-03-22 RCSB 
# 
