data_VRK
# 
_chem_comp.id                                    VRK 
_chem_comp.name                                  "(1~{S},3~{R})-3-(1-adamantyl)-1-(aminomethyl)-3,4-dihydro-1~{H}-isochromene-5,6-diol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H27 N O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-08-09 
_chem_comp.pdbx_modified_date                    2023-11-10 
_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                        329.433 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VRK 
_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        8JLR 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
VRK C1  C1  C 0 1 N N N N N N 109.575 106.231 138.489 1.725  -3.110 0.453  C1  VRK 1  
VRK O2  O1  O 0 1 N N N N N N 114.490 110.260 139.066 5.288  2.075  0.194  O2  VRK 2  
VRK C4  C2  C 0 1 N N N N N N 110.648 105.359 143.059 -1.795 0.113  -0.279 C4  VRK 3  
VRK C5  C3  C 0 1 N N N N N N 110.375 105.930 144.457 -1.999 0.202  1.235  C5  VRK 4  
VRK C6  C4  C 0 1 N N N N N N 110.349 104.816 145.509 -3.469 0.501  1.535  C6  VRK 5  
VRK C7  C5  C 0 1 N N N N N N 111.703 104.112 145.533 -4.343 -0.618 0.968  C7  VRK 6  
VRK C9  C6  C 0 1 N N N N N N 110.901 102.503 143.807 -4.531 0.623  -1.192 C9  VRK 7  
VRK C10 C7  C 0 1 N N N N N N 109.545 103.205 143.788 -3.657 1.743  -0.625 C10 VRK 8  
VRK C11 C8  C 0 1 N N N N N N 109.256 103.809 145.160 -3.860 1.832  0.889  C11 VRK 9  
VRK C2  C9  C 0 1 N N S N N N 110.015 106.877 139.791 1.327  -1.898 -0.391 C2  VRK 10 
VRK C3  C10 C 0 1 N N R N N N 110.657 106.467 142.006 -0.325 -0.187 -0.579 C3  VRK 11 
VRK C8  C11 C 0 1 N N N N N N 111.987 103.517 144.155 -4.140 -0.707 -0.546 C8  VRK 12 
VRK C12 C12 C 0 1 N N N N N N 109.566 104.319 142.738 -2.187 1.443  -0.925 C12 VRK 13 
VRK C13 C13 C 0 1 N N N N N N 112.000 104.634 143.106 -2.670 -1.007 -0.846 C13 VRK 14 
VRK C14 C14 C 0 1 N N N N N N 111.996 107.175 141.896 0.554  0.923  0.000  C14 VRK 15 
VRK C15 C15 C 0 1 Y N N N N N 112.149 107.921 140.594 2.002  0.504  -0.048 C15 VRK 16 
VRK C16 C16 C 0 1 Y N N N N N 111.205 107.784 139.578 2.362  -0.815 -0.228 C16 VRK 17 
VRK C17 C17 C 0 1 Y N N N N N 111.370 108.484 138.384 3.703  -1.167 -0.263 C17 VRK 18 
VRK C18 C18 C 0 1 Y N N N N N 112.457 109.314 138.193 4.683  -0.204 -0.122 C18 VRK 19 
VRK C19 C19 C 0 1 Y N N N N N 113.399 109.458 139.195 4.327  1.123  0.056  C19 VRK 20 
VRK C20 C20 C 0 1 Y N N N N N 113.248 108.767 140.389 2.983  1.477  0.092  C20 VRK 21 
VRK N1  N1  N 0 1 N N N N N N 108.348 105.455 138.669 0.795  -4.217 0.191  N1  VRK 22 
VRK O1  O2  O 0 1 N N N N N N 110.307 105.867 140.757 0.048  -1.427 0.032  O1  VRK 23 
VRK O3  O3  O 0 1 N N N N N N 114.169 108.898 141.388 2.629  2.779  0.266  O3  VRK 24 
VRK H1  H1  H 0 1 N N N N N N 110.373 105.563 138.133 2.738  -3.417 0.193  H1  VRK 25 
VRK H2  H2  H 0 1 N N N N N N 109.395 107.018 137.742 1.686  -2.846 1.510  H2  VRK 26 
VRK H3  H3  H 0 1 N N N N N N 115.009 110.220 139.861 5.574  2.470  -0.642 H3  VRK 27 
VRK H4  H4  H 0 1 N N N N N N 111.167 106.649 144.713 -1.719 -0.746 1.695  H4  VRK 28 
VRK H5  H5  H 0 1 N N N N N N 109.402 106.443 144.452 -1.375 0.999  1.639  H5  VRK 29 
VRK H6  H6  H 0 1 N N N N N N 110.144 105.252 146.498 -3.614 0.564  2.614  H6  VRK 30 
VRK H7  H7  H 0 1 N N N N N N 111.686 103.308 146.284 -4.064 -1.566 1.428  H7  VRK 31 
VRK H8  H8  H 0 1 N N N N N N 112.490 104.837 145.789 -5.391 -0.405 1.182  H8  VRK 32 
VRK H9  H9  H 0 1 N N N N N N 110.890 101.702 144.561 -5.579 0.837  -0.978 H9  VRK 33 
VRK H10 H10 H 0 1 N N N N N N 111.105 102.071 142.816 -4.386 0.560  -2.271 H10 VRK 34 
VRK H11 H11 H 0 1 N N N N N N 108.759 102.478 143.534 -3.936 2.691  -1.085 H11 VRK 35 
VRK H12 H12 H 0 1 N N N N N N 108.281 104.318 145.139 -4.908 2.045  1.103  H12 VRK 36 
VRK H13 H13 H 0 1 N N N N N N 109.237 103.010 145.916 -3.237 2.629  1.293  H13 VRK 37 
VRK H14 H14 H 0 1 N N N N N N 109.182 107.494 140.159 1.275  -2.190 -1.440 H14 VRK 38 
VRK H15 H15 H 0 1 N N N N N N 109.895 107.210 142.283 -0.177 -0.250 -1.657 H15 VRK 39 
VRK H16 H16 H 0 1 N N N N N N 112.966 103.016 144.167 -4.763 -1.505 -0.950 H16 VRK 40 
VRK H17 H17 H 0 1 N N N N N N 108.584 104.815 142.721 -1.563 2.241  -0.521 H17 VRK 41 
VRK H18 H18 H 0 1 N N N N N N 109.772 103.879 141.751 -2.042 1.380  -2.003 H18 VRK 42 
VRK H19 H19 H 0 1 N N N N N N 112.209 104.198 142.118 -2.525 -1.070 -1.925 H19 VRK 43 
VRK H20 H20 H 0 1 N N N N N N 112.788 105.358 143.361 -2.391 -1.955 -0.386 H20 VRK 44 
VRK H21 H21 H 0 1 N N N N N N 112.798 106.426 141.970 0.421  1.834  -0.584 H21 VRK 45 
VRK H22 H22 H 0 1 N N N N N N 112.086 107.891 142.726 0.267  1.110  1.035  H22 VRK 46 
VRK H23 H23 H 0 1 N N N N N N 110.638 108.376 137.598 3.983  -2.201 -0.401 H23 VRK 47 
VRK H24 H24 H 0 1 N N N N N N 112.571 109.850 137.262 5.725  -0.486 -0.149 H24 VRK 48 
VRK H25 H25 H 0 1 N N N N N N 108.083 105.042 137.797 1.037  -5.030 0.737  H25 VRK 49 
VRK H26 H26 H 0 1 N N N N N N 108.505 104.735 139.344 -0.158 -3.936 0.363  H26 VRK 50 
VRK H28 H28 H 0 1 N N N N N N 113.913 108.360 142.128 2.534  3.274  -0.559 H28 VRK 51 
# 
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 
VRK C18 C17 DOUB Y N 1  
VRK C18 C19 SING Y N 2  
VRK C17 C16 SING Y N 3  
VRK C1  N1  SING N N 4  
VRK C1  C2  SING N N 5  
VRK O2  C19 SING N N 6  
VRK C19 C20 DOUB Y N 7  
VRK C16 C2  SING N N 8  
VRK C16 C15 DOUB Y N 9  
VRK C2  O1  SING N N 10 
VRK C20 C15 SING Y N 11 
VRK C20 O3  SING N N 12 
VRK C15 C14 SING N N 13 
VRK O1  C3  SING N N 14 
VRK C14 C3  SING N N 15 
VRK C3  C4  SING N N 16 
VRK C12 C4  SING N N 17 
VRK C12 C10 SING N N 18 
VRK C4  C13 SING N N 19 
VRK C4  C5  SING N N 20 
VRK C13 C8  SING N N 21 
VRK C10 C9  SING N N 22 
VRK C10 C11 SING N N 23 
VRK C9  C8  SING N N 24 
VRK C8  C7  SING N N 25 
VRK C5  C6  SING N N 26 
VRK C11 C6  SING N N 27 
VRK C6  C7  SING N N 28 
VRK C1  H1  SING N N 29 
VRK C1  H2  SING N N 30 
VRK O2  H3  SING N N 31 
VRK C5  H4  SING N N 32 
VRK C5  H5  SING N N 33 
VRK C6  H6  SING N N 34 
VRK C7  H7  SING N N 35 
VRK C7  H8  SING N N 36 
VRK C9  H9  SING N N 37 
VRK C9  H10 SING N N 38 
VRK C10 H11 SING N N 39 
VRK C11 H12 SING N N 40 
VRK C11 H13 SING N N 41 
VRK C2  H14 SING N N 42 
VRK C3  H15 SING N N 43 
VRK C8  H16 SING N N 44 
VRK C12 H17 SING N N 45 
VRK C12 H18 SING N N 46 
VRK C13 H19 SING N N 47 
VRK C13 H20 SING N N 48 
VRK C14 H21 SING N N 49 
VRK C14 H22 SING N N 50 
VRK C17 H23 SING N N 51 
VRK C18 H24 SING N N 52 
VRK N1  H25 SING N N 53 
VRK N1  H26 SING N N 54 
VRK O3  H28 SING N N 55 
# 
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 
VRK InChI            InChI                1.06  "InChI=1S/C20H27NO3/c21-10-17-14-1-2-16(22)19(23)15(14)6-18(24-17)20-7-11-3-12(8-20)5-13(4-11)9-20/h1-2,11-13,17-18,22-23H,3-10,21H2/t11-,12+,13-,17-,18-,20-/m1/s1" 
VRK InChIKey         InChI                1.06  QLJOSZATCBCBDR-HHDLIXMQSA-N                                                                                                                                          
VRK SMILES_CANONICAL CACTVS               3.385 "NC[C@H]1O[C@H](Cc2c(O)c(O)ccc12)C34CC5CC(CC(C5)C3)C4"                                                                                                               
VRK SMILES           CACTVS               3.385 "NC[CH]1O[CH](Cc2c(O)c(O)ccc12)C34CC5CC(CC(C5)C3)C4"                                                                                                                 
VRK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(c2c1[C@H](O[C@H](C2)C34CC5CC(C3)CC(C5)C4)CN)O)O"                                                                                                             
VRK SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(c2c1C(OC(C2)C34CC5CC(C3)CC(C5)C4)CN)O)O"                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           VRK 
_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~{S},3~{R})-3-(1-adamantyl)-1-(aminomethyl)-3,4-dihydro-1~{H}-isochromene-5,6-diol" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VRK "Create component" 2023-08-09 PDBJ 
VRK "Initial release"  2023-11-15 RCSB 
# 
