data_GV3
# 
_chem_comp.id                                    GV3 
_chem_comp.name                                  "5'-S-[3-(N'-phenylcarbamimidamido)propyl]-5'-thioadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H26 N8 O3 S" 
_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                    2024-04-19 
_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                        458.537 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     GV3 
_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        8SHB 
_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 
GV3 N1  N1  N 0 1 Y N N N N N 27.158 0.971  -3.981 -7.970 2.269  0.223  N1  GV3 1  
GV3 C7  C1  C 0 1 N N S N N N 20.735 -0.797 -0.488 -2.953 -2.973 0.171  C7  GV3 2  
GV3 C8  C2  C 0 1 N N S N N N 20.976 -1.963 -1.456 -1.829 -2.032 0.646  C8  GV3 3  
GV3 N2  N2  N 0 1 Y N N N N N 23.374 0.261  -2.840 -4.366 0.438  -0.005 N2  GV3 4  
GV3 C9  C3  C 0 1 N N N N N N 19.790 -2.354 -2.315 -0.584 -2.229 -0.221 C9  GV3 5  
GV3 O1  O1  O 0 1 N N N N N N 21.014 -1.252 0.829  -3.338 -3.862 1.222  O1  GV3 6  
GV3 C1  C4  C 0 1 Y N N N N N 24.819 1.142  -4.244 -5.775 2.049  -0.586 C1  GV3 7  
GV3 C5  C5  C 0 1 N N R N N N 22.714 -0.486 -1.782 -3.757 -0.745 0.609  C5  GV3 8  
GV3 C6  C6  C 0 1 N N R N N N 21.677 0.310  -0.995 -4.120 -2.023 -0.190 C6  GV3 9  
GV3 N3  N3  N 0 1 Y N N N N N 23.561 1.451  -4.737 -4.601 2.224  -1.238 N3  GV3 10 
GV3 C4  C7  C 0 1 Y N N N N N 22.745 0.915  -3.866 -3.772 1.279  -0.898 C4  GV3 11 
GV3 C3  C8  C 0 1 Y N N N N N 26.911 0.284  -2.864 -7.795 1.185  0.956  C3  GV3 12 
GV3 C2  C9  C 0 1 Y N N N N N 24.720 0.411  -3.073 -5.639 0.901  0.212  C2  GV3 13 
GV3 N4  N4  N 0 1 N N N N N N 16.263 -3.990 -5.666 5.723  -0.361 -0.834 N4  GV3 14 
GV3 O2  O2  O 0 1 N N N N N N 22.291 0.997  0.089  -5.370 -2.559 0.248  O2  GV3 15 
GV3 O   O3  O 0 1 N N N N N N 21.998 -1.550 -2.379 -2.313 -0.685 0.512  O   GV3 16 
GV3 N   N5  N 0 1 Y N N N N N 25.734 -0.045 -2.327 -6.665 0.509  0.960  N   GV3 17 
GV3 C   C10 C 0 1 Y N N N N N 26.114 1.431  -4.708 -7.001 2.736  -0.557 C   GV3 18 
GV3 N7  N6  N 0 1 N N N N N N 26.367 2.128  -5.829 -7.194 3.873  -1.322 N7  GV3 19 
GV3 S   S1  S 0 1 N N N N N N 18.991 -1.007 -3.224 0.777  -1.227 0.437  S   GV3 20 
GV3 C10 C11 C 0 1 N N N N N N 17.600 -1.952 -3.912 2.140  -1.588 -0.705 C10 GV3 21 
GV3 C11 C12 C 0 1 N N N N N N 17.456 -1.759 -5.391 3.383  -0.805 -0.279 C11 GV3 22 
GV3 C12 C13 C 0 1 N N N N N N 17.086 -2.947 -6.269 4.532  -1.110 -1.242 C12 GV3 23 
GV3 C13 C14 C 0 1 N N N N N N 15.003 -3.850 -5.218 6.889  -0.476 -1.554 C13 GV3 24 
GV3 N6  N7  N 0 1 N N N N N N 14.310 -4.866 -4.811 6.934  -1.252 -2.600 N6  GV3 25 
GV3 N5  N8  N 0 1 N N N N N N 14.398 -2.608 -5.287 8.007  0.229  -1.171 N5  GV3 26 
GV3 C14 C15 C 0 1 Y N N N N N 13.121 -2.293 -4.778 7.998  0.963  0.019  C14 GV3 27 
GV3 C19 C16 C 0 1 Y N N N N N 12.112 -1.724 -5.544 7.404  0.435  1.158  C19 GV3 28 
GV3 C18 C17 C 0 1 Y N N N N N 10.889 -1.421 -4.966 7.396  1.163  2.332  C18 GV3 29 
GV3 C17 C18 C 0 1 Y N N N N N 10.665 -1.674 -3.631 7.978  2.417  2.374  C17 GV3 30 
GV3 C16 C19 C 0 1 Y N N N N N 11.662 -2.246 -2.866 8.570  2.945  1.241  C16 GV3 31 
GV3 C15 C20 C 0 1 Y N N N N N 12.887 -2.562 -3.434 8.586  2.220  0.066  C15 GV3 32 
GV3 H1  H1  H 0 1 N N N N N N 19.692 -0.458 -0.576 -2.634 -3.536 -0.706 H1  GV3 33 
GV3 H2  H2  H 0 1 N N N N N N 21.312 -2.840 -0.883 -1.589 -2.237 1.689  H2  GV3 34 
GV3 H3  H3  H 0 1 N N N N N N 19.035 -2.811 -1.659 -0.298 -3.281 -0.212 H3  GV3 35 
GV3 H4  H4  H 0 1 N N N N N N 20.136 -3.097 -3.049 -0.801 -1.920 -1.244 H4  GV3 36 
GV3 H5  H5  H 0 1 N N N N N N 20.871 -0.544 1.446  -4.062 -4.458 0.987  H5  GV3 37 
GV3 H6  H6  H 0 1 N N N N N N 23.465 -0.878 -1.081 -4.070 -0.840 1.648  H6  GV3 38 
GV3 H7  H7  H 0 1 N N N N N N 21.133 0.996  -1.661 -4.139 -1.820 -1.260 H7  GV3 39 
GV3 H8  H8  H 0 1 N N N N N N 21.670 0.982  -3.949 -2.763 1.177  -1.269 H8  GV3 40 
GV3 H9  H9  H 0 1 N N N N N N 27.782 -0.051 -2.320 -8.609 0.839  1.576  H9  GV3 41 
GV3 H10 H10 H 0 1 N N N N N N 16.676 -4.896 -5.577 5.690  0.217  -0.055 H10 GV3 42 
GV3 H11 H11 H 0 1 N N N N N N 21.633 1.487  0.568  -5.641 -3.360 -0.222 H11 GV3 43 
GV3 H12 H12 H 0 1 N N N N N N 27.356 2.203  -5.960 -6.478 4.204  -1.887 H12 GV3 44 
GV3 H13 H13 H 0 1 N N N N N N 25.962 1.657  -6.613 -8.044 4.339  -1.293 H13 GV3 45 
GV3 H14 H14 H 0 1 N N N N N N 16.672 -1.624 -3.421 2.358  -2.656 -0.683 H14 GV3 46 
GV3 H15 H15 H 0 1 N N N N N N 17.764 -3.021 -3.709 1.855  -1.295 -1.715 H15 GV3 47 
GV3 H16 H16 H 0 1 N N N N N N 18.419 -1.377 -5.759 3.165  0.263  -0.300 H16 GV3 48 
GV3 H17 H17 H 0 1 N N N N N N 16.678 -0.996 -5.540 3.668  -1.098 0.732  H17 GV3 49 
GV3 H18 H18 H 0 1 N N N N N N 18.023 -3.416 -6.603 4.247  -0.817 -2.252 H18 GV3 50 
GV3 H19 H19 H 0 1 N N N N N N 16.540 -2.557 -7.141 4.751  -2.178 -1.220 H19 GV3 51 
GV3 H20 H20 H 0 1 N N N N N N 13.370 -4.612 -4.584 7.731  -1.276 -3.153 H20 GV3 52 
GV3 H21 H21 H 0 1 N N N N N N 14.908 -1.873 -5.734 8.803  0.215  -1.727 H21 GV3 53 
GV3 H22 H22 H 0 1 N N N N N N 12.280 -1.517 -6.591 6.949  -0.544 1.126  H22 GV3 54 
GV3 H23 H23 H 0 1 N N N N N N 10.106 -0.983 -5.567 6.935  0.753  3.218  H23 GV3 55 
GV3 H24 H24 H 0 1 N N N N N N 9.713  -1.426 -3.184 7.970  2.984  3.293  H24 GV3 56 
GV3 H25 H25 H 0 1 N N N N N N 11.487 -2.448 -1.820 9.024  3.925  1.277  H25 GV3 57 
GV3 H26 H26 H 0 1 N N N N N N 13.660 -3.017 -2.832 9.053  2.632  -0.817 H26 GV3 58 
# 
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 
GV3 C12 N4  SING N N 1  
GV3 C12 C11 SING N N 2  
GV3 N7  C   SING N N 3  
GV3 N4  C13 SING N N 4  
GV3 C19 C18 DOUB Y N 5  
GV3 C19 C14 SING Y N 6  
GV3 C11 C10 SING N N 7  
GV3 N5  C13 SING N N 8  
GV3 N5  C14 SING N N 9  
GV3 C13 N6  DOUB N N 10 
GV3 C18 C17 SING Y N 11 
GV3 C14 C15 DOUB Y N 12 
GV3 N3  C1  SING Y N 13 
GV3 N3  C4  DOUB Y N 14 
GV3 C   C1  DOUB Y N 15 
GV3 C   N1  SING Y N 16 
GV3 C1  C2  SING Y N 17 
GV3 N1  C3  DOUB Y N 18 
GV3 C10 S   SING N N 19 
GV3 C4  N2  SING Y N 20 
GV3 C17 C16 DOUB Y N 21 
GV3 C15 C16 SING Y N 22 
GV3 S   C9  SING N N 23 
GV3 C2  N2  SING Y N 24 
GV3 C2  N   DOUB Y N 25 
GV3 C3  N   SING Y N 26 
GV3 N2  C5  SING N N 27 
GV3 O   C5  SING N N 28 
GV3 O   C8  SING N N 29 
GV3 C9  C8  SING N N 30 
GV3 C5  C6  SING N N 31 
GV3 C8  C7  SING N N 32 
GV3 C6  C7  SING N N 33 
GV3 C6  O2  SING N N 34 
GV3 C7  O1  SING N N 35 
GV3 C7  H1  SING N N 36 
GV3 C8  H2  SING N N 37 
GV3 C9  H3  SING N N 38 
GV3 C9  H4  SING N N 39 
GV3 O1  H5  SING N N 40 
GV3 C5  H6  SING N N 41 
GV3 C6  H7  SING N N 42 
GV3 C4  H8  SING N N 43 
GV3 C3  H9  SING N N 44 
GV3 N4  H10 SING N N 45 
GV3 O2  H11 SING N N 46 
GV3 N7  H12 SING N N 47 
GV3 N7  H13 SING N N 48 
GV3 C10 H14 SING N N 49 
GV3 C10 H15 SING N N 50 
GV3 C11 H16 SING N N 51 
GV3 C11 H17 SING N N 52 
GV3 C12 H18 SING N N 53 
GV3 C12 H19 SING N N 54 
GV3 N6  H20 SING N N 55 
GV3 N5  H21 SING N N 56 
GV3 C19 H22 SING N N 57 
GV3 C18 H23 SING N N 58 
GV3 C17 H24 SING N N 59 
GV3 C16 H25 SING N N 60 
GV3 C15 H26 SING N N 61 
# 
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 
GV3 SMILES           ACDLabs              12.01 "N=C(Nc1ccccc1)NCCCSCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                                                    
GV3 InChI            InChI                1.06  "InChI=1S/C20H26N8O3S/c21-17-14-18(25-10-24-17)28(11-26-14)19-16(30)15(29)13(31-19)9-32-8-4-7-23-20(22)27-12-5-2-1-3-6-12/h1-3,5-6,10-11,13,15-16,19,29-30H,4,7-9H2,(H2,21,24,25)(H3,22,23,27)/t13-,15-,16-,19-/m1/s1" 
GV3 InChIKey         InChI                1.06  PAOYFGCZLHEXFB-NVQRDWNXSA-N                                                                                                                                                                                            
GV3 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCCNC(=N)Nc4ccccc4)[C@@H](O)[C@H]3O"                                                                                                                                                  
GV3 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCCNC(=N)Nc4ccccc4)[CH](O)[CH]3O"                                                                                                                                                        
GV3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\NCCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)/Nc4ccccc4"                                                                                                                                            
GV3 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)NC(=N)NCCCSCC2C(C(C(O2)n3cnc4c3ncnc4N)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 
GV3 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-S-[3-(N'-phenylcarbamimidamido)propyl]-5'-thioadenosine"                                                                    
GV3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]propyl]-3-phenyl-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 
GV3 "Create component" 2023-05-01 RCSB 
GV3 "Initial release"  2024-04-24 RCSB 
# 
