data_YWI
# 
_chem_comp.id                                    YWI 
_chem_comp.name                                  "5'-O-[(R)-(3-{[(1M)-3'-bromo[1,1'-biphenyl]-3-carbonyl]amino}propoxy)(hydroxy)phosphoryl]-2'-deoxyguanosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H28 Br N6 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-01 
_chem_comp.pdbx_modified_date                    2023-06-02 
_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                        663.414 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YWI 
_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        8GB1 
_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.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 
YWI C4     C1  C  0 1 Y N N -4.329  5.719  17.892 9.251   1.563  0.241  C4     YWI 1  
YWI C14    C2  C  0 1 Y N N -11.481 8.751  12.198 -5.462  0.735  -0.843 C14    YWI 2  
YWI C5     C3  C  0 1 Y N N -3.267  5.012  17.357 9.460   2.070  1.529  C5     YWI 3  
YWI C6     C4  C  0 1 N N N -2.568  5.559  16.240 10.422  3.092  1.706  C6     YWI 4  
YWI C11    C5  C  0 1 N N N -12.775 8.163  16.098 -0.944  -1.082 -0.482 C11    YWI 5  
YWI C8     C6  C  0 1 Y N N -4.004  3.825  18.989 7.929   0.544  1.680  C8     YWI 6  
YWI C10    C7  C  0 1 N N N -11.446 7.827  16.757 -0.022  -2.145 0.119  C10    YWI 7  
YWI C12    C8  C  0 1 N N N -13.250 7.226  14.983 -2.374  -1.308 0.014  C12    YWI 8  
YWI C13    C9  C  0 1 N N N -12.509 7.766  12.682 -4.571  -0.292 -0.263 C13    YWI 9  
YWI N1     N1  N  0 1 N N N -3.104  6.787  15.865 11.097  3.533  0.622  N1     YWI 10 
YWI N2     N2  N  0 1 N N N -4.544  8.587  15.949 11.550  3.467  -1.691 N2     YWI 11 
YWI N3     N3  N  0 1 N N N -4.828  6.902  17.505 9.962   2.046  -0.785 N3     YWI 12 
YWI "C1'"  C10 C  0 1 N N R -5.928  5.296  19.896 7.727   -0.210 -0.721 "C1'"  YWI 13 
YWI C15    C11 C  0 1 Y N N -10.511 9.107  13.135 -4.944  1.708  -1.701 C15    YWI 14 
YWI C16    C12 C  0 1 Y N N -9.543  10.037 12.822 -5.776  2.667  -2.243 C16    YWI 15 
YWI C17    C13 C  0 1 Y N N -9.531  10.629 11.573 -7.123  2.671  -1.941 C17    YWI 16 
YWI C18    C14 C  0 1 Y N N -10.458 10.271 10.594 -7.653  1.705  -1.086 C18    YWI 17 
YWI C19    C15 C  0 1 Y N N -10.425 10.932 9.260  -9.103  1.708  -0.768 C19    YWI 18 
YWI C2     C16 C  0 1 N N N -4.170  7.408  16.467 10.849  2.999  -0.608 C2     YWI 19 
YWI "C2'"  C17 C  0 1 N N N -6.139  6.749  20.286 8.622   -1.441 -0.964 "C2'"  YWI 20 
YWI C20    C18 C  0 1 Y N N -9.751  12.140 9.088  -9.936  2.683  -1.314 C20    YWI 21 
YWI C21    C19 C  0 1 Y N N -9.683  12.749 7.847  -11.283 2.681  -1.015 C21    YWI 22 
YWI C22    C20 C  0 1 Y N N -10.235 12.133 6.739  -11.808 1.715  -0.176 C22    YWI 23 
YWI C23    C21 C  0 1 Y N N -10.850 10.909 6.898  -10.985 0.744  0.369  C23    YWI 24 
YWI C24    C22 C  0 1 Y N N -10.944 10.297 8.133  -9.636  0.734  0.072  C24    YWI 25 
YWI C25    C23 C  0 1 Y N N -11.446 9.350  10.939 -6.823  0.732  -0.540 C25    YWI 26 
YWI "C3'"  C24 C  0 1 N N S -7.377  7.169  19.496 7.675   -2.646 -0.748 "C3'"  YWI 27 
YWI "C4'"  C25 C  0 1 N N R -8.146  5.856  19.329 6.279   -2.003 -0.947 "C4'"  YWI 28 
YWI "C5'"  C26 C  0 1 N N N -9.137  5.843  18.185 5.204   -2.811 -0.218 "C5'"  YWI 29 
YWI N5     N4  N  0 1 N N N -12.267 7.298  13.912 -3.256  -0.290 -0.561 N5     YWI 30 
YWI N7     N5  N  0 1 Y N N -3.074  3.830  18.046 8.622   1.408  2.363  N7     YWI 31 
YWI N9     N6  N  0 1 Y N N -4.806  4.963  18.964 8.283   0.604  0.363  N9     YWI 32 
YWI O1B    O1  O  0 1 N N N -8.696  8.736  17.546 2.324   -4.357 -0.485 O1B    YWI 33 
YWI O1G    O2  O  0 1 N N N -13.622 7.696  12.152 -5.023  -1.138 0.483  O1G    YWI 34 
YWI O2     O3  O  0 1 N N N -8.532  6.300  16.976 3.916   -2.266 -0.512 O2     YWI 35 
YWI "O3'"  O4  O  0 1 N N N -8.095  8.159  20.229 7.912   -3.662 -1.724 "O3'"  YWI 36 
YWI O3A    O5  O  0 1 N N N -10.358 7.836  15.899 1.314   -1.934 -0.345 O3A    YWI 37 
YWI O3B    O6  O  0 1 N N N -7.979  7.931  15.219 2.639   -2.919 1.565  O3B    YWI 38 
YWI "O4'"  O7  O  0 1 N N N -7.118  4.853  19.219 6.424   -0.694 -0.355 "O4'"  YWI 39 
YWI O6     O8  O  0 1 N N N -1.606  5.079  15.621 10.636  3.564  2.810  O6     YWI 40 
YWI PB     P1  P  0 1 N N N -8.833  7.774  16.421 2.550   -2.870 0.088  PB     YWI 41 
YWI BR1    BR1 BR 0 0 N N N -11.586 10.038 5.378  -11.710 -0.572 1.516  BR1    YWI 42 
YWI HOG2   H1  H  0 0 N N N -12.688 9.172  15.670 -0.605  -0.092 -0.176 HOG2   YWI 43 
YWI "HO2'" H2  H  0 0 N N N -13.545 8.163  16.883 -0.921  -1.153 -1.569 "HO2'" YWI 44 
YWI H8     H3  H  0 1 N N N -4.127  3.023  19.702 7.184   -0.120 2.093  H8     YWI 45 
YWI HOB2   H4  H  0 0 N N N -11.526 6.823  17.199 -0.045  -2.074 1.206  HOB2   YWI 46 
YWI HOA2   H5  H  0 0 N N N -11.262 8.564  17.553 -0.360  -3.135 -0.188 HOA2   YWI 47 
YWI H17    H6  H  0 1 N N N -14.234 7.549  14.613 -2.712  -2.298 -0.293 H17    YWI 48 
YWI HOG3   H7  H  0 0 N N N -13.320 6.195  15.361 -2.397  -1.237 1.101  HOG3   YWI 49 
YWI HN1    H8  H  0 1 N N N -2.677  7.257  15.092 11.762  4.233  0.719  HN1    YWI 50 
YWI HN22   H9  H  0 0 N N N -5.317  9.084  16.344 12.211  4.168  -1.575 HN22   YWI 51 
YWI HN21   H10 H  0 0 N N N -4.050  8.969  15.168 11.384  3.097  -2.572 HN21   YWI 52 
YWI "H1'"  H11 H  0 1 N N N -5.798  4.710  20.818 7.659   0.384  -1.633 "H1'"  YWI 53 
YWI H19    H12 H  0 1 N N N -10.518 8.650  14.114 -3.891  1.710  -1.940 H19    YWI 54 
YWI H20    H13 H  0 1 N N N -8.794  10.303 13.553 -5.371  3.418  -2.905 H20    YWI 55 
YWI H21    H14 H  0 1 N N N -8.790  11.383 11.351 -7.769  3.424  -2.368 H21    YWI 56 
YWI "H2'"  H15 H  0 1 N N N -5.269  7.360  20.003 9.008   -1.437 -1.983 "H2'"  YWI 57 
YWI H6     H16 H  0 1 N N N -6.316  6.842  21.368 9.442   -1.464 -0.246 H6     YWI 58 
YWI H22    H17 H  0 1 N N N -9.274  12.608 9.937  -9.528  3.438  -1.969 H22    YWI 59 
YWI H23    H18 H  0 1 N N N -9.197  13.708 7.744  -11.930 3.436  -1.438 H23    YWI 60 
YWI H24    H19 H  0 1 N N N -10.185 12.602 5.767  -12.862 1.720  0.058  H24    YWI 61 
YWI H25    H20 H  0 1 N N N -11.418 9.331  8.225  -8.995  -0.024 0.498  H25    YWI 62 
YWI H26    H21 H  0 1 N N N -12.203 9.094  10.213 -7.229  -0.018 0.122  H26    YWI 63 
YWI "H3'"  H22 H  0 1 N N N -7.075  7.548  18.509 7.779   -3.047 0.261  "H3'"  YWI 64 
YWI "H4'"  H23 H  0 1 N N N -8.707  5.682  20.259 6.042   -1.920 -2.007 "H4'"  YWI 65 
YWI "H5''" H24 H  0 0 N N N -9.983  6.501  18.435 5.243   -3.849 -0.549 "H5''" YWI 66 
YWI "H5'"  H25 H  0 1 N N N -9.502  4.816  18.038 5.381   -2.765 0.857  "H5'"  YWI 67 
YWI H18    H26 H  0 1 N N N -11.342 6.974  14.110 -2.895  0.384  -1.157 H18    YWI 68 
YWI H1     H27 H  0 1 N N N -8.028  9.378  17.335 2.256   -4.401 -1.449 H1     YWI 69 
YWI "HO3'" H28 H  0 0 N N N -7.568  8.946  20.298 8.805   -4.032 -1.698 "HO3'" YWI 70 
# 
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 
YWI BR1   C23    SING N N 1  
YWI C22   C23    DOUB Y N 2  
YWI C22   C21    SING Y N 3  
YWI C23   C24    SING Y N 4  
YWI C21   C20    DOUB Y N 5  
YWI C24   C19    DOUB Y N 6  
YWI C20   C19    SING Y N 7  
YWI C19   C18    SING N N 8  
YWI C18   C25    DOUB Y N 9  
YWI C18   C17    SING Y N 10 
YWI C25   C14    SING Y N 11 
YWI C17   C16    DOUB Y N 12 
YWI O1G   C13    DOUB N N 13 
YWI C14   C13    SING N N 14 
YWI C14   C15    DOUB Y N 15 
YWI C13   N5     SING N N 16 
YWI C16   C15    SING Y N 17 
YWI N5    C12    SING N N 18 
YWI C12   C11    SING N N 19 
YWI O3B   PB     DOUB N N 20 
YWI O6    C6     DOUB N N 21 
YWI N1    C6     SING N N 22 
YWI N1    C2     SING N N 23 
YWI O3A   PB     SING N N 24 
YWI O3A   C10    SING N N 25 
YWI N2    C2     SING N N 26 
YWI C11   C10    SING N N 27 
YWI C6    C5     SING N N 28 
YWI PB    O2     SING N N 29 
YWI PB    O1B    SING N N 30 
YWI C2    N3     DOUB N N 31 
YWI O2    "C5'"  SING N N 32 
YWI C5    C4     DOUB Y N 33 
YWI C5    N7     SING Y N 34 
YWI N3    C4     SING N N 35 
YWI C4    N9     SING Y N 36 
YWI N7    C8     DOUB Y N 37 
YWI "C5'" "C4'"  SING N N 38 
YWI N9    C8     SING Y N 39 
YWI N9    "C1'"  SING N N 40 
YWI "O4'" "C4'"  SING N N 41 
YWI "O4'" "C1'"  SING N N 42 
YWI "C4'" "C3'"  SING N N 43 
YWI "C3'" "O3'"  SING N N 44 
YWI "C3'" "C2'"  SING N N 45 
YWI "C1'" "C2'"  SING N N 46 
YWI C11   HOG2   SING N N 47 
YWI C11   "HO2'" SING N N 48 
YWI C8    H8     SING N N 49 
YWI C10   HOB2   SING N N 50 
YWI C10   HOA2   SING N N 51 
YWI C12   H17    SING N N 52 
YWI C12   HOG3   SING N N 53 
YWI N1    HN1    SING N N 54 
YWI N2    HN22   SING N N 55 
YWI N2    HN21   SING N N 56 
YWI "C1'" "H1'"  SING N N 57 
YWI C15   H19    SING N N 58 
YWI C16   H20    SING N N 59 
YWI C17   H21    SING N N 60 
YWI "C2'" "H2'"  SING N N 61 
YWI "C2'" H6     SING N N 62 
YWI C20   H22    SING N N 63 
YWI C21   H23    SING N N 64 
YWI C22   H24    SING N N 65 
YWI C24   H25    SING N N 66 
YWI C25   H26    SING N N 67 
YWI "C3'" "H3'"  SING N N 68 
YWI "C4'" "H4'"  SING N N 69 
YWI "C5'" "H5''" SING N N 70 
YWI "C5'" "H5'"  SING N N 71 
YWI N5    H18    SING N N 72 
YWI O1B   H1     SING N N 73 
YWI "O3'" "HO3'" SING N N 74 
# 
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 
YWI SMILES           ACDLabs              12.01 "Brc1cccc(c1)c1cccc(c1)C(=O)NCCCOP(=O)(O)OCC1OC(CC1O)n1cnc2c1N=C(N)NC2=O"                                                                                                                                                                                     
YWI InChI            InChI                1.06  "InChI=1S/C26H28BrN6O8P/c27-18-7-2-5-16(11-18)15-4-1-6-17(10-15)24(35)29-8-3-9-39-42(37,38)40-13-20-19(34)12-21(41-20)33-14-30-22-23(33)31-26(28)32-25(22)36/h1-2,4-7,10-11,14,19-21,34H,3,8-9,12-13H2,(H,29,35)(H,37,38)(H3,28,31,32,36)/t19-,20+,21+/m0/s1" 
YWI InChIKey         InChI                1.06  YVRCNNGDRZIWPL-PWRODBHTSA-N                                                                                                                                                                                                                                   
YWI SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)OCCCNC(=O)c4cccc(c4)c5cccc(Br)c5)O3"                                                                                                                                                                  
YWI SMILES           CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)OCCCNC(=O)c4cccc(c4)c5cccc(Br)c5)O3"                                                                                                                                                                      
YWI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)C(=O)NCCCOP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)c5cccc(c5)Br"                                                                                                                                                                   
YWI SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)C(=O)NCCCOP(=O)(O)OCC2C(CC(O2)n3cnc4c3N=C(NC4=O)N)O)c5cccc(c5)Br"                                                                                                                                                                                 
# 
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 
YWI "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-(3-{[(1M)-3'-bromo[1,1'-biphenyl]-3-carbonyl]amino}propoxy)(hydroxy)phosphoryl]-2'-deoxyguanosine"                                                          
YWI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methyl 3-[[3-(3-bromophenyl)phenyl]carbonylamino]propyl hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YWI "Create component" 2023-03-01 RCSB 
YWI "Initial release"  2023-06-07 RCSB 
# 
