data_UYP
# 
_chem_comp.id                                    UYP 
_chem_comp.name                                  "1-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-phenyl-urea" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C31 H35 N13 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-09-07 
_chem_comp.pdbx_modified_date                    2025-03-14 
_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                        701.692 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UYP 
_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        8QGC 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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 
UYP C4  C1  C 0 1 Y N N N N N 20.868 11.604 12.949 -5.742 -2.669 0.049  C4  UYP 1  
UYP C5  C2  C 0 1 Y N N N N N 20.535 12.722 12.195 -5.755 -3.113 -1.286 C5  UYP 2  
UYP C6  C3  C 0 1 Y N N N N N 21.536 13.561 11.719 -6.751 -4.030 -1.670 C6  UYP 3  
UYP C8  C4  C 0 1 Y N N N N N 18.752 11.682 12.740 -4.093 -1.727 -1.082 C8  UYP 4  
UYP N1  N1  N 0 1 Y N N N N N 22.799 13.255 12.014 -7.629 -4.431 -0.757 N1  UYP 5  
UYP N3  N2  N 0 1 Y N N N N N 22.147 11.359 13.205 -6.663 -3.127 0.890  N3  UYP 6  
UYP C2  C5  C 0 1 Y N N N N N 23.061 12.167 12.718 -7.576 -3.985 0.485  C2  UYP 7  
UYP CAA C6  C 0 1 N N N N N N 13.134 9.036  12.448 0.726  -1.231 -1.493 CAA UYP 8  
UYP CAC C7  C 0 1 N N N N N N 14.836 10.694 13.085 -0.835 0.550  -1.995 CAC UYP 9  
UYP CAD C8  C 0 1 N N N N N N 16.230 11.072 12.944 -2.011 -0.272 -1.666 CAD UYP 10 
UYP CAE C9  C 0 1 N N N N N N 17.374 11.360 12.848 -2.949 -0.927 -1.403 CAE UYP 11 
UYP CAP C10 C 0 1 N N R N N N 19.564 9.709  14.123 -4.265 -1.086 1.362  CAP UYP 12 
UYP CAR C11 C 0 1 N N R N N N 18.377 7.702  14.592 -3.007 0.705  2.117  CAR UYP 13 
UYP CAS C12 C 0 1 N N N N N N 16.946 8.174  14.417 -1.910 1.625  1.577  CAS UYP 14 
UYP CAU C13 C 0 1 N N N N N N 16.447 6.363  12.715 -1.733 3.830  0.557  CAU UYP 15 
UYP CAX C14 C 0 1 Y N N N N N 15.729 4.933  10.913 -1.470 6.018  -0.341 CAX UYP 16 
UYP CAY C15 C 0 1 Y N N N N N 14.947 4.854  9.773  -1.894 6.841  -1.376 CAY UYP 17 
UYP CAZ C16 C 0 1 Y N N N N N 14.915 3.695  9.010  -1.089 7.877  -1.807 CAZ UYP 18 
UYP CBA C17 C 0 1 Y N N N N N 15.752 2.630  9.318  0.139  8.094  -1.209 CBA UYP 19 
UYP CBB C18 C 0 1 Y N N N N N 16.599 2.727  10.413 0.565  7.276  -0.179 CBB UYP 20 
UYP CBC C19 C 0 1 Y N N N N N 16.608 3.878  11.182 -0.237 6.239  0.257  CBC UYP 21 
UYP CBD C20 C 0 1 N N S N N N 18.824 8.418  15.878 -2.374 -0.548 2.753  CBD UYP 22 
UYP CBF C21 C 0 1 N N R N N N 18.752 9.868  15.404 -2.987 -1.727 1.961  CBF UYP 23 
UYP CBH C22 C 0 1 N N N N N N 14.439 9.930  10.636 1.420  1.080  -1.289 CBH UYP 24 
UYP CBI C23 C 0 1 N N R N N N 15.773 9.832  9.890  2.479  0.761  -0.231 CBI UYP 25 
UYP CBK C24 C 0 1 N N R N N N 17.293 8.468  8.848  4.365  -0.476 0.194  CBK UYP 26 
UYP CBL C25 C 0 1 N N R N N N 17.010 9.759  8.067  4.896  0.964  -0.004 CBL UYP 27 
UYP CBN C26 C 0 1 N N S N N N 15.568 10.064 8.399  3.625  1.795  -0.289 CBN UYP 28 
UYP CBQ C27 C 0 1 Y N N N N N 16.172 6.717  7.408  5.264  -1.953 -1.644 CBQ UYP 29 
UYP CBS C28 C 0 1 Y N N N N N 17.758 5.240  7.569  6.958  -2.893 -0.669 CBS UYP 30 
UYP CBT C29 C 0 1 Y N N N N N 18.102 6.343  8.306  6.366  -2.025 0.264  CBT UYP 31 
UYP CBV C30 C 0 1 Y N N N N N 20.094 5.376  8.940  7.957  -2.630 1.808  CBV UYP 32 
UYP CBX C31 C 0 1 Y N N N N N 18.658 4.184  7.550  8.091  -3.622 -0.271 CBX UYP 33 
UYP N6  N3  N 0 1 N N N N N N 21.267 14.644 10.990 -6.815 -4.503 -2.969 N6  UYP 34 
UYP N7  N4  N 0 1 Y N N N N N 19.222 12.738 12.084 -4.730 -2.507 -1.924 N7  UYP 35 
UYP N9  N5  N 0 1 Y N N N N N 19.748 10.969 13.266 -4.684 -1.802 0.154  N9  UYP 36 
UYP NAB N6  N 0 1 N N N N N N 14.430 9.652  12.102 0.302  0.135  -1.162 NAB UYP 37 
UYP NAT N7  N 0 1 N N N N N N 16.293 7.618  13.188 -2.513 2.865  1.082  NAT UYP 38 
UYP NAW N8  N 0 1 N N N N N N 15.757 6.102  11.596 -2.287 4.971  0.101  NAW UYP 39 
UYP NBP N9  N 0 1 Y N N N N N 17.107 7.198  8.226  5.298  -1.451 -0.377 NBP UYP 40 
UYP NBR N10 N 0 1 Y N N N N N 16.567 5.494  7.026  6.238  -2.799 -1.813 NBR UYP 41 
UYP NBU N11 N 0 1 Y N N N N N 19.260 6.396  8.977  6.895  -1.926 1.480  NBU UYP 42 
UYP NBW N12 N 0 1 Y N N N N N 19.808 4.287  8.241  8.548  -3.458 0.966  NBW UYP 43 
UYP NBY N13 N 0 1 N N N N N N 18.396 3.080  6.858  8.716  -4.493 -1.147 NBY UYP 44 
UYP OAQ O1  O 0 1 N N N N N N 19.031 8.461  13.519 -3.849 0.259  1.041  OAQ UYP 45 
UYP OAV O2  O 0 1 N N N N N N 16.908 5.463  13.422 -0.529 3.671  0.493  OAV UYP 46 
UYP OBE O3  O 0 1 N N N N N N 20.105 8.016  16.391 -2.724 -0.638 4.136  OBE UYP 47 
UYP OBG O4  O 0 1 N N N N N N 19.514 10.691 16.294 -3.320 -2.809 2.832  OBG UYP 48 
UYP OBJ O5  O 0 1 N N N N N N 16.097 8.450  9.720  3.108  -0.507 -0.516 OBJ UYP 49 
UYP OBM O6  O 0 1 N N N N N N 18.006 10.772 8.161  5.540  1.427  1.184  OBM UYP 50 
UYP OBO O7  O 0 1 N N N N N N 15.417 11.471 8.201  3.446  2.797  0.713  OBO UYP 51 
UYP H1  H1  H 0 1 N N N N N N 24.097 11.926 12.905 -8.310 -4.337 1.195  H1  UYP 52 
UYP H2  H2  H 0 1 N N N N N N 13.105 8.822  13.527 1.522  -1.539 -0.815 H2  UYP 53 
UYP H3  H3  H 0 1 N N N N N N 12.319 9.728  12.190 -0.121 -1.910 -1.391 H3  UYP 54 
UYP H4  H4  H 0 1 N N N N N N 13.012 8.099  11.885 1.093  -1.259 -2.520 H4  UYP 55 
UYP H5  H5  H 0 1 N N N N N N 14.211 11.586 12.933 -0.582 0.417  -3.047 H5  UYP 56 
UYP H6  H6  H 0 1 N N N N N N 14.677 10.303 14.101 -1.060 1.600  -1.806 H6  UYP 57 
UYP H7  H7  H 0 1 N N N N N N 20.578 9.453  14.464 -5.069 -1.074 2.098  H7  UYP 58 
UYP H8  H8  H 0 1 N N N N N N 18.524 6.612  14.585 -3.603 1.236  2.859  H8  UYP 59 
UYP H9  H9  H 0 1 N N N N N N 16.945 9.272  14.349 -1.204 1.856  2.374  H9  UYP 60 
UYP H10 H10 H 0 1 N N N N N N 16.363 7.861  15.296 -1.386 1.125  0.762  H10 UYP 61 
UYP H11 H11 H 0 1 N N N N N N 14.354 5.706  9.474  -2.853 6.672  -1.844 H11 UYP 62 
UYP H12 H12 H 0 1 N N N N N N 14.236 3.621  8.173  -1.418 8.517  -2.612 H12 UYP 63 
UYP H13 H13 H 0 1 N N N N N N 15.744 1.736  8.712  0.768  8.905  -1.548 H13 UYP 64 
UYP H14 H14 H 0 1 N N N N N N 17.251 1.904  10.665 1.524  7.448  0.286  H14 UYP 65 
UYP H15 H15 H 0 1 N N N N N N 17.305 3.963  12.003 0.094  5.603  1.065  H15 UYP 66 
UYP H16 H16 H 0 1 N N N N N N 18.052 8.264  16.646 -1.290 -0.529 2.636  H16 UYP 67 
UYP H17 H17 H 0 1 N N N N N N 17.723 10.213 15.224 -2.312 -2.059 1.172  H17 UYP 68 
UYP H18 H18 H 0 1 N N N N N N 14.061 10.953 10.496 1.055  2.096  -1.143 H18 UYP 69 
UYP H19 H19 H 0 1 N N N N N N 13.748 9.216  10.164 1.860  0.990  -2.282 H19 UYP 70 
UYP H20 H20 H 0 1 N N N N N N 16.569 10.452 10.329 2.030  0.747  0.762  H20 UYP 71 
UYP H21 H21 H 0 1 N N N N N N 18.229 8.539  9.421  4.207  -0.679 1.254  H21 UYP 72 
UYP H22 H22 H 0 1 N N N N N N 16.997 9.448  7.012  5.580  1.008  -0.851 H22 UYP 73 
UYP H23 H23 H 0 1 N N N N N N 14.824 9.410  7.921  3.680  2.249  -1.279 H23 UYP 74 
UYP H24 H24 H 0 1 N N N N N N 15.264 7.219  7.108  4.533  -1.691 -2.395 H24 UYP 75 
UYP H25 H25 H 0 1 N N N N N N 21.024 5.428  9.487  8.362  -2.526 2.804  H25 UYP 76 
UYP H26 H26 H 0 1 N N N N N N 22.121 15.106 10.751 -7.507 -5.134 -3.222 H26 UYP 77 
UYP H27 H27 H 0 1 N N N N N N 20.790 14.373 10.154 -6.168 -4.202 -3.627 H27 UYP 78 
UYP H29 H29 H 0 1 N N N N N N 15.691 8.229  12.674 -3.473 2.991  1.133  H29 UYP 79 
UYP H30 H30 H 0 1 N N N N N N 15.205 6.849  11.227 -3.252 5.067  0.081  H30 UYP 80 
UYP H31 H31 H 0 1 N N N N N N 19.153 2.435  6.960  8.372  -4.605 -2.047 H31 UYP 81 
UYP H32 H32 H 0 1 N N N N N N 17.554 2.663  7.201  9.497  -4.991 -0.860 H32 UYP 82 
UYP H33 H33 H 0 1 N N N N N N 20.298 8.507  17.181 -2.352 -1.409 4.586  H33 UYP 83 
UYP H34 H34 H 0 1 N N N N N N 19.034 10.810 17.105 -2.554 -3.243 3.232  H34 UYP 84 
UYP H35 H35 H 0 1 N N N N N N 18.850 10.410 7.918  5.839  2.346  1.137  H35 UYP 85 
UYP H36 H36 H 0 1 N N N N N N 14.522 11.724 8.396  4.168  3.439  0.761  H36 UYP 86 
# 
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 
UYP NBY CBX SING N N 1  
UYP NBR CBQ DOUB Y N 2  
UYP NBR CBS SING Y N 3  
UYP CBQ NBP SING Y N 4  
UYP CBX CBS DOUB Y N 5  
UYP CBX NBW SING Y N 6  
UYP CBS CBT SING Y N 7  
UYP CBL OBM SING N N 8  
UYP CBL CBN SING N N 9  
UYP CBL CBK SING N N 10 
UYP OBO CBN SING N N 11 
UYP NBP CBT SING Y N 12 
UYP NBP CBK SING N N 13 
UYP NBW CBV DOUB Y N 14 
UYP CBT NBU DOUB Y N 15 
UYP CBN CBI SING N N 16 
UYP CBK OBJ SING N N 17 
UYP CBV NBU SING Y N 18 
UYP CAZ CBA DOUB Y N 19 
UYP CAZ CAY SING Y N 20 
UYP CBA CBB SING Y N 21 
UYP OBJ CBI SING N N 22 
UYP CAY CAX DOUB Y N 23 
UYP CBI CBH SING N N 24 
UYP CBB CBC DOUB Y N 25 
UYP CBH NAB SING N N 26 
UYP CAX CBC SING Y N 27 
UYP CAX NAW SING N N 28 
UYP N6  C6  SING N N 29 
UYP NAW CAU SING N N 30 
UYP C6  N1  DOUB Y N 31 
UYP C6  C5  SING Y N 32 
UYP N1  C2  SING Y N 33 
UYP N7  C5  SING Y N 34 
UYP N7  C8  DOUB Y N 35 
UYP NAB CAA SING N N 36 
UYP NAB CAC SING N N 37 
UYP C5  C4  DOUB Y N 38 
UYP CAU NAT SING N N 39 
UYP CAU OAV DOUB N N 40 
UYP C2  N3  DOUB Y N 41 
UYP C8  CAE SING N N 42 
UYP C8  N9  SING Y N 43 
UYP CAE CAD TRIP N N 44 
UYP CAD CAC SING N N 45 
UYP C4  N3  SING Y N 46 
UYP C4  N9  SING Y N 47 
UYP NAT CAS SING N N 48 
UYP N9  CAP SING N N 49 
UYP OAQ CAP SING N N 50 
UYP OAQ CAR SING N N 51 
UYP CAP CBF SING N N 52 
UYP CAS CAR SING N N 53 
UYP CAR CBD SING N N 54 
UYP CBF CBD SING N N 55 
UYP CBF OBG SING N N 56 
UYP CBD OBE SING N N 57 
UYP C2  H1  SING N N 58 
UYP CAA H2  SING N N 59 
UYP CAA H3  SING N N 60 
UYP CAA H4  SING N N 61 
UYP CAC H5  SING N N 62 
UYP CAC H6  SING N N 63 
UYP CAP H7  SING N N 64 
UYP CAR H8  SING N N 65 
UYP CAS H9  SING N N 66 
UYP CAS H10 SING N N 67 
UYP CAY H11 SING N N 68 
UYP CAZ H12 SING N N 69 
UYP CBA H13 SING N N 70 
UYP CBB H14 SING N N 71 
UYP CBC H15 SING N N 72 
UYP CBD H16 SING N N 73 
UYP CBF H17 SING N N 74 
UYP CBH H18 SING N N 75 
UYP CBH H19 SING N N 76 
UYP CBI H20 SING N N 77 
UYP CBK H21 SING N N 78 
UYP CBL H22 SING N N 79 
UYP CBN H23 SING N N 80 
UYP CBQ H24 SING N N 81 
UYP CBV H25 SING N N 82 
UYP N6  H26 SING N N 83 
UYP N6  H27 SING N N 84 
UYP NAT H29 SING N N 85 
UYP NAW H30 SING N N 86 
UYP NBY H31 SING N N 87 
UYP NBY H32 SING N N 88 
UYP OBE H33 SING N N 89 
UYP OBG H34 SING N N 90 
UYP OBM H35 SING N N 91 
UYP OBO H36 SING N N 92 
# 
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 
UYP InChI            InChI                1.06  "InChI=1S/C31H35N13O7/c1-42(11-17-22(46)23(47)29(51-17)43-14-39-19-25(32)35-12-37-27(19)43)9-5-8-18-41-20-26(33)36-13-38-28(20)44(18)30-24(48)21(45)16(50-30)10-34-31(49)40-15-6-3-2-4-7-15/h2-4,6-7,12-14,16-17,21-24,29-30,45-48H,9-11H2,1H3,(H2,32,35,37)(H2,33,36,38)(H2,34,40,49)/t16-,17-,21-,22-,23-,24-,29-,30-/m1/s1" 
UYP InChIKey         InChI                1.06  FBNSVAQFHOUOTK-OZZDRAHTSA-N                                                                                                                                                                                                                                                                                                    
UYP SMILES_CANONICAL CACTVS               3.385 "CN(CC#Cc1nc2c(N)ncnc2n1[C@@H]3O[C@H](CNC(=O)Nc4ccccc4)[C@@H](O)[C@H]3O)C[C@H]5O[C@H]([C@H](O)[C@@H]5O)n6cnc7c(N)ncnc67"                                                                                                                                                                                                       
UYP SMILES           CACTVS               3.385 "CN(CC#Cc1nc2c(N)ncnc2n1[CH]3O[CH](CNC(=O)Nc4ccccc4)[CH](O)[CH]3O)C[CH]5O[CH]([CH](O)[CH]5O)n6cnc7c(N)ncnc67"                                                                                                                                                                                                                  
UYP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(CC#Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CNC(=O)Nc4ccccc4)O)O)N)C[C@@H]5[C@H]([C@H]([C@@H](O5)n6cnc7c6ncnc7N)O)O"                                                                                                                                                                                                    
UYP SMILES           "OpenEye OEToolkits" 2.0.7 "CN(CC#Cc1nc2c(ncnc2n1C3C(C(C(O3)CNC(=O)Nc4ccccc4)O)O)N)CC5C(C(C(O5)n6cnc7c6ncnc7N)O)O"                                                                                                                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           UYP 
_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-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-phenyl-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 
UYP "Create component" 2023-09-07 PDBE 
UYP "Initial release"  2025-03-19 RCSB 
# 
