data_USB
# 
_chem_comp.id                                    USB 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H25 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                     2021-03-11 
_chem_comp.pdbx_modified_date                    2022-08-26 
_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                        460.379 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     USB 
_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        7NU8 
_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 
USB C2    C1  C 0 1 Y N N -12.728 -7.380 -28.745 6.851  -1.200 1.055  C2    USB 1  
USB C4    C2  C 0 1 Y N N -10.631 -7.121 -28.117 4.721  -0.870 0.259  C4    USB 2  
USB C5    C3  C 0 1 Y N N -10.903 -7.574 -26.833 4.850  -2.023 -0.534 C5    USB 3  
USB C6    C4  C 0 1 Y N N -12.238 -7.923 -26.550 6.061  -2.734 -0.477 C6    USB 4  
USB C8    C5  C 0 1 Y N N -8.821  -7.146 -26.886 2.873  -1.209 -0.896 C8    USB 5  
USB N     N1  N 0 1 N N N -0.548  -3.912 -28.566 -7.284 -0.408 -0.054 N     USB 6  
USB CA    C6  C 0 1 N N S -1.746  -3.057 -28.503 -5.908 -0.691 0.376  CA    USB 7  
USB C     C7  C 0 1 N N N -3.026  -3.778 -28.054 -4.968 0.295  -0.268 C     USB 8  
USB O     O1  O 0 1 N N N -4.074  -3.198 -28.013 -5.309 0.898  -1.258 O     USB 9  
USB CB    C8  C 0 1 N N N -1.995  -2.415 -29.872 -5.524 -2.111 -0.045 CB    USB 10 
USB CG    C9  C 0 1 N N N -0.957  -1.383 -30.313 -6.398 -3.119 0.704  CG    USB 11 
USB CD1   C10 C 0 1 N N N -0.985  -0.142 -29.434 -6.101 -4.530 0.193  CD1   USB 12 
USB CD2   C11 C 0 1 N N N -1.157  -1.004 -31.775 -6.092 -3.045 2.201  CD2   USB 13 
USB "C1'" C12 C 0 1 N N R -8.549  -6.235 -29.241 2.865  0.814  0.613  "C1'" USB 14 
USB "C2'" C13 C 0 1 N N R -7.999  -4.847 -28.932 3.270  2.083  -0.179 "C2'" USB 15 
USB "C3'" C14 C 0 1 N N S -6.889  -4.740 -29.975 2.115  3.057  0.155  "C3'" USB 16 
USB "C4'" C15 C 0 1 N N R -6.378  -6.184 -30.088 0.964  2.138  0.608  "C4'" USB 17 
USB "C5'" C16 C 0 1 N N N -5.073  -6.453 -29.375 -0.258 2.354  -0.286 "C5'" USB 18 
USB N1    N2  N 0 1 Y N N -13.139 -7.821 -27.552 7.019  -2.290 0.328  N1    USB 19 
USB N3    N3  N 0 1 Y N N -11.504 -7.003 -29.123 5.737  -0.500 1.031  N3    USB 20 
USB N6    N4  N 0 1 N N N -12.670 -8.295 -25.337 6.246  -3.878 -1.235 N6    USB 21 
USB N7    N5  N 0 1 Y N N -9.747  -7.590 -26.067 3.688  -2.173 -1.214 N7    USB 22 
USB N9    N6  N 0 1 Y N N -9.289  -6.833 -28.135 3.462  -0.382 0.014  N9    USB 23 
USB O1P   O2  O 0 1 N N N -3.374  -7.418 -26.893 -2.664 1.198  -1.911 O1P   USB 24 
USB "O2'" O3  O 0 1 N N N -9.023  -3.887 -29.156 4.521  2.595  0.285  "O2'" USB 25 
USB O2P   O4  O 0 1 N N N -4.519  -5.456 -25.718 -3.464 3.038  -0.380 O2P   USB 26 
USB "O3'" O5  O 0 1 N N N -7.433  -4.272 -31.204 2.497  3.942  1.210  "O3'" USB 27 
USB "O4'" O6  O 0 1 N N N -7.420  -7.031 -29.542 1.427  0.782  0.484  "O4'" USB 28 
USB "O5'" O7  O 0 1 N N N -5.260  -6.173 -27.970 -1.355 1.585  0.212  "O5'" USB 29 
USB OPP   O8  O 0 1 N N N -2.986  -5.068 -27.689 -3.751 0.504  0.259  OPP   USB 30 
USB P     P1  P 0 1 N N N -4.022  -6.089 -26.959 -2.805 1.573  -0.487 P     USB 31 
USB H1    H1  H 0 1 N N N -13.490 -7.320 -29.508 7.656  -0.874 1.697  H1    USB 32 
USB H2    H2  H 0 1 N N N -7.785  -7.038 -26.601 1.876  -1.085 -1.292 H2    USB 33 
USB H3    H3  H 0 1 N N N -0.388  -4.329 -27.671 -7.584 0.500  0.268  H3    USB 34 
USB H4    H4  H 0 1 N N N -0.686  -4.630 -29.249 -7.372 -0.483 -1.056 H4    USB 35 
USB H6    H6  H 0 1 N N N -1.554  -2.246 -27.786 -5.840 -0.603 1.460  H6    USB 36 
USB H7    H7  H 0 1 N N N -2.975  -1.917 -29.840 -5.676 -2.226 -1.119 H7    USB 37 
USB H8    H8  H 0 1 N N N -2.016  -3.218 -30.624 -4.476 -2.290 0.194  H8    USB 38 
USB H9    H9  H 0 1 N N N 0.037   -1.843 -30.217 -7.449 -2.885 0.535  H9    USB 39 
USB H10   H10 H 0 1 N N N -0.839  -0.433 -28.383 -5.050 -4.765 0.361  H10   USB 40 
USB H11   H11 H 0 1 N N N -0.180  0.542  -29.740 -6.723 -5.249 0.727  H11   USB 41 
USB H12   H12 H 0 1 N N N -1.956  0.363  -29.543 -6.318 -4.583 -0.874 H12   USB 42 
USB H13   H13 H 0 1 N N N -0.400  -0.262 -32.069 -6.304 -2.039 2.566  H13   USB 43 
USB H14   H14 H 0 1 N N N -1.054  -1.901 -32.404 -6.715 -3.763 2.735  H14   USB 44 
USB H15   H15 H 0 1 N N N -2.161  -0.576 -31.909 -5.041 -3.279 2.370  H15   USB 45 
USB H16   H16 H 0 1 N N N -9.204  -6.163 -30.122 3.157  0.905  1.659  H16   USB 46 
USB H17   H17 H 0 1 N N N -7.589  -4.801 -27.912 3.309  1.878  -1.249 H17   USB 47 
USB H18   H18 H 0 1 N N N -6.086  -4.083 -29.609 1.825  3.623  -0.730 H18   USB 48 
USB H19   H19 H 0 1 N N N -6.245  -6.417 -31.155 0.708  2.349  1.647  H19   USB 49 
USB H20   H20 H 0 1 N N N -4.785  -7.506 -29.510 -0.525 3.411  -0.286 H20   USB 50 
USB H21   H21 H 0 1 N N N -4.285  -5.803 -29.783 -0.024 2.039  -1.303 H21   USB 51 
USB H22   H22 H 0 1 N N N -13.658 -8.449 -25.367 5.536  -4.196 -1.814 H22   USB 52 
USB H23   H23 H 0 1 N N N -12.209 -9.140 -25.064 7.086  -4.360 -1.188 H23   USB 53 
USB H24   H24 H 0 1 N N N -9.696  -3.980 -28.492 4.818  3.389  -0.180 H24   USB 54 
USB H25   H25 H 0 1 N N N -4.346  -6.027 -24.979 -3.587 3.349  0.527  H25   USB 55 
USB H26   H26 H 0 1 N N N -7.738  -3.379 -31.096 3.254  4.504  0.998  H26   USB 56 
# 
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 
USB CD2   CG    SING N N 1  
USB "O3'" "C3'" SING N N 2  
USB CG    CB    SING N N 3  
USB CG    CD1   SING N N 4  
USB "C4'" "C3'" SING N N 5  
USB "C4'" "O4'" SING N N 6  
USB "C4'" "C5'" SING N N 7  
USB "C3'" "C2'" SING N N 8  
USB CB    CA    SING N N 9  
USB "O4'" "C1'" SING N N 10 
USB "C5'" "O5'" SING N N 11 
USB "C1'" "C2'" SING N N 12 
USB "C1'" N9    SING N N 13 
USB "O2'" "C2'" SING N N 14 
USB N3    C2    DOUB Y N 15 
USB N3    C4    SING Y N 16 
USB C2    N1    SING Y N 17 
USB N     CA    SING N N 18 
USB CA    C     SING N N 19 
USB N9    C4    SING Y N 20 
USB N9    C8    SING Y N 21 
USB C4    C5    DOUB Y N 22 
USB C     O     DOUB N N 23 
USB C     OPP   SING N N 24 
USB "O5'" P     SING N N 25 
USB OPP   P     SING N N 26 
USB N1    C6    DOUB Y N 27 
USB P     O1P   DOUB N N 28 
USB P     O2P   SING N N 29 
USB C8    N7    DOUB Y N 30 
USB C5    C6    SING Y N 31 
USB C5    N7    SING Y N 32 
USB C6    N6    SING N N 33 
USB C2    H1    SING N N 34 
USB C8    H2    SING N N 35 
USB N     H3    SING N N 36 
USB N     H4    SING N N 37 
USB CA    H6    SING N N 38 
USB CB    H7    SING N N 39 
USB CB    H8    SING N N 40 
USB CG    H9    SING N N 41 
USB CD1   H10   SING N N 42 
USB CD1   H11   SING N N 43 
USB CD1   H12   SING N N 44 
USB CD2   H13   SING N N 45 
USB CD2   H14   SING N N 46 
USB CD2   H15   SING N N 47 
USB "C1'" H16   SING N N 48 
USB "C2'" H17   SING N N 49 
USB "C3'" H18   SING N N 50 
USB "C4'" H19   SING N N 51 
USB "C5'" H20   SING N N 52 
USB "C5'" H21   SING N N 53 
USB N6    H22   SING N N 54 
USB N6    H23   SING N N 55 
USB "O2'" H24   SING N N 56 
USB O2P   H25   SING N N 57 
USB "O3'" H26   SING N N 58 
# 
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 
USB InChI            InChI                1.03  "InChI=1S/C16H25N6O8P/c1-7(2)3-8(17)16(25)30-31(26,27)28-4-9-11(23)12(24)15(29-9)22-6-21-10-13(18)19-5-20-14(10)22/h5-9,11-12,15,23-24H,3-4,17H2,1-2H3,(H,26,27)(H2,18,19,20)/t8-,9+,11+,12+,15+/m0/s1" 
USB InChIKey         InChI                1.03  AXWPLGAOCISUCB-OPYVMVOTSA-N                                                                                                                                                                             
USB SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"                                                                                                                        
USB SMILES           CACTVS               3.385 "CC(C)C[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                                              
USB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N"                                                                                                                        
USB SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N"                                                                                                                                               
# 
_pdbx_chem_comp_identifier.comp_id           USB 
_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        "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
USB "Create component" 2021-03-11 PDBE 
USB "Initial release"  2022-08-31 RCSB 
# 
