data_WN9
# 
_chem_comp.id                                    WN9 
_chem_comp.name                                  "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-3-methyl-butanoate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H23 N6 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Valyl adenylate " 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-11 
_chem_comp.pdbx_modified_date                    2024-02-09 
_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                        446.352 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WN9 
_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        8WO2 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
# 
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 
WN9 N1  N   N 0 1 N N N N N N -11.626 -6.464  4.722  7.470  -1.132 -0.264 N1  WN9 1  
WN9 C1  CA  C 0 1 N N S N N N -12.622 -7.307  5.355  6.067  -1.279 -0.674 C1  WN9 2  
WN9 C2  C   C 0 1 N N N N N N -12.511 -8.728  4.812  5.219  -0.275 0.064  C2  WN9 3  
WN9 O1  O   O 0 1 N N N N N N -13.002 -9.568  5.356  5.628  0.227  1.084  O1  WN9 4  
WN9 C3  CB  C 0 1 N N N N N N -13.983 -6.751  5.120  5.585  -2.693 -0.344 C3  WN9 5  
WN9 C4  CG1 C 0 1 N N N N N N -14.008 -5.197  5.396  4.124  -2.847 -0.772 C4  WN9 6  
WN9 C5  CG2 C 0 1 N N N N N N -14.513 -7.055  3.604  6.446  -3.713 -1.093 C5  WN9 7  
WN9 C6  C1* C 0 1 N N R N N N -15.697 -12.705 0.983  -2.568 0.889  -0.560 C6  WN9 8  
WN9 C7  C2  C 0 1 Y N N N N N -17.273 -16.629 -0.217 -6.708 -0.780 -1.026 C7  WN9 9  
WN9 C8  C2* C 0 1 N N R N N N -15.957 -11.941 2.339  -2.858 2.124  0.331  C8  WN9 10 
WN9 C9  C3* C 0 1 N N S N N N -15.971 -10.459 1.837  -1.639 3.031  0.035  C9  WN9 11 
WN9 C10 C4  C 0 1 Y N N N N N -15.785 -15.161 0.787  -4.539 -0.673 -0.275 C10 WN9 12 
WN9 C11 C4* C 0 1 N N R N N N -15.057 -10.410 0.926  -0.573 2.064  -0.514 C11 WN9 13 
WN9 C12 C5  C 0 1 Y N N N N N -15.013 -16.220 1.198  -4.739 -1.867 0.438  C12 WN9 14 
WN9 C13 C5* C 0 1 N N N N N N -13.717 -9.836  1.502  0.682  2.123  0.359  C13 WN9 15 
WN9 C14 C6  C 0 1 Y N N N N N -15.449 -17.530 0.852  -6.001 -2.480 0.365  C14 WN9 16 
WN9 C15 C8  C 0 1 Y N N N N N -14.102 -14.392 1.865  -2.695 -1.236 0.795  C15 WN9 17 
WN9 N2  N1  N 0 1 Y N N N N N -16.563 -17.681 0.158  -6.944 -1.903 -0.373 N2  WN9 18 
WN9 N3  N3  N 0 1 Y N N N N N -16.897 -15.386 0.088  -5.543 -0.170 -0.987 N3  WN9 19 
WN9 N4  N6  N 0 1 N N N N N N -14.676 -18.719 1.256  -6.257 -3.658 1.046  N4  WN9 20 
WN9 N5  N7  N 0 1 Y N N N N N -13.980 -15.719 1.862  -3.575 -2.155 1.069  N5  WN9 21 
WN9 N6  N9  N 0 1 Y N N N N N -15.188 -14.059 1.219  -3.242 -0.299 -0.030 N6  WN9 22 
WN9 O2  O2* O 0 1 N N N N N N -17.124 -12.273 2.859  -4.076 2.761  -0.061 O2  WN9 23 
WN9 O3  O3* O 0 1 N N N N N N -17.298 -10.145 1.222  -1.976 4.017  -0.943 O3  WN9 24 
WN9 O4  O4* O 0 1 N N N N N N -14.824 -11.980 0.365  -1.134 0.741  -0.474 O4  WN9 25 
WN9 O5  O5* O 0 1 N N N N N N -13.041 -10.885 2.228  1.706  1.313  -0.222 O5  WN9 26 
WN9 O6  OAU O 0 1 N N N N N N -10.542 -10.566 2.016  3.029  0.674  1.831  O6  WN9 27 
WN9 O7  OAV O 0 1 N N N N N N -11.433 -11.537 4.099  3.933  2.557  0.413  O7  WN9 28 
WN9 O8  OAW O 0 1 N N N N N N -11.758 -8.968  3.618  4.010  0.062  -0.412 O8  WN9 29 
WN9 P1  PAT P 0 1 N N N N N N -11.670 -10.519 2.988  3.166  1.141  0.433  P1  WN9 30 
WN9 H1  H1  H 0 1 N N N N N N -11.701 -5.533  5.079  7.831  -0.227 -0.529 H1  WN9 31 
WN9 H2  H2  H 0 1 N N N N N N -10.713 -6.823  4.916  7.574  -1.286 0.728  H2  WN9 32 
WN9 H4  H4  H 0 1 N N N N N N -12.435 -7.337  6.439  5.982  -1.107 -1.747 H4  WN9 33 
WN9 H5  H5  H 0 1 N N N N N N -14.690 -7.229  5.814  5.670  -2.865 0.729  H5  WN9 34 
WN9 H6  H6  H 0 1 N N N N N N -13.650 -5.000  6.417  3.781  -3.855 -0.537 H6  WN9 35 
WN9 H7  H7  H 0 1 N N N N N N -13.355 -4.686  4.674  3.511  -2.121 -0.238 H7  WN9 36 
WN9 H8  H8  H 0 1 N N N N N N -15.037 -4.822  5.289  4.040  -2.675 -1.845 H8  WN9 37 
WN9 H9  H9  H 0 1 N N N N N N -15.518 -6.628  3.474  7.486  -3.603 -0.789 H9  WN9 38 
WN9 H10 H10 H 0 1 N N N N N N -13.825 -6.599  2.877  6.102  -4.720 -0.858 H10 WN9 39 
WN9 H11 H11 H 0 1 N N N N N N -14.552 -8.142  3.441  6.361  -3.541 -2.166 H11 WN9 40 
WN9 H12 H12 H 0 1 N N N N N N -16.650 -12.762 0.437  -2.876 1.078  -1.588 H12 WN9 41 
WN9 H13 H13 H 0 1 N N N N N N -18.180 -16.781 -0.784 -7.501 -0.347 -1.618 H13 WN9 42 
WN9 H14 H14 H 0 1 N N N N N N -15.108 -12.097 3.021  -2.889 1.845  1.385  H14 WN9 43 
WN9 H15 H15 H 0 1 N N N N N N -15.779 -9.787  2.687  -1.287 3.508  0.950  H15 WN9 44 
WN9 H16 H16 H 0 1 N N N N N N -15.355 -9.798  0.062  -0.323 2.332  -1.540 H16 WN9 45 
WN9 H17 H17 H 0 1 N N N N N N -13.079 -9.486  0.677  1.030  3.154  0.427  H17 WN9 46 
WN9 H18 H18 H 0 1 N N N N N N -13.934 -8.997  2.179  0.448  1.752  1.357  H18 WN9 47 
WN9 H19 H19 H 0 1 N N N N N N -13.413 -13.701 2.328  -1.681 -1.218 1.167  H19 WN9 48 
WN9 H20 H20 H 0 1 N N N N N N -15.134 -19.544 0.925  -5.561 -4.069 1.582  H20 WN9 49 
WN9 H21 H21 H 0 1 N N N N N N -13.757 -18.668 0.864  -7.132 -4.071 0.987  H21 WN9 50 
WN9 H22 H22 H 0 1 N N N N N N -17.255 -11.800 3.672  -4.300 3.539  0.468  H22 WN9 51 
WN9 H23 H23 H 0 1 N N N N N N -17.973 -10.180 1.889  -2.683 4.617  -0.670 H23 WN9 52 
WN9 H24 H24 H 0 1 N N N N N N -10.614 -11.992 3.943  4.059  2.924  -0.473 H24 WN9 53 
# 
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 
WN9 C7  N3  DOUB Y N 1  
WN9 C7  N2  SING Y N 2  
WN9 N3  C10 SING Y N 3  
WN9 N2  C14 DOUB Y N 4  
WN9 O4  C11 SING N N 5  
WN9 O4  C6  SING N N 6  
WN9 C10 C12 DOUB Y N 7  
WN9 C10 N6  SING Y N 8  
WN9 C14 C12 SING Y N 9  
WN9 C14 N4  SING N N 10 
WN9 C11 C13 SING N N 11 
WN9 C11 C9  SING N N 12 
WN9 C6  N6  SING N N 13 
WN9 C6  C8  SING N N 14 
WN9 C12 N5  SING Y N 15 
WN9 N6  C15 SING Y N 16 
WN9 O3  C9  SING N N 17 
WN9 C13 O5  SING N N 18 
WN9 C9  C8  SING N N 19 
WN9 N5  C15 DOUB Y N 20 
WN9 O6  P1  DOUB N N 21 
WN9 O5  P1  SING N N 22 
WN9 C8  O2  SING N N 23 
WN9 P1  O8  SING N N 24 
WN9 P1  O7  SING N N 25 
WN9 C5  C3  SING N N 26 
WN9 O8  C2  SING N N 27 
WN9 N1  C1  SING N N 28 
WN9 C2  C1  SING N N 29 
WN9 C2  O1  DOUB N N 30 
WN9 C3  C1  SING N N 31 
WN9 C3  C4  SING N N 32 
WN9 N1  H1  SING N N 33 
WN9 N1  H2  SING N N 34 
WN9 C1  H4  SING N N 35 
WN9 C3  H5  SING N N 36 
WN9 C4  H6  SING N N 37 
WN9 C4  H7  SING N N 38 
WN9 C4  H8  SING N N 39 
WN9 C5  H9  SING N N 40 
WN9 C5  H10 SING N N 41 
WN9 C5  H11 SING N N 42 
WN9 C6  H12 SING N N 43 
WN9 C7  H13 SING N N 44 
WN9 C8  H14 SING N N 45 
WN9 C9  H15 SING N N 46 
WN9 C11 H16 SING N N 47 
WN9 C13 H17 SING N N 48 
WN9 C13 H18 SING N N 49 
WN9 C15 H19 SING N N 50 
WN9 N4  H20 SING N N 51 
WN9 N4  H21 SING N N 52 
WN9 O2  H22 SING N N 53 
WN9 O3  H23 SING N N 54 
WN9 O7  H24 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 
WN9 InChI            InChI                1.06  "InChI=1S/C15H23N6O8P/c1-6(2)8(16)15(24)29-30(25,26)27-3-7-10(22)11(23)14(28-7)21-5-20-9-12(17)18-4-19-13(9)21/h4-8,10-11,14,22-23H,3,16H2,1-2H3,(H,25,26)(H2,17,18,19)/t7-,8+,10-,11-,14-/m1/s1" 
WN9 InChIKey         InChI                1.06  KAVINRUMCQFLGF-NIXGFCADSA-N                                                                                                                                                                       
WN9 SMILES_CANONICAL CACTVS               3.385 "CC(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"                                                                                                                   
WN9 SMILES           CACTVS               3.385 "CC(C)[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                                         
WN9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)[C@@H](C(=O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N"                                                                                                               
WN9 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)C(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N"                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           WN9 
_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-3-methyl-butanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
WN9 "Create component" 2023-10-11 PDBC 
WN9 "Initial release"  2024-02-14 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      WN9 
_pdbx_chem_comp_synonyms.name         "Valyl adenylate " 
_pdbx_chem_comp_synonyms.provenance   PUBCHEM 
_pdbx_chem_comp_synonyms.type         ? 
# 
