data_WF9
# 
_chem_comp.id                                    WF9 
_chem_comp.name                                  "(2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}-5-carbamimidamidopentanoic acid (non-preferred name)" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H26 N9 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-02 
_chem_comp.pdbx_modified_date                    2024-10-11 
_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                        503.407 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WF9 
_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        8UAY 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
WF9 N1    N1  N 0 1 Y N N N N N -14.081 -11.314 19.121 6.953   -2.755 0.777  N1    WF9 1  
WF9 C2    C1  C 0 1 Y N N N N N -13.617 -10.474 18.099 6.951   -1.525 1.257  C2    WF9 2  
WF9 N3    N2  N 0 1 Y N N N N N -12.580 -10.943 17.265 5.938   -0.701 1.085  N3    WF9 3  
WF9 C4    C2  C 0 1 Y N N N N N -12.065 -12.172 17.478 4.860   -1.085 0.409  C4    WF9 4  
WF9 C5    C3  C 0 1 Y N N N N N -12.539 -12.959 18.470 4.814   -2.386 -0.122 C5    WF9 5  
WF9 C6    C4  C 0 1 Y N N N N N -13.526 -12.530 19.277 5.920   -3.227 0.088  C6    WF9 6  
WF9 C8    C5  C 0 1 Y N N N N N -10.969 -14.026 17.431 2.952   -1.407 -0.648 C8    WF9 7  
WF9 N6    N3  N 0 1 N N N N N N -13.925 -13.368 20.255 5.932   -4.518 -0.411 N6    WF9 8  
WF9 N7    N4  N 0 1 Y N N N N N -11.853 -14.095 18.442 3.623   -2.517 -0.754 N7    WF9 9  
WF9 N9    N5  N 0 1 Y N N N N N -11.105 -12.827 16.849 3.672   -0.493 0.061  N9    WF9 10 
WF9 "C1'" C6  C 0 1 N N R N N N -10.388 -12.289 15.684 3.255   0.872  0.392  "C1'" WF9 11 
WF9 "O4'" O1  O 0 1 N N N N N N -11.421 -12.391 14.689 1.816   0.985  0.334  "O4'" WF9 12 
WF9 "C2'" C7  C 0 1 N N R N N N -9.379  -13.261 15.145 3.775   1.866  -0.670 "C2'" WF9 13 
WF9 "O2'" O2  O 0 1 N N N N N N -8.119  -12.928 15.649 4.968   2.507  -0.214 "O2'" WF9 14 
WF9 "C3'" C8  C 0 1 N N S N N N -9.409  -12.960 13.654 2.630   2.893  -0.816 "C3'" WF9 15 
WF9 "O3'" O3  O 0 1 N N N N N N -8.557  -11.852 13.372 3.081   4.200  -0.458 "O3'" WF9 16 
WF9 "C4'" C9  C 0 1 N N R N N N -10.805 -12.540 13.415 1.552   2.397  0.178  "C4'" WF9 17 
WF9 "C5'" C10 C 0 1 N N N N N N -11.565 -13.664 12.743 0.153   2.616  -0.400 "C5'" WF9 18 
WF9 "O5'" O4  O 0 1 N N N N N N -12.944 -13.316 12.727 -0.828  2.261  0.577  "O5'" WF9 19 
WF9 P     P1  P 0 1 N N N N N N -13.852 -13.742 11.485 -2.412  2.367  0.308  P     WF9 20 
WF9 OP1   O5  O 0 1 N N N N N N -15.178 -13.080 11.730 -3.200  2.273  1.709  OP1   WF9 21 
WF9 OP2   O6  O 0 1 N N N N N N -13.113 -13.476 10.240 -2.716  3.660  -0.344 OP2   WF9 22 
WF9 N     N6  N 0 1 N N N N N N -14.125 -15.408 11.715 -2.897  1.105  -0.694 N     WF9 23 
WF9 CA    C11 C 0 1 N N S N N N -13.654 -16.419 10.739 -2.609  -0.197 -0.078 CA    WF9 24 
WF9 C     C12 C 0 1 N N N N N N -14.814 -16.933 9.772  -1.281  -0.706 -0.576 C     WF9 25 
WF9 O     O7  O 0 1 N N N N N N -15.262 -16.141 8.969  -0.640  -0.052 -1.363 O     WF9 26 
WF9 OXT   O8  O 0 1 N N N N N N -15.219 -18.111 9.845  -0.811  -1.887 -0.144 OXT   WF9 27 
WF9 CB    C13 C 0 1 N N N N N N -13.201 -17.645 11.573 -3.710  -1.192 -0.452 CB    WF9 28 
WF9 CG    C14 C 0 1 N N N N N N -11.705 -17.585 11.918 -5.037  -0.739 0.160  CG    WF9 29 
WF9 CD    C15 C 0 1 N N N N N N -11.437 -16.904 13.254 -6.137  -1.734 -0.214 CD    WF9 30 
WF9 NE    N7  N 0 1 N N N N N N -12.238 -17.435 14.362 -7.408  -1.299 0.372  NE    WF9 31 
WF9 CZ    C16 C 0 1 N N N N N N -11.743 -17.473 15.620 -8.547  -2.042 0.169  CZ    WF9 32 
WF9 NH2   N8  N 0 1 N N N N N N -12.474 -17.956 16.628 -9.740  -1.634 0.719  NH2   WF9 33 
WF9 NH1   N9  N 0 1 N N N N N N -10.486 -17.028 15.851 -8.497  -3.132 -0.543 NH1   WF9 34 
WF9 H1    H1  H 0 1 N N N N N N -14.043 -9.492  17.954 7.811   -1.181 1.811  H1    WF9 35 
WF9 H2    H2  H 0 1 N N N N N N -10.273 -14.799 17.140 1.969   -1.236 -1.061 H2    WF9 36 
WF9 H3    H3  H 0 1 N N N N N N -14.652 -12.936 20.789 6.701   -5.089 -0.259 H3    WF9 37 
WF9 H4    H4  H 0 1 N N N N N N -14.269 -14.215 19.849 5.171   -4.851 -0.912 H4    WF9 38 
WF9 H5    H5  H 0 1 N N N N N N -9.988  -11.275 15.830 3.618   1.150  1.382  H5    WF9 39 
WF9 H6    H6  H 0 1 N N N N N N -9.669  -14.302 15.349 3.955   1.355  -1.616 H6    WF9 40 
WF9 H7    H7  H 0 1 N N N N N N -8.091  -13.113 16.580 5.337   3.142  -0.843 H7    WF9 41 
WF9 H8    H8  H 0 1 N N N N N N -9.147  -13.852 13.066 2.241   2.889  -1.834 H8    WF9 42 
WF9 H9    H9  H 0 1 N N N N N N -7.652  -12.102 13.520 3.799   4.535  -1.013 H9    WF9 43 
WF9 H10   H10 H 0 1 N N N N N N -10.853 -11.619 12.816 1.653   2.910  1.134  H10   WF9 44 
WF9 H11   H11 H 0 1 N N N N N N -11.423 -14.599 13.305 0.032   3.665  -0.671 H11   WF9 45 
WF9 H12   H12 H 0 1 N N N N N N -11.202 -13.796 11.713 0.024   1.995  -1.287 H12   WF9 46 
WF9 H13   H13 H 0 1 N N N N N N -15.396 -12.524 10.991 -3.047  1.450  2.192  H13   WF9 47 
WF9 H14   H14 H 0 1 N N N N N N -15.116 -15.523 11.783 -2.464  1.178  -1.603 H14   WF9 48 
WF9 H15   H15 H 0 1 N N N N N N -12.815 -16.035 10.140 -2.573  -0.086 1.006  H15   WF9 49 
WF9 H16   H16 H 0 1 N N N N N N -15.897 -18.254 9.195  0.045   -2.172 -0.492 H16   WF9 50 
WF9 H17   H17 H 0 1 N N N N N N -13.780 -17.672 12.508 -3.806  -1.237 -1.537 H17   WF9 51 
WF9 H18   H18 H 0 1 N N N N N N -13.396 -18.560 10.994 -3.452  -2.180 -0.069 H18   WF9 52 
WF9 H19   H19 H 0 1 N N N N N N -11.312 -18.612 11.961 -4.940  -0.694 1.245  H19   WF9 53 
WF9 H20   H20 H 0 1 N N N N N N -11.184 -17.026 11.127 -5.295  0.249  -0.223 H20   WF9 54 
WF9 H21   H21 H 0 1 N N N N N N -10.373 -17.034 13.502 -6.234  -1.778 -1.299 H21   WF9 55 
WF9 H22   H22 H 0 1 N N N N N N -11.660 -15.832 13.148 -5.879  -2.721 0.169  H22   WF9 56 
WF9 H23   H23 H 0 1 N N N N N N -13.162 -17.773 14.185 -7.445  -0.488 0.902  H23   WF9 57 
WF9 H24   H24 H 0 1 N N N N N N -12.092 -17.988 17.552 -9.777  -0.823 1.250  H24   WF9 58 
WF9 H25   H25 H 0 1 N N N N N N -13.403 -18.285 16.459 -10.544 -2.158 0.577  H25   WF9 59 
WF9 H26   H26 H 0 1 N N N N N N -10.228 -17.116 16.813 -9.301  -3.656 -0.686 H26   WF9 60 
# 
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 
WF9 O     C     DOUB N N 1  
WF9 C     OXT   SING N N 2  
WF9 C     CA    SING N N 3  
WF9 OP2   P     DOUB N N 4  
WF9 CA    CB    SING N N 5  
WF9 CA    N     SING N N 6  
WF9 P     N     SING N N 7  
WF9 P     OP1   SING N N 8  
WF9 P     "O5'" SING N N 9  
WF9 CB    CG    SING N N 10 
WF9 CG    CD    SING N N 11 
WF9 "O5'" "C5'" SING N N 12 
WF9 "C5'" "C4'" SING N N 13 
WF9 CD    NE    SING N N 14 
WF9 "O3'" "C3'" SING N N 15 
WF9 "C4'" "C3'" SING N N 16 
WF9 "C4'" "O4'" SING N N 17 
WF9 "C3'" "C2'" SING N N 18 
WF9 NE    CZ    SING N N 19 
WF9 "O4'" "C1'" SING N N 20 
WF9 "C2'" "O2'" SING N N 21 
WF9 "C2'" "C1'" SING N N 22 
WF9 CZ    NH1   DOUB N N 23 
WF9 CZ    NH2   SING N N 24 
WF9 "C1'" N9    SING N N 25 
WF9 N9    C8    SING Y N 26 
WF9 N9    C4    SING Y N 27 
WF9 N3    C4    DOUB Y N 28 
WF9 N3    C2    SING Y N 29 
WF9 C8    N7    DOUB Y N 30 
WF9 C4    C5    SING Y N 31 
WF9 C2    N1    DOUB Y N 32 
WF9 N7    C5    SING Y N 33 
WF9 C5    C6    DOUB Y N 34 
WF9 N1    C6    SING Y N 35 
WF9 C6    N6    SING N N 36 
WF9 C2    H1    SING N N 37 
WF9 C8    H2    SING N N 38 
WF9 N6    H3    SING N N 39 
WF9 N6    H4    SING N N 40 
WF9 "C1'" H5    SING N N 41 
WF9 "C2'" H6    SING N N 42 
WF9 "O2'" H7    SING N N 43 
WF9 "C3'" H8    SING N N 44 
WF9 "O3'" H9    SING N N 45 
WF9 "C4'" H10   SING N N 46 
WF9 "C5'" H11   SING N N 47 
WF9 "C5'" H12   SING N N 48 
WF9 OP1   H13   SING N N 49 
WF9 N     H14   SING N N 50 
WF9 CA    H15   SING N N 51 
WF9 OXT   H16   SING N N 52 
WF9 CB    H17   SING N N 53 
WF9 CB    H18   SING N N 54 
WF9 CG    H19   SING N N 55 
WF9 CG    H20   SING N N 56 
WF9 CD    H21   SING N N 57 
WF9 CD    H22   SING N N 58 
WF9 NE    H23   SING N N 59 
WF9 NH2   H24   SING N N 60 
WF9 NH2   H25   SING N N 61 
WF9 NH1   H26   SING N N 62 
# 
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 
WF9 SMILES           ACDLabs              12.01 "O=C(O)C(CCCNC(=N)N)NP(=O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                                                     
WF9 InChI            InChI                1.06  "InChI=1S/C16H26N9O8P/c17-12-9-13(22-5-21-12)25(6-23-9)14-11(27)10(26)8(33-14)4-32-34(30,31)24-7(15(28)29)2-1-3-20-16(18)19/h5-8,10-11,14,26-27H,1-4H2,(H,28,29)(H2,17,21,22)(H4,18,19,20)(H2,24,30,31)/t7-,8+,10+,11+,14+/m0/s1" 
WF9 InChIKey         InChI                1.06  AXUGFAXGFGAXFD-TWBCTODHSA-N                                                                                                                                                                                                       
WF9 SMILES_CANONICAL CACTVS               3.385 "NC(=N)NCCC[C@H](N[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                                              
WF9 SMILES           CACTVS               3.385 "NC(=N)NCCC[CH](N[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                                                    
WF9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCCC[C@@H](C(=O)O)NP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O"                                                                                                                                        
WF9 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(NC(CCCNC(=N)N)C(=O)O)O)O)O)N"                                                                                                                                                               
# 
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 
WF9 "SYSTEMATIC NAME" ACDLabs              12.01 "(2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}-5-carbamimidamidopentanoic acid (non-preferred name)" 
WF9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]amino]-5-carbamimidamido-pentanoic acid"           
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
WF9 "Create component" 2023-10-02 RCSB 
WF9 "Initial release"  2024-10-16 RCSB 
# 
