data_WFU
# 
_chem_comp.id                                    WFU 
_chem_comp.name                                  "(2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}pentanedioic acid (non-preferred name)" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H21 N6 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;Glutamyl-5'-O-adenosine phosphoramidate
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-03 
_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                        476.335 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WFU 
_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        8UAZ 
_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 
WFU P     P1  P 0 1 N N N N N N 9.444  -8.755  -34.596 -2.720 2.080  0.688  P     WFU 1  
WFU N1    N1  N 0 1 Y N N N N N 10.421 -6.487  -41.421 7.570  -0.089 -1.138 N1    WFU 2  
WFU C2    C1  C 0 1 Y N N N N N 11.011 -5.658  -40.347 6.701  -0.914 -1.695 C2    WFU 3  
WFU N3    N2  N 0 1 Y N N N N N 9.956  -5.306  -39.386 5.422  -0.907 -1.384 N3    WFU 4  
WFU C4    C2  C 0 1 Y N N N N N 8.668  -5.595  -39.523 4.948  -0.055 -0.481 C4    WFU 5  
WFU C5    C3  C 0 1 Y N N N N N 8.252  -6.313  -40.576 5.832  0.843  0.140  C5    WFU 6  
WFU C6    C4  C 0 1 Y N N N N N 9.096  -6.691  -41.513 7.189  0.798  -0.225 C6    WFU 7  
WFU CA    C5  C 0 1 N N S N N N 7.507  -9.520  -33.190 -4.467 0.641  -0.593 CA    WFU 8  
WFU CB    C6  C 0 1 N N N N N N 7.787  -8.559  -31.990 -5.087 -0.751 -0.459 CB    WFU 9  
WFU CD    C7  C 0 1 N N N N N N 8.369  -6.178  -31.646 -4.652 -3.094 0.227  CD    WFU 10 
WFU CG    C8  C 0 1 N N N N N N 7.302  -7.126  -32.217 -4.042 -1.723 0.095  CG    WFU 11 
WFU "C1'" C9  C 0 1 N N R N N N 7.490  -4.486  -37.506 2.461  -0.483 -0.285 "C1'" WFU 12 
WFU OP1   O1  O 0 1 N N N N N N 10.080 -10.130 -34.634 -2.408 2.580  2.045  OP1   WFU 13 
WFU "C2'" C10 C 0 1 N N R N N N 6.444  -5.105  -36.588 2.275  -1.730 0.607  "C2'" WFU 14 
WFU "O2'" O2  O 0 1 N N N N N N 5.924  -4.172  -35.648 2.687  -2.909 -0.087 "O2'" WFU 15 
WFU OP2   O3  O 0 1 N N N N N N 9.923  -7.775  -33.578 -2.934 3.327  -0.308 OP2   WFU 16 
WFU "C3'" C11 C 0 1 N N S N N N 7.242  -6.154  -35.895 0.755  -1.769 0.885  "C3'" WFU 17 
WFU "O3'" O4  O 0 1 N N N N N N 6.573  -6.354  -34.661 0.183  -2.973 0.371  "O3'" WFU 18 
WFU "C4'" C12 C 0 1 N N R N N N 8.680  -5.534  -35.754 0.204  -0.541 0.128  "C4'" WFU 19 
WFU "O4'" O5  O 0 1 N N N N N N 8.724  -4.453  -36.729 1.327  0.359  0.016  "O4'" WFU 20 
WFU "C5'" C13 C 0 1 N N N N N N 9.919  -6.470  -36.039 -0.928 0.112  0.925  "C5'" WFU 21 
WFU "O5'" O6  O 0 1 N N N N N N 9.546  -7.852  -35.995 -1.501 1.172  0.157  "O5'" WFU 22 
WFU OE1   O7  O 0 1 N N N N N N 8.934  -5.379  -32.438 -5.804 -3.276 -0.089 OE1   WFU 23 
WFU OE2   O8  O 0 1 N N N N N N 8.589  -6.231  -30.414 -3.916 -4.114 0.696  OE2   WFU 24 
WFU C     C14 C 0 1 N N N N N N 6.051  -9.924  -33.164 -5.455 1.569  -1.252 C     WFU 25 
WFU OXT   O9  O 0 1 N N N N N N 5.735  -10.718 -32.247 -5.913 1.297  -2.484 OXT   WFU 26 
WFU O     O10 O 0 1 N N N N N N 5.316  -9.434  -34.056 -5.836 2.558  -0.670 O     WFU 27 
WFU N     N3  N 0 1 N N N N N N 7.836  -8.959  -34.513 -4.126 1.156  0.740  N     WFU 28 
WFU N9    N4  N 0 1 Y N N N N N 7.595  -5.288  -38.780 3.711  0.203  0.052  N9    WFU 29 
WFU C8    C15 C 0 1 Y N N N N N 6.515  -5.845  -39.374 3.857  1.214  0.954  C8    WFU 30 
WFU N7    N5  N 0 1 Y N N N N N 6.933  -6.485  -40.464 5.103  1.589  1.005  N7    WFU 31 
WFU N6    N6  N 0 1 N N N N N N 8.583  -7.427  -42.498 8.106  1.658  0.353  N6    WFU 32 
WFU H1    H1  H 0 1 N N N N N N 12.047 -5.360  -40.280 7.053  -1.619 -2.432 H1    WFU 33 
WFU H2    H2  H 0 1 N N N N N N 8.113  -10.425 -33.035 -3.565 0.580  -1.201 H2    WFU 34 
WFU H3    H3  H 0 1 N N N N N N 7.280  -8.959  -31.100 -5.938 -0.707 0.221  H3    WFU 35 
WFU H4    H4  H 0 1 N N N N N N 8.872  -8.533  -31.813 -5.421 -1.096 -1.437 H4    WFU 36 
WFU H5    H5  H 0 1 N N N N N N 7.172  -6.940  -33.293 -3.191 -1.768 -0.585 H5    WFU 37 
WFU H6    H6  H 0 1 N N N N N N 6.344  -6.968  -31.700 -3.708 -1.378 1.073  H6    WFU 38 
WFU H7    H7  H 0 1 N N N N N N 7.181  -3.460  -37.754 2.455  -0.766 -1.338 H7    WFU 39 
WFU H8    H8  H 0 1 N N N N N N 5.643  -5.563  -37.186 2.831  -1.620 1.538  H8    WFU 40 
WFU H9    H9  H 0 1 N N N N N N 5.278  -4.601  -35.099 2.591  -3.723 0.427  H9    WFU 41 
WFU H10   H10 H 0 1 N N N N N N 10.609 -8.172  -33.054 -3.142 3.073  -1.217 H10   WFU 42 
WFU H11   H11 H 0 1 N N N N N N 7.289  -7.075  -36.495 0.560  -1.678 1.954  H11   WFU 43 
WFU H12   H12 H 0 1 N N N N N N 7.029  -7.018  -34.157 0.538  -3.779 0.770  H12   WFU 44 
WFU H13   H13 H 0 1 N N N N N N 8.783  -5.125  -34.738 -0.149 -0.832 -0.861 H13   WFU 45 
WFU H14   H14 H 0 1 N N N N N N 10.692 -6.283  -35.279 -1.693 -0.632 1.145  H14   WFU 46 
WFU H15   H15 H 0 1 N N N N N N 10.321 -6.239  -37.036 -0.531 0.512  1.858  H15   WFU 47 
WFU H16   H16 H 0 1 N N N N N N 9.241  -5.581  -30.180 -4.351 -4.975 0.763  H16   WFU 48 
WFU H17   H17 H 0 1 N N N N N N 4.809  -10.921 -32.309 -6.545 1.922  -2.865 H17   WFU 49 
WFU H18   H18 H 0 1 N N N N N N 7.377  -8.078  -34.630 -4.040 0.403  1.407  H18   WFU 50 
WFU H19   H19 H 0 1 N N N N N N 5.495  -5.782  -39.026 3.057  1.642  1.541  H19   WFU 51 
WFU H20   H20 H 0 1 N N N N N N 9.321  -7.757  -43.087 9.040  1.617  0.093  H20   WFU 52 
WFU H21   H21 H 0 1 N N N N N N 8.092  -8.207  -42.110 7.816  2.301  1.018  H21   WFU 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 
WFU N6    C6    SING N N 1  
WFU C6    N1    DOUB Y N 2  
WFU C6    C5    SING Y N 3  
WFU N1    C2    SING Y N 4  
WFU C5    N7    SING Y N 5  
WFU C5    C4    DOUB Y N 6  
WFU N7    C8    DOUB Y N 7  
WFU C2    N3    DOUB Y N 8  
WFU C4    N3    SING Y N 9  
WFU C4    N9    SING Y N 10 
WFU C8    N9    SING Y N 11 
WFU N9    "C1'" SING N N 12 
WFU "C1'" "O4'" SING N N 13 
WFU "C1'" "C2'" SING N N 14 
WFU "O4'" "C4'" SING N N 15 
WFU "C2'" "C3'" SING N N 16 
WFU "C2'" "O2'" SING N N 17 
WFU "C5'" "O5'" SING N N 18 
WFU "C5'" "C4'" SING N N 19 
WFU "O5'" P     SING N N 20 
WFU "C3'" "C4'" SING N N 21 
WFU "C3'" "O3'" SING N N 22 
WFU OP1   P     DOUB N N 23 
WFU P     N     SING N N 24 
WFU P     OP2   SING N N 25 
WFU N     CA    SING N N 26 
WFU O     C     DOUB N N 27 
WFU CA    C     SING N N 28 
WFU CA    CB    SING N N 29 
WFU C     OXT   SING N N 30 
WFU OE1   CD    DOUB N N 31 
WFU CG    CB    SING N N 32 
WFU CG    CD    SING N N 33 
WFU CD    OE2   SING N N 34 
WFU C2    H1    SING N N 35 
WFU CA    H2    SING N N 36 
WFU CB    H3    SING N N 37 
WFU CB    H4    SING N N 38 
WFU CG    H5    SING N N 39 
WFU CG    H6    SING N N 40 
WFU "C1'" H7    SING N N 41 
WFU "C2'" H8    SING N N 42 
WFU "O2'" H9    SING N N 43 
WFU OP2   H10   SING N N 44 
WFU "C3'" H11   SING N N 45 
WFU "O3'" H12   SING N N 46 
WFU "C4'" H13   SING N N 47 
WFU "C5'" H14   SING N N 48 
WFU "C5'" H15   SING N N 49 
WFU OE2   H16   SING N N 50 
WFU OXT   H17   SING N N 51 
WFU N     H18   SING N N 52 
WFU C8    H19   SING N N 53 
WFU N6    H20   SING N N 54 
WFU N6    H21   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 
WFU SMILES           ACDLabs              12.01 "O=C(O)C(CCC(=O)O)NP(=O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                                              
WFU InChI            InChI                1.06  "InChI=1S/C15H21N6O10P/c16-12-9-13(18-4-17-12)21(5-19-9)14-11(25)10(24)7(31-14)3-30-32(28,29)20-6(15(26)27)1-2-8(22)23/h4-7,10-11,14,24-25H,1-3H2,(H,22,23)(H,26,27)(H2,16,17,18)(H2,20,28,29)/t6-,7+,10+,11+,14+/m0/s1" 
WFU InChIKey         InChI                1.06  CKTPKDBUYLAONN-LTOLZBHSSA-N                                                                                                                                                                                              
WFU SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N[C@@H](CCC(O)=O)C(O)=O)[C@@H](O)[C@H]3O"                                                                                                                                     
WFU SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)N[CH](CCC(O)=O)C(O)=O)[CH](O)[CH]3O"                                                                                                                                             
WFU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(N[C@@H](CCC(=O)O)C(=O)O)O)O)O)N"                                                                                                                                 
WFU SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(NC(CCC(=O)O)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 
WFU "SYSTEMATIC NAME" ACDLabs              12.01 "(2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}pentanedioic acid (non-preferred name)" 
WFU "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]pentanedioic 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 
WFU "Create component" 2023-10-03 RCSB 
WFU "Initial release"  2024-10-16 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      WFU 
_pdbx_chem_comp_synonyms.name         
;Glutamyl-5'-O-adenosine phosphoramidate
;
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
