data_VJ8
# 
_chem_comp.id                                    VJ8 
_chem_comp.name                                  edaGDP 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H25 N7 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[2-(propanoylamino)ethyl]carbamate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-05-18 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        585.356 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VJ8 
_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        7OK3 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              Y 
# 
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 
VJ8 C4  C1  C 0 1 Y N N N N N 46.833 26.900 3.201  -0.031  4.463  0.251  C4  VJ8 1  
VJ8 C5  C2  C 0 1 Y N N N N N 46.944 25.885 4.081  0.777   5.498  -0.232 C5  VJ8 2  
VJ8 C6  C3  C 0 1 N N N N N N 46.045 24.873 4.015  0.328   6.832  -0.087 C6  VJ8 3  
VJ8 C8  C4  C 0 1 Y N N N N N 48.579 27.277 4.481  1.807   3.636  -0.641 C8  VJ8 4  
VJ8 N1  N1  N 0 1 N N N N N N 45.029 24.931 3.097  -0.864  7.046  0.513  N1  VJ8 5  
VJ8 N2  N2  N 0 1 N N N N N N 43.974 26.063 1.274  -2.815  6.242  1.564  N2  VJ8 6  
VJ8 N3  N3  N 0 1 N N N N N N 45.878 26.973 2.249  -1.202  4.751  0.830  N3  VJ8 7  
VJ8 C1A C5  C 0 1 N N R N N N 48.174 29.044 2.741  0.187   1.945  0.302  C1A VJ8 8  
VJ8 C2  C6  C 0 1 N N N N N N 44.956 25.971 2.170  -1.606  5.995  0.964  C2  VJ8 9  
VJ8 C2A C7  C 0 1 N N R N N N 48.393 30.149 3.672  -0.747  1.404  -0.810 C2A VJ8 10 
VJ8 C3A C8  C 0 1 N N S N N N 49.299 31.107 2.911  -0.589  -0.128 -0.650 C3A VJ8 11 
VJ8 C4A C9  C 0 1 N N R N N N 50.178 30.087 2.119  0.747   -0.293 0.100  C4A VJ8 12 
VJ8 C5A C10 C 0 1 N N N N N N 51.513 29.817 2.860  1.708   -1.145 -0.731 C5A VJ8 13 
VJ8 CBC C11 C 0 1 N N N N N N 49.160 32.759 1.228  -2.766  -1.101 -0.548 CBC VJ8 14 
VJ8 CBF C12 C 0 1 N N N N N N 48.967 34.309 -0.643 -4.994  -2.083 -0.621 CBF VJ8 15 
VJ8 CBG C13 C 0 1 N N N N N N 49.500 33.621 -1.913 -6.035  -2.620 0.363  CBG VJ8 16 
VJ8 CBI C14 C 0 1 N N N N N N 51.192 31.880 -1.514 -8.264  -3.602 0.289  CBI VJ8 17 
VJ8 CBJ C15 C 0 1 N N N N N N 52.708 31.528 -1.469 -9.474  -4.081 -0.470 CBJ VJ8 18 
VJ8 CBL C16 C 0 1 N N N N N N 53.007 30.976 -0.097 -10.515 -4.617 0.514  CBL VJ8 19 
VJ8 N7  N4  N 0 1 Y N N N N N 48.026 26.122 4.886  1.885   4.928  -0.765 N7  VJ8 20 
VJ8 N9  N5  N 0 1 Y N N N N N 47.837 27.771 3.476  0.640   3.301  -0.018 N9  VJ8 21 
VJ8 NBE N6  N 0 1 N N N N N N 48.445 33.327 0.287  -3.818  -1.618 0.117  NBE VJ8 22 
VJ8 NBH N7  N 0 1 N N N N N N 50.906 33.134 -1.822 -7.212  -3.085 -0.375 NBH VJ8 23 
VJ8 O2A O1  O 0 1 N N N N N N 47.061 30.816 3.976  -2.099  1.804  -0.579 O2A VJ8 24 
VJ8 O3A O2  O 0 1 N N N N N N 48.497 31.804 1.945  -1.685  -0.673 0.131  O3A VJ8 25 
VJ8 O4A O3  O 0 1 N N N N N N 49.439 28.801 2.129  1.297   1.021  0.288  O4A VJ8 26 
VJ8 O5A O4  O 0 1 N N N N N N 51.271 29.441 4.215  2.906   -1.376 0.014  O5A VJ8 27 
VJ8 O6  O5  O 0 1 N N N N N N 46.075 23.869 4.767  1.000   7.765  -0.493 O6  VJ8 28 
VJ8 OAV O6  O 0 1 N N N N N N 53.684 29.130 4.643  5.256   -2.402 0.593  OAV VJ8 29 
VJ8 OAX O7  O 0 1 N N N N N N 56.108 29.768 4.458  6.199   -4.727 0.317  OAX VJ8 30 
VJ8 OAY O8  O 0 1 N N N N N N 55.070 29.465 6.771  7.768   -2.789 -0.078 OAY VJ8 31 
VJ8 OAZ O9  O 0 1 N N N N N N 52.547 31.373 5.307  3.659   -3.576 -0.969 OAZ VJ8 32 
VJ8 OBA O10 O 0 1 N N N N N N 55.365 27.472 5.261  6.943   -3.412 2.339  OBA VJ8 33 
VJ8 OBB O11 O 0 1 N N N N N N 51.873 29.201 6.550  4.782   -1.483 -1.824 OBB VJ8 34 
VJ8 OBD O12 O 0 1 N N N N N N 50.342 33.061 1.454  -2.793  -1.020 -1.760 OBD VJ8 35 
VJ8 OBK O13 O 0 1 N N N N N N 50.302 31.060 -1.277 -8.237  -3.682 1.499  OBK VJ8 36 
VJ8 PAU P1  P 0 1 N N N N N N 52.350 29.883 5.295  4.140   -2.239 -0.556 PAU VJ8 37 
VJ8 PAW P2  P 0 1 N N N N N N 55.173 28.927 5.366  6.534   -3.362 0.783  PAW VJ8 38 
VJ8 H1  H1  H 0 1 N N N N N N 49.468 27.731 4.893  2.554   2.933  -0.980 H1  VJ8 39 
VJ8 H2  H2  H 0 1 N N N N N N 44.329 24.217 3.092  -1.193  7.951  0.624  H2  VJ8 40 
VJ8 H3  H3  H 0 1 N N N N N N 43.920 26.859 0.671  -3.358  5.504  1.883  H3  VJ8 41 
VJ8 H4  H4  H 0 1 N N N N N N 43.291 25.336 1.205  -3.126  7.155  1.670  H4  VJ8 42 
VJ8 H5  H5  H 0 1 N N N N N N 47.396 29.287 2.002  -0.317  1.928  1.268  H5  VJ8 43 
VJ8 H6  H6  H 0 1 N N N N N N 48.878 29.808 4.598  -0.410  1.730  -1.794 H6  VJ8 44 
VJ8 H7  H7  H 0 1 N N N N N N 49.894 31.757 3.569  -0.540  -0.610 -1.627 H7  VJ8 45 
VJ8 H8  H8  H 0 1 N N N N N N 50.363 30.445 1.096  0.575   -0.765 1.067  H8  VJ8 46 
VJ8 H9  H9  H 0 1 N N N N N N 52.051 29.004 2.350  1.237   -2.099 -0.967 H9  VJ8 47 
VJ8 H10 H10 H 0 1 N N N N N N 52.127 30.730 2.843  1.951   -0.622 -1.656 H10 VJ8 48 
VJ8 H11 H11 H 0 1 N N N N N N 49.786 34.864 -0.161 -4.701  -2.877 -1.309 H11 VJ8 49 
VJ8 H12 H12 H 0 1 N N N N N N 48.164 35.008 -0.920 -5.421  -1.253 -1.185 H12 VJ8 50 
VJ8 H13 H13 H 0 1 N N N N N N 49.441 34.342 -2.742 -5.609  -3.449 0.927  H13 VJ8 51 
VJ8 H14 H14 H 0 1 N N N N N N 48.853 32.758 -2.131 -6.328  -1.826 1.051  H14 VJ8 52 
VJ8 H15 H15 H 0 1 N N N N N N 52.941 30.774 -2.236 -9.901  -3.251 -1.034 H15 VJ8 53 
VJ8 H16 H16 H 0 1 N N N N N N 53.309 32.432 -1.649 -9.181  -4.874 -1.158 H16 VJ8 54 
VJ8 H17 H17 H 0 1 N N N N N N 54.074 30.716 -0.030 -11.391 -4.963 -0.035 H17 VJ8 55 
VJ8 H18 H18 H 0 1 N N N N N N 52.766 31.734 0.663  -10.089 -5.447 1.078  H18 VJ8 56 
VJ8 H19 H19 H 0 1 N N N N N N 52.399 30.076 0.077  -10.808 -3.824 1.202  H19 VJ8 57 
VJ8 H20 H20 H 0 1 N N N N N N 47.483 33.067 0.206  -3.796  -1.682 1.085  H20 VJ8 58 
VJ8 H21 H21 H 0 1 N N N N N N 51.654 33.774 -1.999 -7.234  -3.021 -1.343 H21 VJ8 59 
VJ8 H22 H22 H 0 1 N N N N N N 47.197 31.536 4.581  -2.232  2.762  -0.580 H22 VJ8 60 
VJ8 H23 H23 H 0 1 N N N N N N 55.609 30.243 6.853  8.043   -1.897 0.173  H23 VJ8 61 
VJ8 H24 H24 H 0 1 N N N N N N 56.053 27.287 4.633  7.707   -3.973 2.528  H24 VJ8 62 
VJ8 H25 H25 H 0 1 N N N N N N 51.750 29.848 7.235  5.119   -0.599 -1.626 H25 VJ8 63 
# 
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 
VJ8 CBG NBH SING N N 1  
VJ8 CBG CBF SING N N 2  
VJ8 NBH CBI SING N N 3  
VJ8 CBI CBJ SING N N 4  
VJ8 CBI OBK DOUB N N 5  
VJ8 CBJ CBL SING N N 6  
VJ8 CBF NBE SING N N 7  
VJ8 NBE CBC SING N N 8  
VJ8 CBC OBD DOUB N N 9  
VJ8 CBC O3A SING N N 10 
VJ8 N2  C2  SING N N 11 
VJ8 O3A C3A SING N N 12 
VJ8 C4A O4A SING N N 13 
VJ8 C4A C5A SING N N 14 
VJ8 C4A C3A SING N N 15 
VJ8 O4A C1A SING N N 16 
VJ8 C2  N3  DOUB N N 17 
VJ8 C2  N1  SING N N 18 
VJ8 N3  C4  SING N N 19 
VJ8 C1A N9  SING N N 20 
VJ8 C1A C2A SING N N 21 
VJ8 C5A O5A SING N N 22 
VJ8 C3A C2A SING N N 23 
VJ8 N1  C6  SING N N 24 
VJ8 C4  N9  SING Y N 25 
VJ8 C4  C5  DOUB Y N 26 
VJ8 N9  C8  SING Y N 27 
VJ8 C2A O2A SING N N 28 
VJ8 C6  C5  SING N N 29 
VJ8 C6  O6  DOUB N N 30 
VJ8 C5  N7  SING Y N 31 
VJ8 O5A PAU SING N N 32 
VJ8 OAX PAW DOUB N N 33 
VJ8 C8  N7  DOUB Y N 34 
VJ8 OAV PAU SING N N 35 
VJ8 OAV PAW SING N N 36 
VJ8 OBA PAW SING N N 37 
VJ8 PAU OAZ DOUB N N 38 
VJ8 PAU OBB SING N N 39 
VJ8 PAW OAY SING N N 40 
VJ8 C8  H1  SING N N 41 
VJ8 N1  H2  SING N N 42 
VJ8 N2  H3  SING N N 43 
VJ8 N2  H4  SING N N 44 
VJ8 C1A H5  SING N N 45 
VJ8 C2A H6  SING N N 46 
VJ8 C3A H7  SING N N 47 
VJ8 C4A H8  SING N N 48 
VJ8 C5A H9  SING N N 49 
VJ8 C5A H10 SING N N 50 
VJ8 CBF H11 SING N N 51 
VJ8 CBF H12 SING N N 52 
VJ8 CBG H13 SING N N 53 
VJ8 CBG H14 SING N N 54 
VJ8 CBJ H15 SING N N 55 
VJ8 CBJ H16 SING N N 56 
VJ8 CBL H17 SING N N 57 
VJ8 CBL H18 SING N N 58 
VJ8 CBL H19 SING N N 59 
VJ8 NBE H20 SING N N 60 
VJ8 NBH H21 SING N N 61 
VJ8 O2A H22 SING N N 62 
VJ8 OAY H23 SING N N 63 
VJ8 OBA H24 SING N N 64 
VJ8 OBB H25 SING N N 65 
# 
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 
VJ8 InChI            InChI                1.03  "InChI=1S/C16H25N7O13P2/c1-2-8(24)18-3-4-19-16(27)35-11-7(5-33-38(31,32)36-37(28,29)30)34-14(10(11)25)23-6-20-9-12(23)21-15(17)22-13(9)26/h6-7,10-11,14,25H,2-5H2,1H3,(H,18,24)(H,19,27)(H,31,32)(H2,28,29,30)(H3,17,21,22,26)/t7-,10-,11-,14-/m1/s1" 
VJ8 InChIKey         InChI                1.03  ZYFFWDLDVKYDIX-FRJWGUMJSA-N                                                                                                                                                                                                                           
VJ8 SMILES_CANONICAL CACTVS               3.385 "CCC(=O)NCCNC(=O)O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)N"                                                                                                                                                       
VJ8 SMILES           CACTVS               3.385 "CCC(=O)NCCNC(=O)O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)N"                                                                                                                                                              
VJ8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)NCCNC(=O)O[C@@H]1[C@H](O[C@H]([C@@H]1O)n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O"                                                                                                                                                              
VJ8 SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(=O)NCCNC(=O)OC1C(OC(C1O)n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O"                                                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           VJ8 
_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-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[2-(propanoylamino)ethyl]carbamate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VJ8 "Create component" 2021-05-18 PDBE 
VJ8 "Initial release"  2022-08-03 RCSB 
VJ8 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      VJ8 
_pdbx_chem_comp_synonyms.name         "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[2-(propanoylamino)ethyl]carbamate" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         IUPAC 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            VJ8 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               CBL 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
