data_VJB
# 
_chem_comp.id                                    VJB 
_chem_comp.name                                  bdaGDP 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H29 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-3~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[4-(propanoylamino)butyl]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                        613.409 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VJB 
_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        7OK4 
_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 
VJB C10 C1  C 0 1 N N S N N N 39.061 -5.383  19.259 0.015  -0.074 -0.664 C10 VJB 1  
VJB C15 C2  C 0 1 N N N N N N 41.355 -3.631  23.848 5.930  0.947  0.264  C15 VJB 2  
VJB C17 C3  C 0 1 N N N N N N 39.633 -4.623  25.414 8.385  1.376  0.441  C17 VJB 3  
VJB C20 C4  C 0 1 N N N N N N 37.097 -1.953  24.143 12.048 2.045  -0.449 C20 VJB 4  
VJB C21 C5  C 0 1 N N N N N N 37.099 -2.350  22.667 13.218 2.227  0.521  C21 VJB 5  
VJB C24 C6  C 0 1 N N R N N N 38.016 -5.092  19.925 -1.208 0.424  0.132  C24 VJB 6  
VJB C02 C7  C 0 1 N N N N N N 35.272 -11.450 17.959 -2.793 -6.569 -0.134 C02 VJB 7  
VJB C03 C8  C 0 1 Y N N N N N 35.765 -10.009 17.906 -2.848 -5.114 -0.308 C03 VJB 8  
VJB C05 C9  C 0 1 Y N N N N N 36.176 -7.933  17.526 -3.284 -3.042 -0.757 C05 VJB 9  
VJB C07 C10 C 0 1 N N R N N N 37.956 -7.474  19.243 -1.279 -1.888 0.252  C07 VJB 10 
VJB C08 C11 C 0 1 N N R N N N 38.717 -6.789  18.419 -0.257 -1.584 -0.873 C08 VJB 11 
VJB C12 C12 C 0 1 N N N N N N 40.716 -4.694  20.877 2.364  0.339  -0.596 C12 VJB 12 
VJB C14 C13 C 0 1 N N N N N N 42.281 -3.945  22.676 4.761  0.765  -0.706 C14 VJB 13 
VJB C16 C14 C 0 1 N N N N N N 40.810 -4.906  24.486 7.216  1.194  -0.529 C16 VJB 14 
VJB C19 C15 C 0 1 N N N N N N 38.216 -2.631  24.936 10.782 1.802  0.332  C19 VJB 15 
VJB C25 C16 C 0 1 N N N N N N 37.121 -4.042  19.227 -1.916 1.536  -0.645 C25 VJB 16 
VJB C36 C17 C 0 1 Y N N N N N 36.740 -9.584  18.785 -1.803 -4.353 0.202  C36 VJB 17 
VJB C38 C18 C 0 1 N N N N N N 36.856 -11.875 19.839 -0.771 -6.342 0.975  C38 VJB 18 
VJB N04 N1  N 0 1 Y N N N N N 35.435 -8.962  17.139 -3.726 -4.260 -0.885 N04 VJB 19 
VJB N06 N2  N 0 1 Y N N N N N 36.974 -8.307  18.514 -2.095 -3.056 -0.089 N06 VJB 20 
VJB N13 N3  N 0 1 N N N N N N 41.712 -5.011  21.875 3.530  0.529  0.053  N13 VJB 21 
VJB N18 N4  N 0 1 N N N N N N 38.563 -4.009  24.651 9.616  1.612  -0.318 N18 VJB 22 
VJB N37 N5  N 0 1 N N N N N N 37.323 -10.492 19.782 -0.772 -4.990 0.842  N37 VJB 23 
VJB N39 N6  N 0 1 N N N N N N 37.428 -12.770 20.813 0.277  -6.940 1.621  N39 VJB 24 
VJB N40 N7  N 0 1 N N N N N N 35.833 -12.331 18.929 -1.741 -7.099 0.508  N40 VJB 25 
VJB O01 O1  O 0 1 N N N N N N 34.423 -11.836 17.213 -3.689 -7.282 -0.559 O01 VJB 26 
VJB O09 O2  O 0 1 N N N N N N 39.938 -7.492  18.118 0.938  -2.346 -0.695 O09 VJB 27 
VJB O11 O3  O 0 1 N N N N N N 40.163 -5.742  20.136 1.233  0.122  0.101  O11 VJB 28 
VJB O22 O4  O 0 1 N N N N N N 38.815 -2.041  25.777 10.812 1.777  1.544  O22 VJB 29 
VJB O23 O5  O 0 1 N N N N N N 40.374 -3.568  20.699 2.334  0.364  -1.811 O23 VJB 30 
VJB O26 O6  O 0 1 N N N N N N 36.847 -4.494  17.932 -2.977 2.070  0.150  O26 VJB 31 
VJB O28 O7  O 0 1 N N N N N N 35.267 -2.553  17.469 -5.093 3.516  0.736  O28 VJB 32 
VJB O30 O8  O 0 1 N N N N N N 34.877 -1.125  15.382 -6.466 5.440  -0.149 O30 VJB 33 
VJB O31 O9  O 0 1 N N N N N N 32.934 -1.802  16.784 -7.614 3.202  0.060  O31 VJB 34 
VJB O32 O10 O 0 1 N N N N N N 34.551 -0.120  17.646 -6.990 4.624  2.181  O32 VJB 35 
VJB O33 O11 O 0 1 N N N N N N 36.267 -3.957  15.500 -4.552 2.884  -1.647 O33 VJB 36 
VJB O34 O12 O 0 1 N N N N N N 37.762 -2.394  16.780 -3.070 4.604  -0.544 O34 VJB 37 
VJB O35 O13 O 0 1 N N N N N N 37.153 -6.436  20.028 -2.093 -0.696 0.299  O35 VJB 38 
VJB P27 P1  P 0 1 N N N N N N 36.577 -3.324  16.830 -3.936 3.260  -0.354 P27 VJB 39 
VJB P29 P2  P 0 1 N N N N N N 34.372 -1.360  16.791 -6.539 4.222  0.688  P29 VJB 40 
VJB H1  H1  H 0 1 N N N N N N 39.365 -4.614  18.534 0.081  0.440  -1.623 H1  VJB 41 
VJB H2  H2  H 0 1 N N N N N N 41.916 -3.064  24.605 5.734  1.801  0.913  H2  VJB 42 
VJB H3  H3  H 0 1 N N N N N N 40.512 -3.024  23.485 6.044  0.048  0.870  H3  VJB 43 
VJB H4  H4  H 0 1 N N N N N N 39.277 -5.566  25.855 8.189  2.230  1.090  H4  VJB 44 
VJB H5  H5  H 0 1 N N N N N N 39.952 -3.941  26.216 8.499  0.477  1.047  H5  VJB 45 
VJB H6  H6  H 0 1 N N N N N N 37.225 -0.863  24.215 11.935 2.944  -1.054 H6  VJB 46 
VJB H7  H7  H 0 1 N N N N N N 36.130 -2.239  24.583 12.244 1.192  -1.098 H7  VJB 47 
VJB H8  H8  H 0 1 N N N N N N 36.277 -1.835  22.147 13.022 3.081  1.170  H8  VJB 48 
VJB H9  H9  H 0 1 N N N N N N 38.058 -2.062  22.211 13.331 1.328  1.127  H9  VJB 49 
VJB H10 H10 H 0 1 N N N N N N 36.963 -3.438  22.580 14.134 2.403  -0.044 H10 VJB 50 
VJB H11 H11 H 0 1 N N N N N N 38.237 -4.747  20.946 -0.890 0.794  1.106  H11 VJB 51 
VJB H12 H12 H 0 1 N N N N N N 36.135 -6.941  17.100 -3.782 -2.157 -1.124 H12 VJB 52 
VJB H13 H13 H 0 1 N N N N N N 38.535 -8.095  19.942 -0.769 -2.042 1.203  H13 VJB 53 
VJB H14 H14 H 0 1 N N N N N N 38.194 -6.506  17.494 -0.693 -1.768 -1.855 H14 VJB 54 
VJB H15 H15 H 0 1 N N N N N N 43.262 -4.260  23.060 4.648  1.664  -1.311 H15 VJB 55 
VJB H16 H16 H 0 1 N N N N N N 42.402 -3.045  22.055 4.957  -0.088 -1.355 H16 VJB 56 
VJB H17 H17 H 0 1 N N N N N N 40.478 -5.588  23.689 7.412  0.341  -1.178 H17 VJB 57 
VJB H18 H18 H 0 1 N N N N N N 41.613 -5.384  25.066 7.102  2.093  -1.134 H18 VJB 58 
VJB H19 H19 H 0 1 N N N N N N 37.646 -3.076  19.181 -1.203 2.327  -0.879 H19 VJB 59 
VJB H20 H20 H 0 1 N N N N N N 36.181 -3.922  19.786 -2.325 1.130  -1.570 H20 VJB 60 
VJB H21 H21 H 0 1 N N N N N N 42.006 -5.957  22.012 3.554  0.509  1.022  H21 VJB 61 
VJB H22 H22 H 0 1 N N N N N N 38.076 -4.524  23.945 9.592  1.632  -1.287 H22 VJB 62 
VJB H23 H23 H 0 1 N N N N N N 38.029 -10.168 20.412 -0.036 -4.471 1.204  H23 VJB 63 
VJB H24 H24 H 0 1 N N N N N N 37.117 -13.719 20.864 1.002  -6.400 1.974  H24 VJB 64 
VJB H25 H25 H 0 1 N N N N N N 38.136 -12.442 21.438 0.296  -7.904 1.726  H25 VJB 65 
VJB H26 H26 H 0 1 N N N N N N 40.464 -6.972  17.522 0.803  -3.303 -0.727 H26 VJB 66 
VJB H27 H27 H 0 1 N N N N N N 32.621 -1.848  15.888 -7.714 2.379  0.558  H27 VJB 67 
VJB H28 H28 H 0 1 N N N N N N 34.949 0.569   17.126 -7.854 5.055  2.228  H28 VJB 68 
VJB H29 H29 H 0 1 N N N N N N 38.111 -2.372  15.897 -2.637 4.910  0.264  H29 VJB 69 
# 
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 
VJB O30 P29 DOUB N N 1  
VJB O33 P27 DOUB N N 2  
VJB O34 P27 SING N N 3  
VJB O31 P29 SING N N 4  
VJB P29 O28 SING N N 5  
VJB P29 O32 SING N N 6  
VJB P27 O28 SING N N 7  
VJB P27 O26 SING N N 8  
VJB N04 C05 DOUB Y N 9  
VJB N04 C03 SING Y N 10 
VJB O01 C02 DOUB N N 11 
VJB C05 N06 SING Y N 12 
VJB C03 C02 SING N N 13 
VJB C03 C36 DOUB Y N 14 
VJB O26 C25 SING N N 15 
VJB C02 N40 SING N N 16 
VJB O09 C08 SING N N 17 
VJB C08 C07 SING N N 18 
VJB C08 C10 SING N N 19 
VJB N06 C36 SING Y N 20 
VJB N06 C07 SING N N 21 
VJB C36 N37 SING N N 22 
VJB N40 C38 DOUB N N 23 
VJB C25 C24 SING N N 24 
VJB C07 O35 SING N N 25 
VJB C10 C24 SING N N 26 
VJB C10 O11 SING N N 27 
VJB N37 C38 SING N N 28 
VJB C38 N39 SING N N 29 
VJB C24 O35 SING N N 30 
VJB O11 C12 SING N N 31 
VJB O23 C12 DOUB N N 32 
VJB C12 N13 SING N N 33 
VJB N13 C14 SING N N 34 
VJB C21 C20 SING N N 35 
VJB C14 C15 SING N N 36 
VJB C15 C16 SING N N 37 
VJB C20 C19 SING N N 38 
VJB C16 C17 SING N N 39 
VJB N18 C19 SING N N 40 
VJB N18 C17 SING N N 41 
VJB C19 O22 DOUB N N 42 
VJB C10 H1  SING N N 43 
VJB C15 H2  SING N N 44 
VJB C15 H3  SING N N 45 
VJB C17 H4  SING N N 46 
VJB C17 H5  SING N N 47 
VJB C20 H6  SING N N 48 
VJB C20 H7  SING N N 49 
VJB C21 H8  SING N N 50 
VJB C21 H9  SING N N 51 
VJB C21 H10 SING N N 52 
VJB C24 H11 SING N N 53 
VJB C05 H12 SING N N 54 
VJB C07 H13 SING N N 55 
VJB C08 H14 SING N N 56 
VJB C14 H15 SING N N 57 
VJB C14 H16 SING N N 58 
VJB C16 H17 SING N N 59 
VJB C16 H18 SING N N 60 
VJB C25 H19 SING N N 61 
VJB C25 H20 SING N N 62 
VJB N13 H21 SING N N 63 
VJB N18 H22 SING N N 64 
VJB N37 H23 SING N N 65 
VJB N39 H24 SING N N 66 
VJB N39 H25 SING N N 67 
VJB O09 H26 SING N N 68 
VJB O31 H27 SING N N 69 
VJB O32 H28 SING N N 70 
VJB O34 H29 SING N N 71 
# 
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 
VJB InChI            InChI                1.03  "InChI=1S/C18H29N7O13P2/c1-2-10(26)20-5-3-4-6-21-18(29)37-13-9(7-35-40(33,34)38-39(30,31)32)36-16(12(13)27)25-8-22-11-14(25)23-17(19)24-15(11)28/h8-9,12-13,16,27H,2-7H2,1H3,(H,20,26)(H,21,29)(H,33,34)(H2,30,31,32)(H3,19,23,24,28)/t9-,12-,13-,16-/m1/s1" 
VJB InChIKey         InChI                1.03  AUZGVMRTRAGZKN-RVXWVPLUSA-N                                                                                                                                                                                                                                  
VJB SMILES_CANONICAL CACTVS               3.385 "CCC(=O)NCCCCNC(=O)O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)N=C(N)Nc23"                                                                                                                                                            
VJB SMILES           CACTVS               3.385 "CCC(=O)NCCCCNC(=O)O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)N=C(N)Nc23"                                                                                                                                                                   
VJB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)NCCCCNC(=O)O[C@@H]1[C@H](O[C@H]([C@@H]1O)n2cnc3c2NC(=NC3=O)N)COP(=O)(O)OP(=O)(O)O"                                                                                                                                                                   
VJB SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(=O)NCCCCNC(=O)OC1C(OC(C1O)n2cnc3c2NC(=NC3=O)N)COP(=O)(O)OP(=O)(O)O"                                                                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           VJB 
_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-3~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[4-(propanoylamino)butyl]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 
VJB "Create component" 2021-05-18 PDBE 
VJB "Initial release"  2022-08-03 RCSB 
VJB "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      VJB 
_pdbx_chem_comp_synonyms.name         "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[4-(propanoylamino)butyl]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                            VJB 
_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               C21 
_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      ? 
# 
