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 2022-07-29 _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 # 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.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 39.061 -5.383 19.259 0.015 -0.074 -0.664 C10 VJB 1 VJB C15 C2 C 0 1 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 39.633 -4.623 25.414 8.385 1.376 0.441 C17 VJB 3 VJB C20 C4 C 0 1 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 37.099 -2.350 22.667 13.218 2.227 0.521 C21 VJB 5 VJB C24 C6 C 0 1 N N R 38.016 -5.092 19.925 -1.208 0.424 0.132 C24 VJB 6 VJB C02 C7 C 0 1 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 35.765 -10.009 17.906 -2.848 -5.114 -0.308 C03 VJB 8 VJB C05 C9 C 0 1 Y 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 37.956 -7.474 19.243 -1.279 -1.888 0.252 C07 VJB 10 VJB C08 C11 C 0 1 N N R 38.717 -6.789 18.419 -0.257 -1.584 -0.873 C08 VJB 11 VJB C12 C12 C 0 1 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 42.281 -3.945 22.676 4.761 0.765 -0.706 C14 VJB 13 VJB C16 C14 C 0 1 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 38.216 -2.631 24.936 10.782 1.802 0.332 C19 VJB 15 VJB C25 C16 C 0 1 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 36.740 -9.584 18.785 -1.803 -4.353 0.202 C36 VJB 17 VJB C38 C18 C 0 1 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 35.435 -8.962 17.139 -3.726 -4.260 -0.885 N04 VJB 19 VJB N06 N2 N 0 1 Y 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 41.712 -5.011 21.875 3.530 0.529 0.053 N13 VJB 21 VJB N18 N4 N 0 1 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 37.323 -10.492 19.782 -0.772 -4.990 0.842 N37 VJB 23 VJB N39 N6 N 0 1 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 35.833 -12.331 18.929 -1.741 -7.099 0.508 N40 VJB 25 VJB O01 O1 O 0 1 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 39.938 -7.492 18.118 0.938 -2.346 -0.695 O09 VJB 27 VJB O11 O3 O 0 1 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 38.815 -2.041 25.777 10.812 1.777 1.544 O22 VJB 29 VJB O23 O5 O 0 1 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 36.847 -4.494 17.932 -2.977 2.070 0.150 O26 VJB 31 VJB O28 O7 O 0 1 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 34.877 -1.125 15.382 -6.466 5.440 -0.149 O30 VJB 33 VJB O31 O9 O 0 1 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 34.551 -0.120 17.646 -6.990 4.624 2.181 O32 VJB 35 VJB O33 O11 O 0 1 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 37.762 -2.394 16.780 -3.070 4.604 -0.544 O34 VJB 37 VJB O35 O13 O 0 1 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 36.577 -3.324 16.830 -3.936 3.260 -0.354 P27 VJB 39 VJB P29 P2 P 0 1 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 39.365 -4.614 18.534 0.081 0.440 -1.623 H1 VJB 41 VJB H2 H2 H 0 1 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 40.512 -3.024 23.485 6.044 0.048 0.870 H3 VJB 43 VJB H4 H4 H 0 1 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 39.952 -3.941 26.216 8.499 0.477 1.047 H5 VJB 45 VJB H6 H6 H 0 1 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 36.130 -2.239 24.583 12.244 1.192 -1.098 H7 VJB 47 VJB H8 H8 H 0 1 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 38.058 -2.062 22.211 13.331 1.328 1.127 H9 VJB 49 VJB H10 H10 H 0 1 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 38.237 -4.747 20.946 -0.890 0.794 1.106 H11 VJB 51 VJB H12 H12 H 0 1 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 38.535 -8.095 19.942 -0.769 -2.042 1.203 H13 VJB 53 VJB H14 H14 H 0 1 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 43.262 -4.260 23.060 4.648 1.664 -1.311 H15 VJB 55 VJB H16 H16 H 0 1 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 40.478 -5.588 23.689 7.412 0.341 -1.178 H17 VJB 57 VJB H18 H18 H 0 1 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 37.646 -3.076 19.181 -1.203 2.327 -0.879 H19 VJB 59 VJB H20 H20 H 0 1 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 42.006 -5.957 22.012 3.554 0.509 1.022 H21 VJB 61 VJB H22 H22 H 0 1 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 38.029 -10.168 20.412 -0.036 -4.471 1.204 H23 VJB 63 VJB H24 H24 H 0 1 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 38.136 -12.442 21.438 0.296 -7.904 1.726 H25 VJB 65 VJB H26 H26 H 0 1 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 32.621 -1.848 15.888 -7.714 2.379 0.558 H27 VJB 67 VJB H28 H28 H 0 1 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 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 # _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 #