data_VDG # _chem_comp.id VDG _chem_comp.name "(2S)-2-[[(2S,3S,4S)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-[(2R,3S,4R,5R)-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H25 N5 O13" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-07-19 _chem_comp.pdbx_modified_date 2023-10-13 _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 507.406 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VDG _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 8K3P _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 VDG C20 C1 C 0 1 N N S 114.486 141.069 94.154 -1.320 -3.438 -0.129 C20 VDG 1 VDG C21 C2 C 0 1 N N R 114.826 140.681 92.699 -2.529 -2.505 -0.383 C21 VDG 2 VDG C22 C3 C 0 1 N N R 116.114 140.451 92.670 -2.283 -1.369 0.642 C22 VDG 3 VDG C24 C4 C 0 1 N N N 117.358 141.720 96.628 0.743 -1.850 -1.590 C24 VDG 4 VDG C26 C5 C 0 1 N N N 116.511 138.541 91.290 -2.528 0.481 -0.915 C26 VDG 5 VDG C28 C6 C 0 1 N N S 113.214 143.017 98.617 4.383 -1.182 0.980 C28 VDG 6 VDG C19 C7 C 0 1 N N R 115.861 141.657 94.702 -0.283 -2.533 0.562 C19 VDG 7 VDG C23 C8 C 0 1 N N S 115.961 141.469 96.206 1.009 -2.501 -0.257 C23 VDG 8 VDG C25 C9 C 0 1 N N N 116.507 138.275 93.575 -3.965 0.386 0.951 C25 VDG 9 VDG C27 C10 C 0 1 N N N 114.116 142.004 97.912 3.335 -1.969 0.236 C27 VDG 10 VDG C29 C11 C 0 1 N N S 113.546 142.969 100.105 4.552 0.190 0.324 C29 VDG 11 VDG C30 C12 C 0 1 N N N 116.768 136.917 93.421 -4.570 1.525 0.551 C30 VDG 12 VDG C31 C13 C 0 1 N N S 114.555 144.074 100.428 3.266 1.000 0.499 C31 VDG 13 VDG C32 C14 C 0 1 N N N 116.892 136.422 92.124 -4.127 2.161 -0.634 C32 VDG 14 VDG C33 C15 C 0 1 N N N 116.918 135.980 94.665 -5.702 2.111 1.355 C33 VDG 15 VDG C34 C16 C 0 1 N N N 114.443 144.458 101.911 3.478 2.416 -0.042 C34 VDG 16 VDG C35 C17 C 0 1 N N N 116.572 145.161 102.619 2.240 4.420 -0.428 C35 VDG 17 VDG N14 N1 N 0 1 N N N 116.380 139.058 92.502 -2.939 -0.133 0.209 N14 VDG 18 VDG N15 N2 N 0 1 N N N 115.082 142.465 96.878 2.027 -1.736 0.466 N15 VDG 19 VDG N16 N3 N 0 1 N N N 116.757 137.263 91.097 -3.113 1.618 -1.337 N16 VDG 20 VDG N17 N4 N 0 1 N N N 111.834 142.647 98.422 5.661 -1.906 0.938 N17 VDG 21 VDG N18 N5 N 0 1 N N N 116.959 145.474 103.972 1.111 5.155 -0.403 N18 VDG 22 VDG O01 O1 O 0 1 N N N 116.750 140.947 94.132 -0.848 -1.213 0.634 O01 VDG 23 VDG O02 O2 O 0 1 N N N 113.561 141.998 94.173 -1.693 -4.518 0.730 O02 VDG 24 VDG O03 O3 O 0 1 N N N 114.505 141.838 91.773 -3.760 -3.180 -0.112 O03 VDG 25 VDG O04 O4 O 0 1 N N N 118.042 142.602 96.042 1.342 -0.849 -1.903 O04 VDG 26 VDG O05 O5 O 0 1 N N N 117.845 141.077 97.548 -0.161 -2.381 -2.428 O05 VDG 27 VDG O06 O6 O 0 1 N N N 116.403 139.222 90.378 -1.611 0.006 -1.557 O06 VDG 28 VDG O07 O7 O 0 1 N N N 114.051 140.855 98.193 3.668 -2.813 -0.569 O07 VDG 29 VDG O08 O8 O 0 1 N N N 112.374 143.178 100.841 5.639 0.882 0.940 O08 VDG 30 VDG O09 O9 O 0 1 N N N 114.269 145.182 99.654 2.929 1.066 1.886 O09 VDG 31 VDG O10 O10 O 0 1 N N N 117.114 135.286 91.941 -4.657 3.190 -1.014 O10 VDG 32 VDG O11 O11 O 0 1 N N N 118.017 136.429 95.434 -5.955 1.286 2.494 O11 VDG 33 VDG O12 O12 O 0 1 N N N 115.341 145.546 102.158 2.226 3.148 0.015 O12 VDG 34 VDG O13 O13 O 0 1 N N N 117.325 144.567 101.905 3.272 4.904 -0.850 O13 VDG 35 VDG H1 H1 H 0 1 N N N 114.220 140.170 94.729 -0.926 -3.820 -1.071 H1 VDG 36 VDG H2 H2 H 0 1 N N N 114.230 139.803 92.411 -2.515 -2.119 -1.402 H2 VDG 37 VDG H3 H3 H 0 1 N N N 116.620 141.031 91.884 -2.632 -1.663 1.632 H3 VDG 38 VDG H4 H4 H 0 1 N N N 113.410 144.026 98.224 4.072 -1.053 2.017 H4 VDG 39 VDG H5 H5 H 0 1 N N N 115.916 142.727 94.454 -0.076 -2.905 1.566 H5 VDG 40 VDG H6 H6 H 0 1 N N N 115.656 140.447 96.476 1.364 -3.520 -0.415 H6 VDG 41 VDG H7 H7 H 0 1 N N N 116.407 138.696 94.565 -4.290 -0.113 1.852 H7 VDG 42 VDG H8 H8 H 0 1 N N N 113.992 141.993 100.344 4.758 0.061 -0.739 H8 VDG 43 VDG H9 H9 H 0 1 N N N 115.571 143.702 100.230 2.456 0.519 -0.049 H9 VDG 44 VDG H10 H10 H 0 1 N N N 116.001 136.018 95.271 -5.431 3.114 1.686 H10 VDG 45 VDG H11 H11 H 0 1 N N N 117.095 134.947 94.332 -6.598 2.162 0.737 H11 VDG 46 VDG H12 H12 H 0 1 N N N 113.412 144.766 102.140 4.226 2.928 0.563 H12 VDG 47 VDG H13 H13 H 0 1 N N N 114.717 143.598 102.540 3.821 2.362 -1.076 H13 VDG 48 VDG H14 H14 H 0 1 N N N 115.140 143.434 96.637 1.761 -1.061 1.110 H14 VDG 49 VDG H15 H15 H 0 1 N N N 116.844 136.916 90.163 -2.803 2.048 -2.149 H15 VDG 50 VDG H16 H16 H 0 1 N N N 111.243 143.309 98.883 6.014 -1.961 -0.006 H16 VDG 51 VDG H17 H17 H 0 1 N N N 111.626 142.639 97.444 6.338 -1.480 1.553 H17 VDG 52 VDG H19 H19 H 0 1 N N N 117.857 145.194 104.313 0.288 4.769 -0.065 H19 VDG 53 VDG H20 H20 H 0 1 N N N 116.330 145.971 104.570 1.122 6.071 -0.721 H20 VDG 54 VDG H21 H21 H 0 1 N N N 113.361 142.228 95.073 -2.345 -5.120 0.345 H21 VDG 55 VDG H22 H22 H 0 1 N N N 113.571 142.009 91.791 -3.915 -3.954 -0.671 H22 VDG 56 VDG H23 H23 H 0 1 N N N 118.739 141.362 97.695 -0.297 -1.928 -3.272 H23 VDG 57 VDG H24 H24 H 0 1 N N N 112.573 143.149 101.769 5.523 1.032 1.889 H24 VDG 58 VDG H25 H25 H 0 1 N N N 114.891 145.873 99.848 3.607 1.483 2.436 H25 VDG 59 VDG H26 H26 H 0 1 N N N 118.122 135.869 96.195 -6.673 1.604 3.058 H26 VDG 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 VDG O06 C26 DOUB N N 1 VDG N16 C26 SING N N 2 VDG N16 C32 SING N N 3 VDG C26 N14 SING N N 4 VDG O03 C21 SING N N 5 VDG O10 C32 DOUB N N 6 VDG C32 C30 SING N N 7 VDG N14 C22 SING N N 8 VDG N14 C25 SING N N 9 VDG C22 C21 SING N N 10 VDG C22 O01 SING N N 11 VDG C21 C20 SING N N 12 VDG C30 C25 DOUB N N 13 VDG C30 C33 SING N N 14 VDG O01 C19 SING N N 15 VDG C20 O02 SING N N 16 VDG C20 C19 SING N N 17 VDG C33 O11 SING N N 18 VDG C19 C23 SING N N 19 VDG O04 C24 DOUB N N 20 VDG C23 C24 SING N N 21 VDG C23 N15 SING N N 22 VDG C24 O05 SING N N 23 VDG N15 C27 SING N N 24 VDG C27 O07 DOUB N N 25 VDG C27 C28 SING N N 26 VDG N17 C28 SING N N 27 VDG C28 C29 SING N N 28 VDG O09 C31 SING N N 29 VDG C29 C31 SING N N 30 VDG C29 O08 SING N N 31 VDG C31 C34 SING N N 32 VDG O13 C35 DOUB N N 33 VDG C34 O12 SING N N 34 VDG O12 C35 SING N N 35 VDG C35 N18 SING N N 36 VDG C20 H1 SING N N 37 VDG C21 H2 SING N N 38 VDG C22 H3 SING N N 39 VDG C28 H4 SING N N 40 VDG C19 H5 SING N N 41 VDG C23 H6 SING N N 42 VDG C25 H7 SING N N 43 VDG C29 H8 SING N N 44 VDG C31 H9 SING N N 45 VDG C33 H10 SING N N 46 VDG C33 H11 SING N N 47 VDG C34 H12 SING N N 48 VDG C34 H13 SING N N 49 VDG N15 H14 SING N N 50 VDG N16 H15 SING N N 51 VDG N17 H16 SING N N 52 VDG N17 H17 SING N N 53 VDG N18 H19 SING N N 54 VDG N18 H20 SING N N 55 VDG O02 H21 SING N N 56 VDG O03 H22 SING N N 57 VDG O05 H23 SING N N 58 VDG O08 H24 SING N N 59 VDG O09 H25 SING N N 60 VDG O11 H26 SING N N 61 # 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 VDG InChI InChI 1.06 "InChI=1S/C17H25N5O13/c18-6(8(25)5(24)3-34-16(19)32)13(29)20-7(15(30)31)11-9(26)10(27)14(35-11)22-1-4(2-23)12(28)21-17(22)33/h1,5-11,14,23-27H,2-3,18H2,(H2,19,32)(H,20,29)(H,30,31)(H,21,28,33)/t5-,6-,7-,8+,9-,10+,11+,14+/m0/s1" VDG InChIKey InChI 1.06 YFZNSPMAOIVQRP-YVKGXWRCSA-N VDG SMILES_CANONICAL CACTVS 3.385 "N[C@@H]([C@H](O)[C@@H](O)COC(N)=O)C(=O)N[C@@H]([C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=C(CO)C(=O)NC2=O)C(O)=O" VDG SMILES CACTVS 3.385 "N[CH]([CH](O)[CH](O)COC(N)=O)C(=O)N[CH]([CH]1O[CH]([CH](O)[CH]1O)N2C=C(CO)C(=O)NC2=O)C(O)=O" VDG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)[C@@H](C(=O)O)NC(=O)[C@H]([C@@H]([C@H](COC(=O)N)O)O)N)O)O)CO" VDG SMILES "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1C2C(C(C(O2)C(C(=O)O)NC(=O)C(C(C(COC(=O)N)O)O)N)O)O)CO" # _pdbx_chem_comp_identifier.comp_id VDG _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~{S})-2-[[(2~{S},3~{S},4~{S})-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-[(2~{R},3~{S},4~{R},5~{R})-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic 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 VDG "Create component" 2023-07-19 PDBJ VDG "Initial release" 2023-10-18 RCSB #