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 
# 
