data_VBA
# 
_chem_comp.id                                    VBA 
_chem_comp.name                                  "[(1R,2R,3S,4R)-4-{[5-(1-benzyl-1H-pyrazole-3-carbonyl)pyrimidin-4-yl]amino}-2,3-dihydroxycyclopentyl]methyl sulfamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H24 N6 O6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-07-22 
_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                        488.517 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VBA 
_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        6XOI 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
VBA C4  C1  C 0 1 N N N N N N 34.756 -2.918  26.104 -3.207 -0.225 -0.439 C4  VBA 1  
VBA C5  C2  C 0 1 N N R N N N 33.791 -3.239  24.932 -4.437 -1.076 -0.034 C5  VBA 2  
VBA C8  C3  C 0 1 N N N N N N 32.376 -3.057  25.437 -5.554 -0.179 0.503  C8  VBA 3  
VBA C10 C4  C 0 1 Y N N N N N 37.875 -3.409  27.463 0.411  -1.137 -0.560 C10 VBA 4  
VBA C15 C5  C 0 1 Y N N N N N 38.465 -3.505  28.725 1.633  -0.436 -0.477 C15 VBA 5  
VBA C17 C6  C 0 1 Y N N N N N 38.505 -4.722  30.982 2.949  1.704  -0.010 C17 VBA 6  
VBA C21 C7  C 0 1 Y N N N N N 40.029 -5.472  32.445 4.457  3.297  0.208  C21 VBA 7  
VBA C22 C8  C 0 1 Y N N N N N 39.880 -5.054  31.142 3.151  3.030  0.440  C22 VBA 8  
VBA C24 C9  C 0 1 Y N N N N N 37.565 -6.931  34.393 7.003  0.843  -0.090 C24 VBA 9  
VBA C26 C10 C 0 1 Y N N N N N 37.258 -9.346  34.353 8.160  -0.141 1.762  C26 VBA 10 
VBA C28 C11 C 0 1 Y N N N N N 35.336 -7.892  34.695 7.493  -1.501 -0.093 C28 VBA 11 
VBA C25 C12 C 0 1 Y N N N N N 38.096 -8.226  34.264 7.611  0.968  1.146  C25 VBA 12 
VBA C27 C13 C 0 1 Y N N N N N 35.880 -9.178  34.566 8.100  -1.375 1.143  C27 VBA 13 
VBA C29 C14 C 0 1 Y N N N N N 36.186 -6.778  34.618 6.944  -0.391 -0.709 C29 VBA 14 
VBA C23 C15 C 0 1 N N N N N N 38.434 -5.714  34.327 6.400  2.051  -0.758 C23 VBA 15 
VBA N20 N1  N 0 1 Y N N N N N 38.776 -5.378  32.970 4.999  2.187  -0.350 N20 VBA 16 
VBA N19 N2  N 0 1 Y N N N N N 37.824 -4.935  32.121 4.107  1.270  -0.468 N19 VBA 17 
VBA C16 C16 C 0 1 N N N N N N 37.788 -4.224  29.806 1.682  0.946  0.033  C16 VBA 18 
VBA O18 O1  O 0 1 N N N N N N 36.580 -4.367  29.676 0.680  1.461  0.489  O18 VBA 19 
VBA C14 C17 C 0 1 Y N N N N N 39.673 -2.870  28.936 2.796  -1.092 -0.893 C14 VBA 20 
VBA N13 N3  N 0 1 Y N N N N N 40.305 -2.174  27.966 2.706  -2.332 -1.344 N13 VBA 21 
VBA C12 C18 C 0 1 Y N N N N N 39.676 -2.134  26.786 1.544  -2.954 -1.406 C12 VBA 22 
VBA N11 N4  N 0 1 Y N N N N N 38.505 -2.724  26.508 0.420  -2.382 -1.027 N11 VBA 23 
VBA N9  N5  N 0 1 N N N N N N 36.637 -4.020  27.220 -0.767 -0.545 -0.159 N9  VBA 24 
VBA C3  C19 C 0 1 N N R N N N 35.983 -3.850  25.895 -2.041 -1.241 -0.358 C3  VBA 25 
VBA C2  C20 C 0 1 N N S N N N 35.185 -5.135  25.620 -2.380 -2.108 0.872  C2  VBA 26 
VBA O7  O2  O 0 1 N N N N N N 36.108 -6.079  25.074 -2.008 -3.467 0.631  O7  VBA 27 
VBA C1  C21 C 0 1 N N R N N N 34.085 -4.731  24.607 -3.906 -2.003 1.078  C1  VBA 28 
VBA O6  O3  O 0 1 N N N N N N 34.582 -4.824  23.255 -4.507 -3.294 0.968  O6  VBA 29 
VBA O30 O4  O 0 1 N N N N N N 31.501 -3.327  24.379 -6.049 0.649  -0.550 O30 VBA 30 
VBA S31 S1  S 0 1 N N N N N N 30.031 -3.992  24.679 -7.170 1.587  -0.126 S31 VBA 31 
VBA O33 O5  O 0 1 N N N N N N 29.395 -3.899  23.376 -7.671 2.178  -1.317 O33 VBA 32 
VBA O34 O6  O 0 1 N N N N N N 30.351 -5.270  25.275 -7.984 0.855  0.780  O34 VBA 33 
VBA N32 N6  N 0 1 N N N N N N 29.417 -2.778  25.669 -6.481 2.811  0.749  N32 VBA 34 
VBA H1  H1  H 0 1 N N N N N N 35.064 -1.863  26.071 -3.318 0.156  -1.454 H1  VBA 35 
VBA H2  H2  H 0 1 N N N N N N 34.273 -3.129  27.069 -3.056 0.594  0.265  H2  VBA 36 
VBA H3  H3  H 0 1 N N N N N N 33.997 -2.597  24.063 -4.792 -1.660 -0.883 H3  VBA 37 
VBA H4  H4  H 0 1 N N N N N N 32.234 -2.023  25.784 -6.364 -0.800 0.889  H4  VBA 38 
VBA H5  H5  H 0 1 N N N N N N 32.184 -3.753  26.267 -5.164 0.447  1.305  H5  VBA 39 
VBA H6  H6  H 0 1 N N N N N N 40.932 -5.799  32.938 4.971  4.221  0.426  H6  VBA 40 
VBA H7  H7  H 0 1 N N N N N N 40.653 -4.991  30.390 2.416  3.691  0.877  H7  VBA 41 
VBA H8  H8  H 0 1 N N N N N N 37.672 -10.339 34.258 8.634  -0.043 2.727  H8  VBA 42 
VBA H9  H9  H 0 1 N N N N N N 34.276 -7.760  34.852 7.446  -2.465 -0.576 H9  VBA 43 
VBA H10 H10 H 0 1 N N N N N N 39.155 -8.359  34.096 7.657  1.933  1.630  H10 VBA 44 
VBA H11 H11 H 0 1 N N N N N N 35.237 -10.043 34.631 8.528  -2.242 1.625  H11 VBA 45 
VBA H12 H12 H 0 1 N N N N N N 35.774 -5.787  34.734 6.470  -0.489 -1.674 H12 VBA 46 
VBA H13 H13 H 0 1 N N N N N N 39.359 -5.905  34.891 6.952  2.944  -0.464 H13 VBA 47 
VBA H14 H14 H 0 1 N N N N N N 37.897 -4.867  34.780 6.453  1.932  -1.840 H14 VBA 48 
VBA H15 H15 H 0 1 N N N N N N 40.129 -2.932  29.913 3.753  -0.594 -0.848 H15 VBA 49 
VBA H16 H16 H 0 1 N N N N N N 40.152 -1.580  25.990 1.513  -3.966 -1.781 H16 VBA 50 
VBA H17 H17 H 0 1 N N N N N N 36.000 -3.669  27.906 -0.753 0.332  0.254  H17 VBA 51 
VBA H18 H18 H 0 1 N N N N N N 36.649 -3.542  25.076 -2.004 -1.852 -1.259 H18 VBA 52 
VBA H19 H19 H 0 1 N N N N N N 34.725 -5.503  26.549 -1.859 -1.729 1.752  H19 VBA 53 
VBA H20 H20 H 0 1 N N N N N N 36.762 -6.297  25.727 -2.196 -4.063 1.369  H20 VBA 54 
VBA H21 H21 H 0 1 N N N N N N 33.182 -5.341  24.757 -4.120 -1.573 2.057  H21 VBA 55 
VBA H22 H22 H 0 1 N N N N N N 34.765 -5.733  23.046 -4.214 -3.924 1.641  H22 VBA 56 
VBA H23 H23 H 0 1 N N N N N N 29.848 -2.832  26.570 -5.522 2.821  0.899  H23 VBA 57 
VBA H24 H24 H 0 1 N N N N N N 29.609 -1.886  25.261 -7.035 3.519  1.113  H24 VBA 58 
# 
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 
VBA O6  C1  SING N N 1  
VBA O33 S31 DOUB N N 2  
VBA O30 S31 SING N N 3  
VBA O30 C8  SING N N 4  
VBA C1  C5  SING N N 5  
VBA C1  C2  SING N N 6  
VBA S31 O34 DOUB N N 7  
VBA S31 N32 SING N N 8  
VBA C5  C8  SING N N 9  
VBA C5  C4  SING N N 10 
VBA O7  C2  SING N N 11 
VBA C2  C3  SING N N 12 
VBA C3  C4  SING N N 13 
VBA C3  N9  SING N N 14 
VBA N11 C12 DOUB Y N 15 
VBA N11 C10 SING Y N 16 
VBA C12 N13 SING Y N 17 
VBA N9  C10 SING N N 18 
VBA C10 C15 DOUB Y N 19 
VBA N13 C14 DOUB Y N 20 
VBA C15 C14 SING Y N 21 
VBA C15 C16 SING N N 22 
VBA O18 C16 DOUB N N 23 
VBA C16 C17 SING N N 24 
VBA C17 C22 SING Y N 25 
VBA C17 N19 DOUB Y N 26 
VBA C22 C21 DOUB Y N 27 
VBA N19 N20 SING Y N 28 
VBA C21 N20 SING Y N 29 
VBA N20 C23 SING N N 30 
VBA C25 C26 DOUB Y N 31 
VBA C25 C24 SING Y N 32 
VBA C23 C24 SING N N 33 
VBA C26 C27 SING Y N 34 
VBA C24 C29 DOUB Y N 35 
VBA C27 C28 DOUB Y N 36 
VBA C29 C28 SING Y N 37 
VBA C4  H1  SING N N 38 
VBA C4  H2  SING N N 39 
VBA C5  H3  SING N N 40 
VBA C8  H4  SING N N 41 
VBA C8  H5  SING N N 42 
VBA C21 H6  SING N N 43 
VBA C22 H7  SING N N 44 
VBA C26 H8  SING N N 45 
VBA C28 H9  SING N N 46 
VBA C25 H10 SING N N 47 
VBA C27 H11 SING N N 48 
VBA C29 H12 SING N N 49 
VBA C23 H13 SING N N 50 
VBA C23 H14 SING N N 51 
VBA C14 H15 SING N N 52 
VBA C12 H16 SING N N 53 
VBA N9  H17 SING N N 54 
VBA C3  H18 SING N N 55 
VBA C2  H19 SING N N 56 
VBA O7  H20 SING N N 57 
VBA C1  H21 SING N N 58 
VBA O6  H22 SING N N 59 
VBA N32 H23 SING N N 60 
VBA N32 H24 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 
VBA SMILES           ACDLabs              12.01 "C1C(COS(=O)(N)=O)C(C(C1Nc2c(cncn2)C(c4ccn(Cc3ccccc3)n4)=O)O)O"                                                                                                                                                          
VBA InChI            InChI                1.03  "InChI=1S/C21H24N6O6S/c22-34(31,32)33-11-14-8-17(20(30)18(14)28)25-21-15(9-23-12-24-21)19(29)16-6-7-27(26-16)10-13-4-2-1-3-5-13/h1-7,9,12,14,17-18,20,28,30H,8,10-11H2,(H2,22,31,32)(H,23,24,25)/t14-,17-,18-,20+/m1/s1" 
VBA InChIKey         InChI                1.03  AGIKMOLYLSSZIM-ZESCBINXSA-N                                                                                                                                                                                              
VBA SMILES_CANONICAL CACTVS               3.385 "N[S](=O)(=O)OC[C@H]1C[C@@H](Nc2ncncc2C(=O)c3ccn(Cc4ccccc4)n3)[C@H](O)[C@@H]1O"                                                                                                                                          
VBA SMILES           CACTVS               3.385 "N[S](=O)(=O)OC[CH]1C[CH](Nc2ncncc2C(=O)c3ccn(Cc4ccccc4)n3)[CH](O)[CH]1O"                                                                                                                                                
VBA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Cn2ccc(n2)C(=O)c3cncnc3N[C@@H]4C[C@@H]([C@H]([C@H]4O)O)COS(=O)(=O)N"                                                                                                                                          
VBA SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Cn2ccc(n2)C(=O)c3cncnc3NC4CC(C(C4O)O)COS(=O)(=O)N"                                                                                                                                                            
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
VBA "SYSTEMATIC NAME" ACDLabs              12.01 "[(1R,2R,3S,4R)-4-{[5-(1-benzyl-1H-pyrazole-3-carbonyl)pyrimidin-4-yl]amino}-2,3-dihydroxycyclopentyl]methyl sulfamate"                      
VBA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[5-[1-(phenylmethyl)pyrazol-3-yl]carbonylpyrimidin-4-yl]amino]cyclopentyl]methyl sulfamate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VBA "Create component" 2020-07-22 RCSB 
VBA "Initial release"  2021-03-24 RCSB 
VBA "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            VBA 
_pdbx_chem_comp_pcm.modified_residue_id                GLY 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               C-terminal 
_pdbx_chem_comp_pcm.comp_id_linking_atom               N32 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   C 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
