data_BGI
# 
_chem_comp.id                                    BGI 
_chem_comp.name                                  "(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name)" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H25 N5 O10" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Nikkomycin Z" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-11-15 
_chem_comp.pdbx_modified_date                    2022-07-08 
_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                        495.440 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     BGI 
_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        7STN 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
BGI C13  C1  C 0 1 N N N 141.145 122.190 96.776  -1.440 -2.621 -0.162 C13  BGI 1  
BGI C17  C2  C 0 1 N N R 140.459 120.053 94.092  2.148  -1.854 -0.388 C17  BGI 2  
BGI C20  C3  C 0 1 N N R 139.227 119.716 92.268  3.613  -0.119 -0.729 C20  BGI 3  
BGI C24  C4  C 0 1 N N N 135.380 119.736 92.427  3.937  2.946  1.299  C24  BGI 4  
BGI C28  C5  C 0 1 N N N 137.556 118.690 90.637  4.551  2.072  -1.205 C28  BGI 5  
BGI C01  C6  C 0 1 N N N 141.180 121.221 99.399  -3.724 -1.373 1.157  C01  BGI 6  
BGI C02  C7  C 0 1 N N S 142.518 121.588 98.794  -3.344 -1.037 -0.287 C02  BGI 7  
BGI C03  C8  C 0 1 N N S 143.448 122.171 99.872  -4.602 -0.664 -1.072 C03  BGI 8  
BGI C04  C9  C 0 1 Y N N 143.985 121.106 100.872 -5.174 0.618  -0.525 C04  BGI 9  
BGI C06  C10 C 0 1 Y N N 145.130 120.696 102.835 -6.054 1.775  1.263  C06  BGI 10 
BGI C07  C11 C 0 1 Y N N 144.968 119.325 102.689 -6.212 2.919  0.494  C07  BGI 11 
BGI C08  C12 C 0 1 Y N N 144.289 118.817 101.590 -5.833 2.891  -0.844 C08  BGI 12 
BGI C09  C13 C 0 1 Y N N 143.792 119.740 100.670 -5.306 1.716  -1.355 C09  BGI 13 
BGI C12  C14 C 0 1 N N S 142.303 122.636 97.686  -2.680 -2.253 -0.936 C12  BGI 14 
BGI C16  C15 C 0 1 N N S 139.965 120.359 95.381  0.910  -2.292 0.396  C16  BGI 15 
BGI C18  C16 C 0 1 N N S 140.541 121.361 93.203  3.433  -2.298 0.346  C18  BGI 16 
BGI C19  C17 C 0 1 N N R 139.520 121.333 92.521  4.419  -1.130 0.116  C19  BGI 17 
BGI C23  C18 C 0 1 N N N 136.775 119.971 92.766  3.627  1.685  0.929  C23  BGI 18 
BGI C25  C19 C 0 1 N N N 135.041 118.997 91.225  4.577  3.799  0.368  C25  BGI 19 
BGI C32  C20 C 0 1 N N N 139.306 119.093 96.001  0.891  -1.599 1.734  C32  BGI 20 
BGI N05  N1  N 0 1 Y N N 144.641 121.538 101.935 -5.548 0.677  0.739  N05  BGI 21 
BGI N15  N2  N 0 1 N N N 141.101 120.806 96.269  -0.296 -1.934 -0.356 N15  BGI 22 
BGI N22  N3  N 0 1 N N N 137.846 119.472 91.906  3.939  1.253  -0.331 N22  BGI 23 
BGI N27  N4  N 0 1 N N N 136.075 118.484 90.349  4.862  3.337  -0.866 N27  BGI 24 
BGI N35  N5  N 0 1 N N N 141.974 123.915 98.262  -3.616 -3.385 -0.927 N35  BGI 25 
BGI O10  O1  O 0 1 N N N 145.497 118.443 103.661 -6.734 4.049  1.039  O10  BGI 26 
BGI O11  O2  O 0 1 N N N 144.527 122.772 99.248  -4.269 -0.486 -2.450 O11  BGI 27 
BGI O14  O3  O 0 1 N N N 140.292 122.955 96.488  -1.472 -3.530 0.639  O14  BGI 28 
BGI O21  O4  O 0 1 N N N 139.492 119.138 93.374  2.228  -0.413 -0.438 O21  BGI 29 
BGI O26  O5  O 0 1 N N N 133.901 118.810 90.956  4.865  4.941  0.679  O26  BGI 30 
BGI O29  O6  O 0 1 N N N 138.402 118.277 89.933  4.827  1.665  -2.317 O29  BGI 31 
BGI O30  O7  O 0 1 N N N 139.756 122.010 91.229  5.570  -1.578 -0.603 O30  BGI 32 
BGI O31  O8  O 0 1 N N N 141.761 121.307 92.311  3.943  -3.506 -0.223 O31  BGI 33 
BGI O33  O9  O 0 1 N N N 139.903 118.456 96.909  1.902  -1.780 2.598  O33  BGI 34 
BGI O34  O10 O 0 1 N N N 138.177 118.708 95.598  -0.035 -0.880 2.029  O34  BGI 35 
BGI H171 H1  H 0 0 N N N 141.454 119.587 94.141  2.125  -2.268 -1.396 H171 BGI 36 
BGI H201 H2  H 0 0 N N N 139.889 119.390 91.452  3.815  -0.265 -1.790 H201 BGI 37 
BGI H241 H3  H 0 0 N N N 134.597 120.111 93.069  3.696  3.300  2.291  H241 BGI 38 
BGI H011 H4  H 0 0 N N N 141.328 120.472 100.191 -4.518 -2.119 1.159  H011 BGI 39 
BGI H013 H5  H 0 0 N N N 140.712 122.120 99.827  -2.853 -1.768 1.679  H013 BGI 40 
BGI H012 H6  H 0 0 N N N 140.527 120.804 98.618  -4.072 -0.471 1.660  H012 BGI 41 
BGI H021 H7  H 0 0 N N N 142.984 120.692 98.359  -2.649 -0.197 -0.293 H021 BGI 42 
BGI H031 H8  H 0 0 N N N 142.879 122.916 100.447 -5.340 -1.461 -0.977 H031 BGI 43 
BGI H061 H9  H 0 0 N N N 145.661 121.082 103.693 -6.349 1.785  2.302  H061 BGI 44 
BGI H081 H10 H 0 0 N N N 144.152 117.755 101.453 -5.944 3.765  -1.469 H081 BGI 45 
BGI H091 H11 H 0 0 N N N 143.256 119.395 99.798  -5.001 1.658  -2.389 H091 BGI 46 
BGI H121 H12 H 0 0 N N N 143.221 122.713 97.085  -2.408 -2.013 -1.964 H121 BGI 47 
BGI H161 H13 H 0 0 N N N 139.211 121.158 95.327  0.937  -3.371 0.546  H161 BGI 48 
BGI H181 H14 H 0 0 N N N 140.614 122.233 93.870  3.239  -2.430 1.410  H181 BGI 49 
BGI H191 H15 H 0 0 N N N 138.634 121.760 93.014  4.711  -0.685 1.067  H191 BGI 50 
BGI H231 H16 H 0 0 N N N 137.022 120.520 93.663  3.136  1.020  1.625  H231 BGI 51 
BGI H151 H17 H 0 0 N N N 141.826 120.162 96.514  -0.271 -1.204 -0.994 H151 BGI 52 
BGI H271 H18 H 0 0 N N N 135.807 117.978 89.529  5.304  3.915  -1.508 H271 BGI 53 
BGI H351 H19 H 0 0 N N N 142.720 124.215 98.856  -3.224 -4.181 -1.407 H351 BGI 54 
BGI H352 H20 H 0 0 N N N 141.839 124.585 97.532  -3.882 -3.626 0.016  H352 BGI 55 
BGI H101 H22 H 0 0 N N N 145.928 118.944 104.343 -6.074 4.642  1.424  H101 BGI 56 
BGI H111 H23 H 0 0 N N N 145.110 123.137 99.904  -3.616 0.209  -2.611 H111 BGI 57 
BGI H301 H24 H 0 0 N N N 139.923 122.933 91.380  6.113  -2.215 -0.119 H301 BGI 58 
BGI H311 H25 H 0 0 N N N 142.546 121.329 92.846  4.750  -3.830 0.200  H311 BGI 59 
BGI H2   H26 H 0 1 N N N 139.371 117.717 97.180  1.845  -1.314 3.444  H2   BGI 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 
BGI O29 C28  DOUB N N 1  
BGI N27 C28  SING N N 2  
BGI N27 C25  SING N N 3  
BGI C28 N22  SING N N 4  
BGI O26 C25  DOUB N N 5  
BGI C25 C24  SING N N 6  
BGI O30 C19  SING N N 7  
BGI N22 C20  SING N N 8  
BGI N22 C23  SING N N 9  
BGI C20 C19  SING N N 10 
BGI C20 O21  SING N N 11 
BGI O31 C18  SING N N 12 
BGI C24 C23  DOUB N N 13 
BGI C19 C18  SING N N 14 
BGI C18 C17  SING N N 15 
BGI O21 C17  SING N N 16 
BGI C17 C16  SING N N 17 
BGI C16 C32  SING N N 18 
BGI C16 N15  SING N N 19 
BGI O34 C32  DOUB N N 20 
BGI C32 O33  SING N N 21 
BGI N15 C13  SING N N 22 
BGI O14 C13  DOUB N N 23 
BGI C13 C12  SING N N 24 
BGI C12 N35  SING N N 25 
BGI C12 C02  SING N N 26 
BGI C02 C01  SING N N 27 
BGI C02 C03  SING N N 28 
BGI O11 C03  SING N N 29 
BGI C03 C04  SING N N 30 
BGI C09 C04  DOUB Y N 31 
BGI C09 C08  SING Y N 32 
BGI C04 N05  SING Y N 33 
BGI C08 C07  DOUB Y N 34 
BGI N05 C06  DOUB Y N 35 
BGI C07 C06  SING Y N 36 
BGI C07 O10  SING N N 37 
BGI C17 H171 SING N N 38 
BGI C20 H201 SING N N 39 
BGI C24 H241 SING N N 40 
BGI C01 H011 SING N N 41 
BGI C01 H013 SING N N 42 
BGI C01 H012 SING N N 43 
BGI C02 H021 SING N N 44 
BGI C03 H031 SING N N 45 
BGI C06 H061 SING N N 46 
BGI C08 H081 SING N N 47 
BGI C09 H091 SING N N 48 
BGI C12 H121 SING N N 49 
BGI C16 H161 SING N N 50 
BGI C18 H181 SING N N 51 
BGI C19 H191 SING N N 52 
BGI C23 H231 SING N N 53 
BGI N15 H151 SING N N 54 
BGI N27 H271 SING N N 55 
BGI N35 H351 SING N N 56 
BGI N35 H352 SING N N 57 
BGI O10 H101 SING N N 58 
BGI O11 H111 SING N N 59 
BGI O30 H301 SING N N 60 
BGI O31 H311 SING N N 61 
BGI O33 H2   SING N N 62 
# 
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 
BGI SMILES           ACDLabs              12.01 "Oc1ccc(nc1)C(O)C(C)C(N)C(=O)NC(C1OC(N2C=CC(=O)NC2=O)C(O)C1O)C(=O)O"                                                                                                                                                                  
BGI InChI            InChI                1.03  "InChI=1S/C20H25N5O10/c1-7(13(28)9-3-2-8(26)6-22-9)11(21)17(31)24-12(19(32)33)16-14(29)15(30)18(35-16)25-5-4-10(27)23-20(25)34/h2-7,11-16,18,26,28-30H,21H2,1H3,(H,24,31)(H,32,33)(H,23,27,34)/t7-,11-,12-,13-,14-,15+,16+,18+/m0/s1" 
BGI InChIKey         InChI                1.03  WWJFFVUVFNBJTN-VHDFTHOZSA-N                                                                                                                                                                                                           
BGI SMILES_CANONICAL CACTVS               3.385 "C[C@@H]([C@H](N)C(=O)N[C@@H]([C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)C(O)=O)[C@H](O)c3ccc(O)cn3"                                                                                                                               
BGI SMILES           CACTVS               3.385 "C[CH]([CH](N)C(=O)N[CH]([CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O)C(O)=O)[CH](O)c3ccc(O)cn3"                                                                                                                                          
BGI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]([C@@H](c1ccc(cn1)O)O)[C@@H](C(=O)N[C@@H]([C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)C(=O)O)N"                                                                                                                           
BGI SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C(c1ccc(cn1)O)O)C(C(=O)NC(C2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)C(=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 
BGI "SYSTEMATIC NAME" ACDLabs              12.01 "(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name)"               
BGI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S},3~{S},4~{S})-2-azanyl-3-methyl-4-oxidanyl-4-(5-oxidanylpyridin-2-yl)butanoyl]amino]-2-[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      BGI 
_pdbx_chem_comp_synonyms.name         "Nikkomycin Z" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
BGI "Create component" 2021-11-15 RCSB 
BGI "Initial release"  2022-07-13 RCSB 
# 
