data_BJ9
# 
_chem_comp.id                                    BJ9 
_chem_comp.name                                  "1-{(2R,3R,4S,5R)-5-[(S)-{[(2S,3S,4S)-2-amino-5-(carbamoyloxy)-3,4-dihydroxypentanoyl]amino}(carboxy)methyl]-3,4-dihydroxyoxolan-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid (non-preferred name)" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H23 N5 O14" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Polyoxin d" 
_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                        521.390 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     BJ9 
_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        7STO 
_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 
BJ9 C10  C1  C 0 1 N N R 129.446 97.559  91.891  3.480  -2.109 0.170  C10  BJ9 1  
BJ9 C15  C2  C 0 1 N N N 127.873 97.068  96.090  0.174  -1.996 1.452  C15  BJ9 2  
BJ9 C21  C3  C 0 1 N N S 132.029 95.594  97.011  -3.568 -1.582 -1.023 C21  BJ9 3  
BJ9 C22  C4  C 0 1 N N S 131.966 96.031  98.479  -3.901 -0.308 -0.244 C22  BJ9 4  
BJ9 C24  C5  C 0 1 N N N 132.093 93.739  99.529  -5.555 1.547  0.012  C24  BJ9 5  
BJ9 C26  C6  C 0 1 N N N 130.715 92.735  101.186 -7.147 3.325  0.010  C26  BJ9 6  
BJ9 C01  C7  C 0 1 N N N 127.321 99.587  92.313  4.506  1.034  -0.903 C01  BJ9 7  
BJ9 C02  C8  C 0 1 N N N 126.479 100.733 91.979  4.978  2.230  -0.396 C02  BJ9 8  
BJ9 C03  C9  C 0 1 N N N 125.608 100.684 90.806  4.439  2.696  0.893  C03  BJ9 9  
BJ9 C06  C10 C 0 1 N N N 126.423 98.280  90.237  3.097  0.783  0.968  C06  BJ9 10 
BJ9 C09  C11 C 0 1 N N R 128.175 97.253  91.836  3.071  -0.928 -0.746 C09  BJ9 11 
BJ9 C11  C12 C 0 1 N N S 130.002 96.597  92.921  2.398  -3.166 -0.160 C11  BJ9 12 
BJ9 C12  C13 C 0 1 N N R 128.852 96.421  93.937  1.240  -2.345 -0.759 C12  BJ9 13 
BJ9 C14  C14 C 0 1 N N S 129.002 97.350  95.135  -0.030 -2.555 0.068  C14  BJ9 14 
BJ9 C19  C15 C 0 1 N N N 130.691 95.802  96.361  -2.414 -2.289 -0.360 C19  BJ9 15 
BJ9 C23  C16 C 0 1 N N S 132.824 95.066  99.342  -5.150 0.343  -0.841 C23  BJ9 16 
BJ9 C34  C17 C 0 1 N N N 126.502 101.977 92.860  5.988  3.013  -1.120 C34  BJ9 17 
BJ9 N05  N1  N 0 1 N N N 125.570 99.514  89.957  3.514  1.937  1.517  N05  BJ9 18 
BJ9 N08  N2  N 0 1 N N N 127.323 98.391  91.482  3.570  0.340  -0.207 N08  BJ9 19 
BJ9 N18  N3  N 0 1 N N N 130.331 97.138  95.794  -1.152 -1.868 -0.576 N18  BJ9 20 
BJ9 N28  N4  N 0 1 N N N 130.843 91.705  102.199 -8.178 4.010  -0.523 N28  BJ9 21 
BJ9 N31  N5  N 0 1 N N N 133.040 96.400  96.301  -4.741 -2.467 -1.038 N31  BJ9 22 
BJ9 O04  O1  O 0 1 N N N 124.942 101.599 90.558  4.820  3.742  1.384  O04  BJ9 23 
BJ9 O07  O2  O 0 1 N N N 126.397 97.327  89.553  2.266  0.119  1.556  O07  BJ9 24 
BJ9 O13  O3  O 0 1 N N N 127.773 96.737  93.307  1.628  -0.962 -0.715 O13  BJ9 25 
BJ9 O16  O4  O 0 1 N N N 126.677 97.418  95.779  -0.544 -1.113 1.859  O16  BJ9 26 
BJ9 O17  O5  O 0 1 N N N 128.085 96.499  97.171  1.153  -2.477 2.233  O17  BJ9 27 
BJ9 O20  O6  O 0 1 N N N 129.906 94.892  96.300  -2.621 -3.237 0.368  O20  BJ9 28 
BJ9 O25  O7  O 0 1 N N N 131.787 93.591  100.917 -6.667 2.235  -0.619 O25  BJ9 29 
BJ9 O27  O8  O 0 1 N N N 129.708 92.846  100.593 -6.651 3.690  1.057  O27  BJ9 30 
BJ9 O29  O9  O 0 1 N N N 133.048 95.634  100.583 -6.218 -0.605 -0.864 O29  BJ9 31 
BJ9 O30  O10 O 0 1 N N N 132.459 97.308  98.587  -4.144 -0.637 1.126  O30  BJ9 32 
BJ9 O32  O11 O 0 1 N N N 130.280 95.431  92.337  2.891  -4.106 -1.115 O32  BJ9 33 
BJ9 O33  O12 O 0 1 N N N 130.136 97.327  90.576  4.782  -2.591 -0.169 O33  BJ9 34 
BJ9 O35  O13 O 0 1 N N N 127.581 102.420 93.273  6.434  4.177  -0.608 O35  BJ9 35 
BJ9 O36  O14 O 0 1 N N N 125.420 102.561 93.162  6.421  2.611  -2.183 O36  BJ9 36 
BJ9 H101 H1  H 0 0 N N N 129.620 98.593  92.223  3.435  -1.821 1.220  H101 BJ9 37 
BJ9 H211 H2  H 0 0 N N N 132.299 94.529  96.964  -3.296 -1.322 -2.046 H211 BJ9 38 
BJ9 H221 H3  H 0 0 N N N 130.922 95.977  98.823  -3.063 0.386  -0.307 H221 BJ9 39 
BJ9 H241 H4  H 0 0 N N N 131.164 93.739  98.941  -5.854 1.205  1.003  H241 BJ9 40 
BJ9 H242 H5  H 0 0 N N N 132.736 92.910  99.199  -4.710 2.229  0.103  H242 BJ9 41 
BJ9 H011 H6  H 0 0 N N N 127.951 99.627  93.189  4.876  0.658  -1.845 H011 BJ9 42 
BJ9 H091 H7  H 0 0 N N N 127.987 96.427  91.134  3.437  -1.085 -1.761 H091 BJ9 43 
BJ9 H111 H8  H 0 0 N N N 130.873 97.044  93.422  2.074  -3.676 0.747  H111 BJ9 44 
BJ9 H121 H9  H 0 0 N N N 128.848 95.379  94.289  1.064  -2.650 -1.791 H121 BJ9 45 
BJ9 H141 H10 H 0 0 N N N 128.931 98.392  94.789  -0.247 -3.621 0.135  H141 BJ9 46 
BJ9 H231 H11 H 0 0 N N N 133.773 94.879  98.819  -4.936 0.674  -1.858 H231 BJ9 47 
BJ9 H051 H12 H 0 0 N N N 124.965 99.514  89.161  3.149  2.225  2.368  H051 BJ9 48 
BJ9 H181 H13 H 0 0 N N N 130.981 97.895  95.855  -0.987 -1.110 -1.158 H181 BJ9 49 
BJ9 H281 H14 H 0 0 N N N 130.075 91.093  102.390 -8.575 3.718  -1.359 H281 BJ9 50 
BJ9 H282 H15 H 0 0 N N N 131.699 91.607  102.707 -8.524 4.795  -0.070 H282 BJ9 51 
BJ9 H311 H16 H 0 0 N N N 133.934 96.266  96.729  -4.568 -3.287 -1.600 H311 BJ9 52 
BJ9 H1   H17 H 0 1 N N N 133.082 96.114  95.344  -5.013 -2.723 -0.100 H1   BJ9 53 
BJ9 H2   H19 H 0 1 N N N 127.267 96.400  97.643  1.245  -2.087 3.113  H2   BJ9 54 
BJ9 H291 H20 H 0 0 N N N 133.573 95.044  101.112 -6.462 -0.944 0.008  H291 BJ9 55 
BJ9 H301 H21 H 0 0 N N N 132.423 97.586  99.495  -4.879 -1.252 1.258  H301 BJ9 56 
BJ9 H321 H22 H 0 0 N N N 130.629 94.828  92.983  3.659  -4.610 -0.811 H321 BJ9 57 
BJ9 H331 H23 H 0 0 N N N 131.054 97.559  90.654  5.046  -3.385 0.316  H331 BJ9 58 
BJ9 H3   H24 H 0 1 N N N 127.425 103.196 93.798  7.098  4.657  -1.121 H3   BJ9 59 
# 
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 
BJ9 O07 C06  DOUB N N 1  
BJ9 N05 C06  SING N N 2  
BJ9 N05 C03  SING N N 3  
BJ9 C06 N08  SING N N 4  
BJ9 O04 C03  DOUB N N 5  
BJ9 O33 C10  SING N N 6  
BJ9 C03 C02  SING N N 7  
BJ9 N08 C09  SING N N 8  
BJ9 N08 C01  SING N N 9  
BJ9 C09 C10  SING N N 10 
BJ9 C09 O13  SING N N 11 
BJ9 C10 C11  SING N N 12 
BJ9 C02 C01  DOUB N N 13 
BJ9 C02 C34  SING N N 14 
BJ9 O32 C11  SING N N 15 
BJ9 C34 O36  DOUB N N 16 
BJ9 C34 O35  SING N N 17 
BJ9 C11 C12  SING N N 18 
BJ9 O13 C12  SING N N 19 
BJ9 C12 C14  SING N N 20 
BJ9 C14 N18  SING N N 21 
BJ9 C14 C15  SING N N 22 
BJ9 O16 C15  DOUB N N 23 
BJ9 N18 C19  SING N N 24 
BJ9 C15 O17  SING N N 25 
BJ9 O20 C19  DOUB N N 26 
BJ9 N31 C21  SING N N 27 
BJ9 C19 C21  SING N N 28 
BJ9 C21 C22  SING N N 29 
BJ9 C22 O30  SING N N 30 
BJ9 C22 C23  SING N N 31 
BJ9 C23 C24  SING N N 32 
BJ9 C23 O29  SING N N 33 
BJ9 C24 O25  SING N N 34 
BJ9 O27 C26  DOUB N N 35 
BJ9 O25 C26  SING N N 36 
BJ9 C26 N28  SING N N 37 
BJ9 C10 H101 SING N N 38 
BJ9 C21 H211 SING N N 39 
BJ9 C22 H221 SING N N 40 
BJ9 C24 H241 SING N N 41 
BJ9 C24 H242 SING N N 42 
BJ9 C01 H011 SING N N 43 
BJ9 C09 H091 SING N N 44 
BJ9 C11 H111 SING N N 45 
BJ9 C12 H121 SING N N 46 
BJ9 C14 H141 SING N N 47 
BJ9 C23 H231 SING N N 48 
BJ9 N05 H051 SING N N 49 
BJ9 N18 H181 SING N N 50 
BJ9 N28 H281 SING N N 51 
BJ9 N28 H282 SING N N 52 
BJ9 N31 H311 SING N N 53 
BJ9 N31 H1   SING N N 54 
BJ9 O17 H2   SING N N 55 
BJ9 O29 H291 SING N N 56 
BJ9 O30 H301 SING N N 57 
BJ9 O32 H321 SING N N 58 
BJ9 O33 H331 SING N N 59 
BJ9 O35 H3   SING N N 60 
# 
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 
BJ9 SMILES           ACDLabs              12.01 "NC(=O)OCC(O)C(O)C(N)C(=O)NC(C1OC(N2C=C(C(=O)NC2=O)C(=O)O)C(O)C1O)C(=O)O"                                                                                                                                                                    
BJ9 InChI            InChI                1.03  "InChI=1S/C17H23N5O14/c18-5(7(24)4(23)2-35-16(19)33)12(28)20-6(15(31)32)10-8(25)9(26)13(36-10)22-1-3(14(29)30)11(27)21-17(22)34/h1,4-10,13,23-26H,2,18H2,(H2,19,33)(H,20,28)(H,29,30)(H,31,32)(H,21,27,34)/t4-,5-,6-,7+,8-,9+,10+,13+/m0/s1" 
BJ9 InChIKey         InChI                1.03  JPFWJDMDPLEUBD-ITJAGOAWSA-N                                                                                                                                                                                                                  
BJ9 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(C(O)=O)C(=O)NC2=O)C(O)=O"                                                                                                                                
BJ9 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(C(O)=O)C(=O)NC2=O)C(O)=O"                                                                                                                                            
BJ9 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)C(=O)O"                                                                                                                            
BJ9 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)C(=O)O"                                                                                                                                                                
# 
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 
BJ9 "SYSTEMATIC NAME" ACDLabs              12.01 "1-{(2R,3R,4S,5R)-5-[(S)-{[(2S,3S,4S)-2-amino-5-(carbamoyloxy)-3,4-dihydroxypentanoyl]amino}(carboxy)methyl]-3,4-dihydroxyoxolan-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid (non-preferred name)"                              
BJ9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(2~{R},3~{R},4~{S},5~{R})-5-[(1~{S})-1-[[(2~{S},3~{S},4~{S})-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidine-5-carboxylic 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 
BJ9 "Create component" 2021-11-15 RCSB 
BJ9 "Initial release"  2022-07-13 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      BJ9 
_pdbx_chem_comp_synonyms.name         "Polyoxin d" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
