data_YJI
# 
_chem_comp.id                                    YJI 
_chem_comp.name                                  "N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2-hydroxyethyl)sulfanyl]ethyl}-beta-alaninamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H27 N2 O8 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-08 
_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                        402.401 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YJI 
_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        8G3I 
_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 
YJI C01  C1  C 0 1 N N N N N N -51.490 21.730 -3.239 3.150   -0.731 -2.086 C01  YJI 1  
YJI C02  C2  C 0 1 N N N N N N -52.989 21.786 -2.997 4.189   -1.173 -1.054 C02  YJI 2  
YJI C03  C3  C 0 1 N N N N N N -53.466 23.172 -3.407 4.336   -0.092 0.018  C03  YJI 3  
YJI C09  C4  C 0 1 N N R N N N -53.204 21.520 -1.509 3.736   -2.481 -0.402 C09  YJI 4  
YJI C10  C5  C 0 1 N N N N N N -54.624 21.063 -1.176 2.482   -2.234 0.398  C10  YJI 5  
YJI C12  C6  C 0 1 N N N N N N -53.737 19.681 0.730  0.135   -1.598 0.548  C12  YJI 6  
YJI C13  C7  C 0 1 N N N N N N -54.210 19.021 2.018  -1.026  -1.298 -0.402 C13  YJI 7  
YJI C14  C8  C 0 1 N N N N N N -53.783 17.584 2.276  -2.255  -0.954 0.400  C14  YJI 8  
YJI C16  C9  C 0 1 N N N N N N -52.016 15.954 3.042  -4.602  -0.318 0.550  C16  YJI 9  
YJI C17  C10 C 0 1 N N N N N N -51.377 15.851 4.417  -5.764  -0.018 -0.400 C17  YJI 10 
YJI C19  C11 C 0 1 N N N N N N -52.096 14.021 6.619  -8.489  0.714  -0.714 C19  YJI 11 
YJI C20  C12 C 0 1 N N N N N N -51.967 12.797 5.731  -9.818  1.083  -0.051 C20  YJI 12 
YJI C25  C13 C 0 1 N N N N N N -53.649 20.714 -3.851 5.536   -1.390 -1.748 C25  YJI 13 
YJI N11  N1  N 0 1 N N N N N N -54.853 20.163 -0.062 1.330   -1.932 -0.232 N11  YJI 14 
YJI N15  N2  N 0 1 N N N N N N -52.455 17.313 2.788  -3.408  -0.652 -0.230 N15  YJI 15 
YJI O04  O1  O 0 1 N N N N N N -53.458 23.230 -4.802 4.759   1.129  -0.592 O04  YJI 16 
YJI O06  O2  O 0 1 N N N N N N -55.244 24.796 -5.812 3.625   2.993  0.875  O06  YJI 17 
YJI O07  O3  O 0 1 N N N N N N -53.336 25.799 -4.646 5.984   2.217  1.328  O07  YJI 18 
YJI O21  O4  O 0 1 N N N N N N -51.432 11.772 6.517  -10.800 1.333  -1.059 O21  YJI 19 
YJI O22  O5  O 0 1 N N N N N N -54.539 16.705 2.056  -2.207  -0.949 1.612  O22  YJI 20 
YJI O23  O6  O 0 1 N N N N N N -55.546 21.450 -1.804 2.511   -2.308 1.608  O23  YJI 21 
YJI O24  O7  O 0 1 N N N N N N -52.981 22.700 -0.795 4.765   -2.964 0.463  O24  YJI 22 
YJI P05  P1  P 0 1 N N N N N N -53.775 24.667 -5.531 5.015   2.483  0.242  P05  YJI 23 
YJI S18  S1  S 0 1 N N N N N N -52.657 15.418 5.619  -7.243  0.396  0.565  S18  YJI 24 
YJI H012 H1  H 0 0 N N N N N N -50.991 22.498 -2.630 2.223   -0.467 -1.578 H012 YJI 25 
YJI H013 H2  H 0 0 N N N N N N -51.110 20.736 -2.959 3.525   0.135  -2.631 H013 YJI 26 
YJI H011 H3  H 0 0 N N N N N N -51.283 21.914 -4.304 2.962   -1.546 -2.785 H011 YJI 27 
YJI H032 H4  H 0 0 N N N N N N -52.790 23.937 -2.997 3.376   0.062  0.512  H032 YJI 28 
YJI H031 H5  H 0 0 N N N N N N -54.485 23.343 -3.031 5.076   -0.407 0.753  H031 YJI 29 
YJI H091 H6  H 0 0 N N N N N N -52.500 20.738 -1.187 3.533   -3.222 -1.175 H091 YJI 30 
YJI H122 H7  H 0 0 N N N N N N -53.170 18.946 0.139  0.337   -0.721 1.164  H122 YJI 31 
YJI H121 H8  H 0 0 N N N N N N -53.085 20.530 0.982  -0.128  -2.440 1.189  H121 YJI 32 
YJI H131 H9  H 0 0 N N N N N N -53.837 19.630 2.855  -0.763  -0.457 -1.043 H131 YJI 33 
YJI H132 H10 H 0 0 N N N N N N -55.310 19.041 2.012  -1.228  -2.175 -1.018 H132 YJI 34 
YJI H162 H11 H 0 0 N N N N N N -52.883 15.278 2.994  -4.401  0.559  1.166  H162 YJI 35 
YJI H161 H12 H 0 0 N N N N N N -51.280 15.662 2.278  -4.865  -1.159 1.191  H161 YJI 36 
YJI H172 H13 H 0 0 N N N N N N -50.600 15.072 4.407  -5.501  0.824  -1.041 H172 YJI 37 
YJI H171 H14 H 0 0 N N N N N N -50.925 16.816 4.689  -5.965  -0.895 -1.015 H171 YJI 38 
YJI H191 H15 H 0 0 N N N N N N -51.119 14.257 7.066  -8.622  -0.181 -1.322 H191 YJI 39 
YJI H192 H16 H 0 0 N N N N N N -52.826 13.822 7.417  -8.158  1.537  -1.347 H192 YJI 40 
YJI H202 H17 H 0 0 N N N N N N -51.297 13.013 4.886  -10.149 0.260  0.582  H202 YJI 41 
YJI H201 H18 H 0 0 N N N N N N -52.956 12.502 5.349  -9.684  1.978  0.557  H201 YJI 42 
YJI H251 H19 H 0 0 N N N N N N -53.290 19.722 -3.538 5.888   -0.445 -2.161 H251 YJI 43 
YJI H253 H20 H 0 0 N N N N N N -54.741 20.765 -3.725 6.261   -1.763 -1.024 H253 YJI 44 
YJI H252 H21 H 0 0 N N N N N N -53.394 20.879 -4.908 5.418   -2.116 -2.552 H252 YJI 45 
YJI H111 H22 H 0 0 N N N N N N -55.784 19.874 0.161  1.291   -1.936 -1.201 H111 YJI 46 
YJI H151 H23 H 0 0 N N N N N N -51.832 18.074 2.969  -3.447  -0.656 -1.199 H151 YJI 47 
YJI H1   H24 H 0 1 N N N N N N -55.585 25.565 -5.371 2.942   3.187  0.219  H1   YJI 48 
YJI H211 H26 H 0 0 N N N N N N -51.337 10.986 5.992  -11.669 1.573  -0.710 H211 YJI 49 
YJI H241 H27 H 0 0 N N N N N N -53.114 22.540 0.132  4.998   -2.354 1.177  H241 YJI 50 
YJI O1   O8  O 0 1 N Y N N N N -52.168 24.334 -6.333 5.605   3.614  -0.740 O1   YJI 51 
YJI H2   H28 H 0 1 N Y N N N N -51.514 24.935 -5.995 5.784   4.459  -0.304 H2   YJI 52 
# 
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 
YJI O06 P05  SING N N 1  
YJI P05 O04  SING N N 2  
YJI P05 O07  DOUB N N 3  
YJI O04 C03  SING N N 4  
YJI C25 C02  SING N N 5  
YJI C03 C02  SING N N 6  
YJI C01 C02  SING N N 7  
YJI C02 C09  SING N N 8  
YJI O23 C10  DOUB N N 9  
YJI C09 C10  SING N N 10 
YJI C09 O24  SING N N 11 
YJI C10 N11  SING N N 12 
YJI N11 C12  SING N N 13 
YJI C12 C13  SING N N 14 
YJI C13 C14  SING N N 15 
YJI O22 C14  DOUB N N 16 
YJI C14 N15  SING N N 17 
YJI N15 C16  SING N N 18 
YJI C16 C17  SING N N 19 
YJI C17 S18  SING N N 20 
YJI S18 C19  SING N N 21 
YJI C20 O21  SING N N 22 
YJI C20 C19  SING N N 23 
YJI C01 H012 SING N N 24 
YJI C01 H013 SING N N 25 
YJI C01 H011 SING N N 26 
YJI C03 H032 SING N N 27 
YJI C03 H031 SING N N 28 
YJI C09 H091 SING N N 29 
YJI C12 H122 SING N N 30 
YJI C12 H121 SING N N 31 
YJI C13 H131 SING N N 32 
YJI C13 H132 SING N N 33 
YJI C16 H162 SING N N 34 
YJI C16 H161 SING N N 35 
YJI C17 H172 SING N N 36 
YJI C17 H171 SING N N 37 
YJI C19 H191 SING N N 38 
YJI C19 H192 SING N N 39 
YJI C20 H202 SING N N 40 
YJI C20 H201 SING N N 41 
YJI C25 H251 SING N N 42 
YJI C25 H253 SING N N 43 
YJI C25 H252 SING N N 44 
YJI N11 H111 SING N N 45 
YJI N15 H151 SING N N 46 
YJI O06 H1   SING N N 47 
YJI O21 H211 SING N N 48 
YJI O24 H241 SING N N 49 
YJI P05 O1   SING N N 50 
YJI O1  H2   SING N N 51 
# 
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 
YJI SMILES           ACDLabs              12.01 "O=C(NCCSCCO)CCNC(=O)C(O)C(C)(C)COP(=O)(O)O"                                                                                                                 
YJI InChI            InChI                1.06  "InChI=1S/C13H27N2O8PS/c1-13(2,9-23-24(20,21)22)11(18)12(19)15-4-3-10(17)14-5-7-25-8-6-16/h11,16,18H,3-9H2,1-2H3,(H,14,17)(H,15,19)(H2,20,21,22)/t11-/m0/s1" 
YJI InChIKey         InChI                1.06  IGYAFBQHDWNTQK-NSHDSACASA-N                                                                                                                                  
YJI SMILES_CANONICAL CACTVS               3.385 "CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)NCCSCCO"                                                                                                          
YJI SMILES           CACTVS               3.385 "CC(C)(CO[P](O)(O)=O)[CH](O)C(=O)NCCC(=O)NCCSCCO"                                                                                                            
YJI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSCCO)O"                                                                                                             
YJI SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)O)C(C(=O)NCCC(=O)NCCSCCO)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 
YJI "SYSTEMATIC NAME" ACDLabs              12.01 "N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2-hydroxyethyl)sulfanyl]ethyl}-beta-alaninamide"                                      
YJI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{R})-4-[[3-[2-(2-hydroxyethylsulfanyl)ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YJI "Create component" 2023-02-08 RCSB 
YJI "Initial release"  2023-06-14 RCSB 
YJI "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YJI 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               P05 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
