data_BY3
# 
_chem_comp.id                                    BY3 
_chem_comp.name                                  "(E)-3-[(3S)-3-chloro-2-oxo-2,3-dihydro-1H-indol-3-yl]-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H19 Cl N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-04-24 
_chem_comp.pdbx_modified_date                    2023-08-18 
_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                        483.796 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ? 
_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        8SL7 
_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 
BY3 C13  C1  C  0 1 N N N -3.278  0.758  -2.447 0.134  -0.867 0.616  C13  BY3 1  
BY3 C15  C2  C  0 1 N N S -4.959  -0.011 -0.730 -2.074 -0.642 1.502  C15  BY3 2  
BY3 C20  C3  C  0 1 N N S -6.863  -0.184 -2.619 -3.082 0.170  -0.635 C20  BY3 3  
BY3 C22  C4  C  0 1 Y N N -8.136  -0.854 -2.087 -2.718 1.600  -0.309 C22  BY3 4  
BY3 C28  C5  C  0 1 Y N N -10.152 -2.693 -1.401 -2.571 4.342  -0.043 C28  BY3 5  
BY3 C01  C6  C  0 1 N N N 1.047   -1.703 -3.227 1.852  -5.143 -1.347 C01  BY3 6  
BY3 C02  C7  C  0 1 Y N N 0.129   -0.479 -3.431 2.059  -3.708 -0.936 C02  BY3 7  
BY3 C04  C8  C  0 1 Y N N -0.092  1.613  -4.398 3.471  -1.891 -0.773 C04  BY3 8  
BY3 C05  C9  C  0 1 Y N N -1.379  1.771  -3.860 2.486  -1.110 -0.205 C05  BY3 9  
BY3 C06  C10 C  0 1 N N N -2.126  3.076  -4.181 2.771  0.319  0.180  C06  BY3 10 
BY3 C12  C11 C  0 1 Y N N -1.896  0.747  -3.069 1.219  -1.664 0.012  C12  BY3 11 
BY3 C16  C12 C  0 1 N N N -5.147  -1.312 -0.016 -2.371 -1.295 2.827  C16  BY3 12 
BY3 C19  C13 C  0 1 N N N -6.185  0.626  -1.426 -3.343 -0.623 0.647  C19  BY3 13 
BY3 C23  C14 C  0 1 Y N N -8.037  -2.308 -2.434 -3.695 2.395  -0.894 C23  BY3 14 
BY3 C25  C15 C  0 1 N N N -6.140  -1.237 -3.199 -4.351 0.290  -1.452 C25  BY3 15 
BY3 C27  C16 C  0 1 Y N N -9.033  -3.169 -2.087 -3.611 3.779  -0.753 C27  BY3 16 
BY3 C29  C17 C  0 1 Y N N -10.254 -1.300 -1.063 -1.604 3.539  0.534  C29  BY3 17 
BY3 C30  C18 C  0 1 Y N N -9.225  -0.411 -1.432 -1.680 2.164  0.399  C30  BY3 18 
BY3 C31  C19 C  0 1 Y N N -1.143  -0.405 -2.858 1.009  -3.000 -0.367 C31  BY3 19 
BY3 N03  N1  N  0 1 Y N N 0.568   0.512  -4.159 3.235  -3.143 -1.115 N03  BY3 20 
BY3 N14  N2  N  0 1 N N N -3.636  0.092  -1.346 -1.029 -1.398 0.808  N14  BY3 21 
BY3 N24  N3  N  0 1 N N N -6.673  -2.466 -3.183 -4.633 1.600  -1.553 N24  BY3 22 
BY3 O07  O1  O  0 1 N N N -2.290  3.853  -2.959 4.127  0.637  -0.138 O07  BY3 23 
BY3 O09  O2  O  0 1 N N N -4.822  3.936  -2.743 4.827  2.354  1.725  O09  BY3 24 
BY3 O10  O3  O  0 1 N N N -3.595  5.645  -1.621 6.271  2.125  -0.460 O10  BY3 25 
BY3 O11  O4  O  0 1 N N N -3.744  5.682  -4.022 3.955  3.127  -0.514 O11  BY3 26 
BY3 O17  O5  O  0 1 N N N -5.737  -1.373 1.097  -3.302 -0.771 3.640  O17  BY3 27 
BY3 O18  O6  O  0 1 N N N -4.695  -2.330 -0.515 -1.771 -2.290 3.158  O18  BY3 28 
BY3 O26  O7  O  0 1 N N N -5.124  -1.081 -3.727 -4.992 -0.623 -1.926 O26  BY3 29 
BY3 O32  O8  O  0 1 N N N -1.648  -1.488 -2.060 -0.199 -3.589 -0.180 O32  BY3 30 
BY3 P08  P1  P  0 1 N N N -3.642  4.801  -2.829 4.777  2.084  0.139  P08  BY3 31 
BY3 CL21 CL1 CL 0 0 N N N -7.288  0.980  -3.944 -1.775 -0.610 -1.603 CL21 BY3 32 
BY3 H131 H1  H  0 0 N N N -4.036  1.354  -2.934 0.313  0.159  0.902  H131 BY3 33 
BY3 H281 H3  H  0 0 N N N -10.943 -3.374 -1.124 -2.511 5.415  0.062  H281 BY3 34 
BY3 H013 H4  H  0 0 N N N 1.995   -1.544 -3.762 1.506  -5.178 -2.380 H013 BY3 35 
BY3 H011 H5  H  0 0 N N N 1.249   -1.835 -2.154 2.794  -5.685 -1.261 H011 BY3 36 
BY3 H012 H6  H  0 0 N N N 0.551   -2.603 -3.620 1.107  -5.604 -0.699 H012 BY3 37 
BY3 H041 H7  H  0 0 N N N 0.347   2.393  -5.002 4.452  -1.471 -0.939 H041 BY3 38 
BY3 H062 H8  H  0 0 N N N -1.547  3.660  -4.912 2.103  0.983  -0.369 H062 BY3 39 
BY3 H061 H9  H  0 0 N N N -3.115  2.839  -4.601 2.610  0.446  1.251  H061 BY3 40 
BY3 H191 H10 H  0 0 N N N -5.866  1.598  -1.829 -3.625 -1.644 0.392  H191 BY3 41 
BY3 H192 H11 H  0 0 N N N -6.955  0.783  -0.656 -4.151 -0.152 1.207  H192 BY3 42 
BY3 H271 H12 H  0 0 N N N -8.958  -4.216 -2.341 -4.363 4.413  -1.201 H271 BY3 43 
BY3 H291 H13 H  0 0 N N N -11.118 -0.935 -0.527 -0.791 3.984  1.089  H291 BY3 44 
BY3 H301 H14 H  0 0 N N N -9.311  0.637  -1.187 -0.927 1.534  0.849  H301 BY3 45 
BY3 H241 H15 H  0 0 N N N -6.283  -3.303 -3.567 -5.401 1.953  -2.030 H241 BY3 46 
BY3 H2   H16 H  0 1 N N N -5.405  4.121  -3.470 5.350  1.707  2.218  H2   BY3 47 
BY3 H3   H17 H  0 1 N N N -3.640  6.560  -1.872 6.724  2.969  -0.329 H3   BY3 48 
BY3 H4   H18 H  0 1 N N N -5.742  -2.272 1.405  -3.458 -1.225 4.480  H4   BY3 49 
BY3 H321 H19 H  0 0 N N N -2.520  -1.274 -1.751 -0.295 -4.027 0.677  H321 BY3 50 
BY3 H1   H20 H  0 1 N N N -4.843  0.673  0.124  -1.733 0.380  1.669  H1   BY3 51 
# 
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 
BY3 C04  N03  SING Y N 1  
BY3 C04  C05  DOUB Y N 2  
BY3 C06  C05  SING N N 3  
BY3 C06  O07  SING N N 4  
BY3 N03  C02  DOUB Y N 5  
BY3 O11  P08  DOUB N N 6  
BY3 CL21 C20  SING N N 7  
BY3 C05  C12  SING Y N 8  
BY3 O26  C25  DOUB N N 9  
BY3 C02  C01  SING N N 10 
BY3 C02  C31  SING Y N 11 
BY3 C25  N24  SING N N 12 
BY3 C25  C20  SING N N 13 
BY3 N24  C23  SING N N 14 
BY3 C12  C31  DOUB Y N 15 
BY3 C12  C13  SING N N 16 
BY3 O07  P08  SING N N 17 
BY3 C31  O32  SING N N 18 
BY3 P08  O09  SING N N 19 
BY3 P08  O10  SING N N 20 
BY3 C20  C22  SING N N 21 
BY3 C20  C19  SING N N 22 
BY3 C13  N14  DOUB N N 23 
BY3 C23  C27  SING Y N 24 
BY3 C23  C22  DOUB Y N 25 
BY3 C27  C28  DOUB Y N 26 
BY3 C22  C30  SING Y N 27 
BY3 C30  C29  DOUB Y N 28 
BY3 C19  C15  SING N N 29 
BY3 C28  C29  SING Y N 30 
BY3 N14  C15  SING N N 31 
BY3 C15  C16  SING N N 32 
BY3 O18  C16  DOUB N N 33 
BY3 C16  O17  SING N N 34 
BY3 C13  H131 SING N N 35 
BY3 C28  H281 SING N N 36 
BY3 C01  H013 SING N N 37 
BY3 C01  H011 SING N N 38 
BY3 C01  H012 SING N N 39 
BY3 C04  H041 SING N N 40 
BY3 C06  H062 SING N N 41 
BY3 C06  H061 SING N N 42 
BY3 C19  H191 SING N N 43 
BY3 C19  H192 SING N N 44 
BY3 C27  H271 SING N N 45 
BY3 C29  H291 SING N N 46 
BY3 C30  H301 SING N N 47 
BY3 N24  H241 SING N N 48 
BY3 O09  H2   SING N N 49 
BY3 O10  H3   SING N N 50 
BY3 O17  H4   SING N N 51 
BY3 O32  H321 SING N N 52 
BY3 C15  H1   SING N N 53 
# 
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 
BY3 SMILES           ACDLabs              12.01 "O=P(O)(O)OCc1cnc(C)c(O)c1/C=N/C(CC1(Cl)c2ccccc2NC1=O)C(=O)O"                                                                                                                                             
BY3 InChI            InChI                1.06  "InChI=1S/C19H19ClN3O8P/c1-10-16(24)12(11(7-21-10)9-31-32(28,29)30)8-22-15(17(25)26)6-19(20)13-4-2-3-5-14(13)23-18(19)27/h2-5,7-8,15,24H,6,9H2,1H3,(H,23,27)(H,25,26)(H2,28,29,30)/b22-8+/t15-,19-/m0/s1" 
BY3 InChIKey         InChI                1.06  BXXCZCGSFDLCHB-ABVQHWRVSA-N                                                                                                                                                                               
BY3 SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](C[C@@]2(Cl)C(=O)Nc3ccccc23)C(O)=O)c1O"                                                                                                                                  
BY3 SMILES           CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](C[C]2(Cl)C(=O)Nc3ccccc23)C(O)=O)c1O"                                                                                                                                      
BY3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(C[C@@]2(c3ccccc3NC2=O)Cl)C(=O)O)O"                                                                                                                                       
BY3 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(CC2(c3ccccc3NC2=O)Cl)C(=O)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 
BY3 "SYSTEMATIC NAME" ACDLabs              12.01 "(E)-3-[(3S)-3-chloro-2-oxo-2,3-dihydro-1H-indol-3-yl]-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine"                   
BY3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[(3~{S})-3-chloranyl-2-oxidanylidene-1~{H}-indol-3-yl]-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic 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 
BY3 "Create component" 2023-04-24 RCSB 
BY3 "Initial release"  2023-08-23 RCSB 
# 
