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 #