data_PN9 # _chem_comp.id PN9 _chem_comp.name "(4Z)-4-({[(1E)-1-carboxy-3-(methylsulfanyl)propylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H19 N2 O7 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "PLP-Met adduct intermediate in zwitterionic form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-01-14 _chem_comp.pdbx_modified_date 2022-05-27 _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 378.338 _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 7TCS _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 PN9 N1 N1 N 1 1 N N N -9.811 -1.988 3.680 2.309 0.794 0.102 N1 PN9 1 PN9 C4 C1 C 0 1 N N N -14.286 -3.408 4.986 1.610 -4.897 -1.544 C4 PN9 2 PN9 C5 C2 C 0 1 N N N -5.934 -0.449 4.483 -0.272 4.023 -0.305 C5 PN9 3 PN9 C6 C3 C 0 1 N N N -5.584 0.996 4.527 0.235 5.433 -0.468 C6 PN9 4 PN9 C7 C4 C 0 1 N N N -7.168 -0.889 4.138 0.611 3.007 -0.126 C7 PN9 5 PN9 C8 C5 C 0 1 N N N -7.418 -2.281 4.112 0.121 1.686 0.027 C8 PN9 6 PN9 C10 C6 C 0 1 N N N -6.393 -3.182 4.470 -1.276 1.472 -0.013 C10 PN9 7 PN9 C13 C7 C 0 1 N N N -11.131 -2.257 3.454 3.150 -0.191 0.392 C13 PN9 8 PN9 C1 C8 C 0 1 N N N -11.935 -1.181 3.317 4.527 0.025 0.322 C1 PN9 9 PN9 C11 C9 C 0 1 N N N -6.634 -4.669 4.471 -1.838 0.083 0.146 C11 PN9 10 PN9 C12 C10 C 0 1 N N N -5.189 -2.682 4.827 -2.103 2.527 -0.194 C12 PN9 11 PN9 C2 C11 C 0 1 N N N -11.606 -3.693 3.389 2.618 -1.541 0.798 C2 PN9 12 PN9 C3 C12 C 0 1 N N N -11.706 -4.358 4.765 2.418 -2.406 -0.448 C3 PN9 13 PN9 C9 C13 C 0 1 N N N -8.759 -2.831 3.769 1.010 0.606 0.214 C9 PN9 14 PN9 N2 N2 N 0 1 N N N -4.966 -1.354 4.833 -1.608 3.782 -0.332 N2 PN9 15 PN9 O1 O1 O 0 1 N N N -11.465 -0.039 3.475 5.005 1.237 -0.043 O1 PN9 16 PN9 O2 O2 O 0 1 N N N -13.117 -1.331 3.026 5.300 -0.880 0.589 O2 PN9 17 PN9 O3 O3 O 0 1 N N N -6.967 -6.664 1.212 -3.887 -1.875 1.464 O3 PN9 18 PN9 O4 O4 O 0 1 N N N -7.053 -7.619 3.544 -3.920 -2.154 -1.044 O4 PN9 19 PN9 O5 O5 O -1 1 N N N -8.043 -0.057 3.815 1.948 3.254 -0.095 O5 PN9 20 PN9 O6 O6 O 0 1 N N N -8.860 -6.029 2.791 -5.745 -0.727 0.199 O6 PN9 21 PN9 O7 O7 O 0 1 N N N -6.541 -5.201 3.111 -3.264 0.135 0.070 O7 PN9 22 PN9 P1 P1 P 0 1 N N N -7.414 -6.467 2.641 -4.197 -1.171 0.200 P1 PN9 23 PN9 S1 S1 S 0 1 N N N -12.757 -3.434 5.919 1.778 -4.031 0.041 S1 PN9 24 PN9 H8 H1 H 0 1 N N N -15.056 -2.869 5.558 0.919 -4.350 -2.185 H8 PN9 25 PN9 H6 H2 H 0 1 N N N -14.120 -2.899 4.025 2.584 -4.959 -2.029 H6 PN9 26 PN9 H7 H3 H 0 1 N N N -14.621 -4.440 4.802 1.226 -5.902 -1.370 H7 PN9 27 PN9 H11 H5 H 0 1 N N N -4.533 1.110 4.831 -0.609 6.111 -0.595 H11 PN9 28 PN9 H9 H6 H 0 1 N N N -5.727 1.438 3.530 0.802 5.720 0.418 H9 PN9 29 PN9 H10 H7 H 0 1 N N N -6.233 1.509 5.252 0.880 5.488 -1.345 H10 PN9 30 PN9 H14 H10 H 0 1 N N N -7.638 -4.873 4.872 -1.455 -0.557 -0.648 H14 PN9 31 PN9 H13 H11 H 0 1 N N N -5.879 -5.158 5.104 -1.541 -0.321 1.114 H13 PN9 32 PN9 H15 H12 H 0 1 N N N -4.395 -3.357 5.111 -3.171 2.369 -0.225 H15 PN9 33 PN9 H3 H13 H 0 1 N N N -12.600 -3.711 2.919 3.329 -2.025 1.467 H3 PN9 34 PN9 H2 H14 H 0 1 N N N -10.898 -4.268 2.773 1.664 -1.416 1.311 H2 PN9 35 PN9 H4 H15 H 0 1 N N N -12.126 -5.367 4.638 1.707 -1.921 -1.116 H4 PN9 36 PN9 H5 H16 H 0 1 N N N -10.696 -4.433 5.193 3.372 -2.530 -0.960 H5 PN9 37 PN9 H12 H17 H 0 1 N N N -8.889 -3.889 3.594 0.625 -0.376 0.449 H12 PN9 38 PN9 H16 H18 H 0 1 N N N -4.064 -1.017 5.102 -2.222 4.523 -0.457 H16 PN9 39 PN9 H20 H19 H 0 1 N N N -12.148 0.607 3.336 5.970 1.289 -0.063 H20 PN9 40 PN9 H21 H20 H 0 1 N N N -6.596 -8.284 3.043 -4.103 -1.758 -1.907 H21 PN9 41 PN9 H22 H21 H 0 1 N N N -9.258 -5.949 1.932 -6.366 -1.465 0.274 H22 PN9 42 PN9 H1 H22 H 0 1 N N N -9.590 -1.020 3.797 2.651 1.654 -0.190 H1 PN9 43 # # 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 PN9 O3 P1 DOUB N N 1 PN9 P1 O6 SING N N 2 PN9 P1 O7 SING N N 3 PN9 P1 O4 SING N N 4 PN9 O2 C1 DOUB N N 5 PN9 O7 C11 SING N N 6 PN9 C1 C13 SING N N 7 PN9 C1 O1 SING N N 8 PN9 C2 C13 SING N N 9 PN9 C2 C3 SING N N 10 PN9 C13 N1 DOUB N N 11 PN9 N1 C9 SING N N 12 PN9 C9 C8 DOUB N Z 13 PN9 O5 C7 SING N N 14 PN9 C8 C7 SING N N 15 PN9 C8 C10 SING N N 16 PN9 C7 C5 DOUB N N 17 PN9 C10 C11 SING N N 18 PN9 C10 C12 DOUB N N 19 PN9 C5 C6 SING N N 20 PN9 C5 N2 SING N N 21 PN9 C3 S1 SING N N 22 PN9 C12 N2 SING N N 23 PN9 C4 S1 SING N N 24 PN9 C4 H8 SING N N 25 PN9 C4 H6 SING N N 26 PN9 C4 H7 SING N N 27 PN9 C6 H11 SING N N 28 PN9 C6 H9 SING N N 29 PN9 C6 H10 SING N N 30 PN9 C11 H14 SING N N 31 PN9 C11 H13 SING N N 32 PN9 C12 H15 SING N N 33 PN9 C2 H3 SING N N 34 PN9 C2 H2 SING N N 35 PN9 C3 H4 SING N N 36 PN9 C3 H5 SING N N 37 PN9 C9 H12 SING N N 38 PN9 N2 H16 SING N N 39 PN9 O1 H20 SING N N 40 PN9 O4 H21 SING N N 41 PN9 O6 H22 SING N N 42 PN9 N1 H1 SING N N 43 # # 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 PN9 SMILES ACDLabs 12.01 "O=C(O)C(\CCSC)=[NH+]\C=C1/C([O-])=C(C)NC=C1COP(=O)(O)O" PN9 InChI InChI 1.03 "InChI=1S/C13H19N2O7PS/c1-8-12(16)10(6-15-11(13(17)18)3-4-24-2)9(5-14-8)7-22-23(19,20)21/h5-6,14,16H,3-4,7H2,1-2H3,(H,17,18)(H2,19,20,21)/b10-6-,15-11+" PN9 InChIKey InChI 1.03 UNHRYMFMFMQCNK-JNVWRRHBSA-N PN9 SMILES_CANONICAL CACTVS 3.385 "CSCCC(=[NH+]\C=C1/C(=C(C)NC=C1CO[P](O)(O)=O)[O-])C(O)=O" PN9 SMILES CACTVS 3.385 "CSCCC(=[NH+]C=C1C(=C(C)NC=C1CO[P](O)(O)=O)[O-])C(O)=O" PN9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=C(/C(=C\[NH+]=C(/CCSC)\C(=O)O)/C(=CN1)COP(=O)(O)O)[O-]" PN9 SMILES "OpenEye OEToolkits" 2.0.7 "CC1=C(C(=C[NH+]=C(CCSC)C(=O)O)C(=CN1)COP(=O)(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 PN9 "SYSTEMATIC NAME" ACDLabs 12.01 "(4Z)-4-({[(1E)-1-carboxy-3-(methylsulfanyl)propylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate" PN9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(4~{Z})-2-methyl-4-[(4-methylsulfanyl-1-oxidanyl-1-oxidanylidene-butan-2-ylidene)azaniumylmethylidene]-5-(phosphonooxymethyl)-1~{H}-pyridin-3-olate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PN9 _pdbx_chem_comp_synonyms.name "PLP-Met adduct intermediate in zwitterionic form" _pdbx_chem_comp_synonyms.provenance PDB _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 PN9 "Create component" 2022-01-14 RCSB PN9 "Modify synonyms" 2022-01-19 RCSB PN9 "Initial release" 2022-06-01 RCSB ##