data_Y3D # _chem_comp.id Y3D _chem_comp.name "(1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-02-01 _chem_comp.pdbx_modified_date 2022-02-11 _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 372.267 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y3D _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 7LK0 _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 Y3D C15 C1 C 0 1 N N N 65.872 -49.997 -5.016 -0.329 0.040 0.144 C15 Y3D 1 Y3D C17 C2 C 0 1 N N S 64.427 -51.493 -6.172 -2.505 1.011 0.327 C17 Y3D 2 Y3D C18 C3 C 0 1 N N N 64.267 -50.617 -7.391 -3.502 0.995 -0.850 C18 Y3D 3 Y3D C19 C4 C 0 1 N N R 63.980 -51.501 -8.589 -4.825 1.500 -0.219 C19 Y3D 4 Y3D C20 C5 C 0 1 N N N 63.688 -52.918 -8.066 -4.785 0.858 1.190 C20 Y3D 5 Y3D C21 C6 C 0 1 N N N 64.131 -52.925 -6.593 -3.324 0.932 1.598 C21 Y3D 6 Y3D C01 C7 C 0 1 Y N N 67.242 -50.453 -1.717 0.967 -3.492 -0.016 C01 Y3D 7 Y3D C03 C8 C 0 1 Y N N 68.470 -48.821 -2.808 2.774 -2.062 -0.125 C03 Y3D 8 Y3D C04 C9 C 0 1 Y N N 67.674 -48.953 -3.936 1.963 -0.948 -0.043 C04 Y3D 9 Y3D C05 C10 C 0 1 Y N N 66.634 -49.863 -3.940 0.577 -1.121 0.053 C05 Y3D 10 Y3D C06 C11 C 0 1 Y N N 66.408 -50.633 -2.815 0.075 -2.433 0.066 C06 Y3D 11 Y3D C07 C12 C 0 1 N N N 66.997 -51.286 -0.461 0.446 -4.906 -0.003 C07 Y3D 12 Y3D C09 C13 C 0 1 N N N 67.951 -48.111 -5.181 2.561 0.435 -0.062 C09 Y3D 13 Y3D C23 C14 C 0 1 N N N 64.536 -51.209 -9.978 -6.014 1.004 -1.000 C23 Y3D 14 Y3D N02 N1 N 0 1 Y N N 68.240 -49.578 -1.734 2.263 -3.277 -0.109 N02 Y3D 15 Y3D N16 N2 N 0 1 N N N 65.023 -51.177 -5.109 -1.605 -0.141 0.237 N16 Y3D 16 Y3D O08 O1 O 0 1 N N N 65.372 -51.577 -2.767 -1.260 -2.659 0.157 O08 Y3D 17 Y3D O10 O2 O 0 1 N N N 67.104 -46.998 -5.253 3.982 0.339 -0.170 O10 Y3D 18 Y3D O12 O3 O 0 1 N N N 66.193 -47.245 -7.635 4.520 2.523 -1.316 O12 Y3D 19 Y3D O13 O4 O 0 1 N N N 68.401 -46.007 -7.352 4.861 2.414 1.183 O13 Y3D 20 Y3D O14 O5 O 0 1 N N N 66.068 -45.138 -6.652 6.464 1.151 -0.474 O14 Y3D 21 Y3D O22 O6 O 0 1 N N N 64.233 -53.881 -5.900 -2.895 0.926 2.727 O22 Y3D 22 Y3D O24 O7 O 0 1 N N N 65.745 -50.873 -10.099 -7.257 1.237 -0.551 O24 Y3D 23 Y3D O25 O8 O 0 1 N N N 63.794 -51.309 -10.985 -5.849 0.396 -2.032 O25 Y3D 24 Y3D P11 P1 P 0 1 N N N 66.924 -46.326 -6.746 4.948 1.626 -0.218 P11 Y3D 25 Y3D H1 H1 H 0 1 N N N 65.880 -49.254 -5.800 0.075 1.042 0.136 H1 Y3D 26 Y3D H2 H2 H 0 1 N N N 63.414 -51.301 -5.789 -1.928 1.936 0.313 H2 Y3D 27 Y3D H3 H3 H 0 1 N N N 65.193 -50.049 -7.563 -3.173 1.669 -1.641 H3 Y3D 28 Y3D H4 H4 H 0 1 N N N 63.431 -49.918 -7.238 -3.622 -0.017 -1.237 H4 Y3D 29 Y3D H5 H5 H 0 1 N N N 62.941 -51.187 -8.769 -4.831 2.588 -0.150 H5 Y3D 30 Y3D H6 H6 H 0 1 N N N 62.613 -53.140 -8.143 -5.403 1.427 1.885 H6 Y3D 31 Y3D H7 H7 H 0 1 N N N 64.259 -53.663 -8.640 -5.117 -0.179 1.146 H7 Y3D 32 Y3D H8 H8 H 0 1 N N N 69.278 -48.104 -2.799 3.843 -1.935 -0.204 H8 Y3D 33 Y3D H9 H9 H 0 1 N N N 67.739 -51.020 0.306 0.247 -5.229 -1.025 H9 Y3D 34 Y3D H10 H10 H 0 1 N N N 65.986 -51.084 -0.078 1.189 -5.564 0.448 H10 Y3D 35 Y3D H11 H11 H 0 1 N N N 67.089 -52.354 -0.706 -0.476 -4.949 0.577 H11 Y3D 36 Y3D H12 H12 H 0 1 N N N 67.797 -48.734 -6.074 2.168 0.989 -0.914 H12 Y3D 37 Y3D H13 H13 H 0 1 N N N 68.994 -47.764 -5.151 2.301 0.956 0.860 H13 Y3D 38 Y3D H14 H14 H 0 1 N N N 65.373 -52.006 -1.919 -1.710 -2.710 -0.698 H14 Y3D 39 Y3D H15 H15 H 0 1 N N N 68.516 -46.476 -8.170 5.128 1.886 1.948 H15 Y3D 40 Y3D H16 H16 H 0 1 N N N 65.286 -45.268 -7.176 7.103 1.876 -0.515 H16 Y3D 41 Y3D H17 H17 H 0 1 N N N 65.944 -50.730 -11.017 -7.989 0.900 -1.086 H17 Y3D 42 # # 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 Y3D O25 C23 DOUB N N 1 Y3D O24 C23 SING N N 2 Y3D C23 C19 SING N N 3 Y3D C19 C20 SING N N 4 Y3D C19 C18 SING N N 5 Y3D C20 C21 SING N N 6 Y3D O12 P11 DOUB N N 7 Y3D C18 C17 SING N N 8 Y3D O13 P11 SING N N 9 Y3D P11 O14 SING N N 10 Y3D P11 O10 SING N N 11 Y3D C21 C17 SING N N 12 Y3D C21 O22 DOUB N N 13 Y3D C17 N16 SING N N 14 Y3D O10 C09 SING N N 15 Y3D C09 C04 SING N N 16 Y3D N16 C15 DOUB N N 17 Y3D C15 C05 SING N N 18 Y3D C05 C04 DOUB Y N 19 Y3D C05 C06 SING Y N 20 Y3D C04 C03 SING Y N 21 Y3D C06 O08 SING N N 22 Y3D C06 C01 DOUB Y N 23 Y3D C03 N02 DOUB Y N 24 Y3D N02 C01 SING Y N 25 Y3D C01 C07 SING N N 26 Y3D C15 H1 SING N N 27 Y3D C17 H2 SING N N 28 Y3D C18 H3 SING N N 29 Y3D C18 H4 SING N N 30 Y3D C19 H5 SING N N 31 Y3D C20 H6 SING N N 32 Y3D C20 H7 SING N N 33 Y3D C03 H8 SING N N 34 Y3D C07 H9 SING N N 35 Y3D C07 H10 SING N N 36 Y3D C07 H11 SING N N 37 Y3D C09 H12 SING N N 38 Y3D C09 H13 SING N N 39 Y3D O08 H14 SING N N 40 Y3D O13 H15 SING N N 41 Y3D O14 H16 SING N N 42 Y3D O24 H17 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 Y3D SMILES ACDLabs 12.01 "[C@H](c1c(cnc(C)c1O)COP(=O)(O)O)=NC2CC(CC2=O)C(O)=O" Y3D InChI InChI 1.03 "InChI=1S/C14H17N2O8P/c1-7-13(18)10(9(4-15-7)6-24-25(21,22)23)5-16-11-2-8(14(19)20)3-12(11)17/h4-5,8,11,18H,2-3,6H2,1H3,(H,19,20)(H2,21,22,23)/b16-5+/t8-,11+/m1/s1" Y3D InChIKey InChI 1.03 XLGFWCHBZWEILL-SNTOBFBISA-N Y3D SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H]2C[C@H](CC2=O)C(O)=O)c1O" Y3D SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[CH]2C[CH](CC2=O)C(O)=O)c1O" Y3D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2C[C@H](CC2=O)C(=O)O)O" Y3D SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2CC(CC2=O)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 Y3D "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid" Y3D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},3~{S})-3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanylidene-cyclopentane-1-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 Y3D "Create component" 2021-02-01 RCSB Y3D "Initial release" 2022-02-16 RCSB ##