data_PDG # _chem_comp.id PDG _chem_comp.name "N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H19 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-04-25 _chem_comp.pdbx_modified_date 2020-06-17 _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 378.272 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PDG _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1X2A _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 PDG N1 N1 N 0 1 Y N N 40.416 103.523 -11.097 1.683 3.695 0.490 N1 PDG 1 PDG C2 C2 C 0 1 Y N N 40.019 104.639 -11.827 0.471 3.933 0.029 C2 PDG 2 PDG C2A C2A C 0 1 N N N 41.074 105.728 -11.680 -0.094 5.328 0.103 C2A PDG 3 PDG C3 C3 C 0 1 Y N N 38.744 104.567 -12.556 -0.292 2.912 -0.520 C3 PDG 4 PDG O3 O3 O 0 1 N N N 38.501 105.724 -13.213 -1.540 3.163 -0.994 O3 PDG 5 PDG C4 C4 C 0 1 Y N N 37.898 103.406 -12.548 0.245 1.630 -0.587 C4 PDG 6 PDG C4A C4A C 0 1 N N N 36.555 103.313 -13.317 -0.547 0.493 -1.180 C4A PDG 7 PDG C5 C5 C 0 1 Y N N 38.461 102.338 -11.739 1.521 1.423 -0.090 C5 PDG 8 PDG C6 C6 C 0 1 Y N N 39.668 102.378 -11.036 2.218 2.490 0.447 C6 PDG 9 PDG C5A C5A C 0 1 N N N 37.771 100.990 -11.557 2.144 0.052 -0.135 C5A PDG 10 PDG OP4 OP4 O 0 1 N N N 37.280 100.364 -12.678 3.453 0.104 0.435 OP4 PDG 11 PDG P P P 0 1 N N N 36.683 98.874 -12.691 4.055 -1.387 0.355 P PDG 12 PDG OP1 OP1 O 0 1 N N N 37.450 97.992 -13.527 4.003 -1.866 -1.044 OP1 PDG 13 PDG OP2 OP2 O 0 1 N N N 35.213 99.104 -12.989 5.584 -1.376 0.861 OP2 PDG 14 PDG OP3 OP3 O 0 1 N N N 36.879 98.350 -11.278 3.187 -2.367 1.291 OP3 PDG 15 PDG NA NA N 0 1 N N N 36.052 104.742 -13.471 -1.334 -0.158 -0.125 NA PDG 16 PDG CAA CAA C 0 1 N N R 34.774 104.984 -12.697 -2.077 -1.251 -0.766 CAA PDG 17 PDG CBA CBA C 0 1 N N N 33.631 104.021 -13.087 -3.332 -1.563 0.051 CBA PDG 18 PDG CGA CGA C 0 1 N N N 32.447 103.935 -12.100 -4.275 -0.359 0.018 CGA PDG 19 PDG CDA CDA C 0 1 N N N 32.901 103.755 -10.641 -5.511 -0.667 0.824 CDA PDG 20 PDG OE1 OE1 O 0 1 N N N 32.918 104.757 -9.967 -6.485 0.251 0.936 OE1 PDG 21 PDG OE2 OE2 O 0 1 N N N 33.193 102.587 -10.337 -5.626 -1.739 1.368 OE2 PDG 22 PDG CA CA C 0 1 N N N 34.373 106.454 -12.898 -1.205 -2.478 -0.837 CA PDG 23 PDG OA OA O 0 1 N N N 35.366 107.256 -12.436 -0.080 -2.446 -0.397 OA PDG 24 PDG OXT OXT O 0 1 N N N 33.249 106.881 -13.436 -1.678 -3.607 -1.387 OXT PDG 25 PDG H2A1 1H2A H 0 0 N N N 40.755 106.622 -12.265 0.164 5.874 -0.805 H2A1 PDG 26 PDG H2A2 2H2A H 0 0 N N N 41.286 105.972 -10.613 -1.179 5.276 0.200 H2A2 PDG 27 PDG H2A3 3H2A H 0 0 N N N 42.092 105.374 -11.965 0.324 5.844 0.968 H2A3 PDG 28 PDG HO3 HO3 H 0 1 N N N 37.677 105.677 -13.684 -2.152 3.023 -0.258 HO3 PDG 29 PDG H4A1 1H4A H 0 0 N N N 36.635 102.765 -14.284 -1.217 0.878 -1.948 H4A1 PDG 30 PDG H4A2 2H4A H 0 0 N N N 35.814 102.632 -12.835 0.136 -0.232 -1.624 H4A2 PDG 31 PDG H6 H6 H 0 1 N N N 40.024 101.519 -10.442 3.213 2.335 0.835 H6 PDG 32 PDG H5A1 1H5A H 0 0 N N N 38.459 100.295 -11.021 1.528 -0.645 0.434 H5A1 PDG 33 PDG H5A2 2H5A H 0 0 N N N 36.952 101.095 -10.807 2.211 -0.284 -1.170 H5A2 PDG 34 PDG HP2 HP2 H 0 1 N N N 34.859 98.222 -12.996 5.906 -2.286 0.798 HP2 PDG 35 PDG HP3 HP3 H 0 1 N N N 36.525 97.468 -11.285 3.248 -2.020 2.192 HP3 PDG 36 PDG HNA HNA H 0 1 N N N 35.940 104.990 -14.454 -0.675 -0.588 0.506 HNA PDG 37 PDG HAA HAA H 0 1 N N N 34.962 104.775 -11.618 -2.366 -0.952 -1.774 HAA PDG 38 PDG HBA1 1HBA H 0 0 N N N 33.255 104.274 -14.105 -3.836 -2.431 -0.374 HBA1 PDG 39 PDG HBA2 2HBA H 0 0 N N N 34.043 103.001 -13.271 -3.051 -1.776 1.082 HBA2 PDG 40 PDG HGA1 1HGA H 0 0 N N N 31.775 104.818 -12.203 -3.771 0.509 0.444 HGA1 PDG 41 PDG HGA2 2HGA H 0 0 N N N 31.734 103.131 -12.399 -4.557 -0.146 -1.013 HGA2 PDG 42 PDG HE1 HE1 H 0 1 N N N 33.198 104.645 -9.066 -7.278 0.053 1.453 HE1 PDG 43 PDG HXT HXT H 0 1 N N N 33.001 107.789 -13.560 -1.119 -4.395 -1.432 HXT PDG 44 # # 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 PDG N1 C2 DOUB Y N 1 PDG N1 C6 SING Y N 2 PDG C2 C2A SING N N 3 PDG C2 C3 SING Y N 4 PDG C2A H2A1 SING N N 5 PDG C2A H2A2 SING N N 6 PDG C2A H2A3 SING N N 7 PDG C3 O3 SING N N 8 PDG C3 C4 DOUB Y N 9 PDG O3 HO3 SING N N 10 PDG C4 C4A SING N N 11 PDG C4 C5 SING Y N 12 PDG C4A NA SING N N 13 PDG C4A H4A1 SING N N 14 PDG C4A H4A2 SING N N 15 PDG C5 C6 DOUB Y N 16 PDG C5 C5A SING N N 17 PDG C6 H6 SING N N 18 PDG C5A OP4 SING N N 19 PDG C5A H5A1 SING N N 20 PDG C5A H5A2 SING N N 21 PDG OP4 P SING N N 22 PDG P OP1 DOUB N N 23 PDG P OP2 SING N N 24 PDG P OP3 SING N N 25 PDG OP2 HP2 SING N N 26 PDG OP3 HP3 SING N N 27 PDG NA CAA SING N N 28 PDG NA HNA SING N N 29 PDG CAA CBA SING N N 30 PDG CAA CA SING N N 31 PDG CAA HAA SING N N 32 PDG CBA CGA SING N N 33 PDG CBA HBA1 SING N N 34 PDG CBA HBA2 SING N N 35 PDG CGA CDA SING N N 36 PDG CGA HGA1 SING N N 37 PDG CGA HGA2 SING N N 38 PDG CDA OE1 SING N N 39 PDG CDA OE2 DOUB N N 40 PDG OE1 HE1 SING N N 41 PDG CA OA DOUB N N 42 PDG CA OXT SING N N 43 PDG OXT HXT SING N N 44 # # 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 PDG SMILES ACDLabs 10.04 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCC(=O)O" PDG SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CCC(O)=O)C(O)=O)c1O" PDG SMILES CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCC(O)=O)C(O)=O)c1O" PDG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCC(=O)O)C(=O)O)O" PDG SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCC(=O)O)C(=O)O)O" PDG InChI InChI 1.03 "InChI=1S/C13H19N2O9P/c1-7-12(18)9(8(4-14-7)6-24-25(21,22)23)5-15-10(13(19)20)2-3-11(16)17/h4,10,15,18H,2-3,5-6H2,1H3,(H,16,17)(H,19,20)(H2,21,22,23)/t10-/m1/s1" PDG InChIKey InChI 1.03 JMRKOGDJNHPMHS-SNVBAGLBSA-N # # 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 PDG "SYSTEMATIC NAME" ACDLabs 10.04 "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid" PDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanedioic 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 PDG "Create component" 2005-04-25 RCSB PDG "Modify descriptor" 2011-06-04 RCSB PDG "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PDG _pdbx_chem_comp_synonyms.name "N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##