data_PPD # _chem_comp.id PPD _chem_comp.name "2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H17 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "PYRIDOXYL-ASPARTIC ACID-5-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 364.245 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PPD _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 1ARG _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 PPD N1 N1 N 0 1 Y N N 3.702 26.817 26.653 3.866 0.664 0.325 N1 PPD 1 PPD C2 C2 C 0 1 Y N N 4.696 25.987 26.333 3.811 0.436 -0.971 C2 PPD 2 PPD C2A C2A C 0 1 N N N 4.685 24.596 26.925 5.015 0.723 -1.831 C2A PPD 3 PPD C3 C3 C 0 1 Y N N 5.665 26.480 25.447 2.654 -0.058 -1.554 C3 PPD 4 PPD O3 O3 O 0 1 N N N 6.669 25.635 25.154 2.601 -0.291 -2.892 O3 PPD 5 PPD C4 C4 C 0 1 Y N N 5.598 27.784 24.957 1.551 -0.324 -0.748 C4 PPD 6 PPD C4A C4A C 0 1 N N N 6.572 28.321 24.061 0.276 -0.868 -1.338 C4A PPD 7 PPD C5 C5 C 0 1 Y N N 4.493 28.563 25.342 1.653 -0.070 0.609 C5 PPD 8 PPD C6 C6 C 0 1 Y N N 3.556 28.081 26.198 2.838 0.429 1.116 C6 PPD 9 PPD C5A C5A C 0 1 N N N 4.436 30.041 24.868 0.485 -0.335 1.524 C5A PPD 10 PPD O4P O4P O 0 1 N N N 4.029 30.126 23.516 0.842 0.005 2.865 O4P PPD 11 PPD P P P 0 1 N N N 3.836 31.483 22.721 -0.444 -0.300 3.782 P PPD 12 PPD O1P O1P O 0 1 N N N 2.706 31.225 21.816 -0.792 -1.735 3.680 O1P PPD 13 PPD O2P O2P O 0 1 N N N 5.191 31.700 22.013 -0.110 0.063 5.314 O2P PPD 14 PPD O3P O3P O 0 1 N N N 3.616 32.601 23.645 -1.687 0.589 3.277 O3P PPD 15 PPD N N N 0 1 N N N 7.885 27.733 24.396 -0.593 0.245 -1.737 N PPD 16 PPD CA CA C 0 1 N N S 9.038 27.849 23.486 -1.811 -0.351 -2.301 CA PPD 17 PPD CB CB C 0 1 N N N 9.372 29.277 23.155 -2.998 0.581 -2.053 CB PPD 18 PPD CG CG C 0 1 N N N 9.643 30.163 24.347 -3.177 0.782 -0.570 CG PPD 19 PPD OD1 OD1 O 0 1 N N N 9.528 31.404 24.187 -2.432 0.235 0.207 OD1 PPD 20 PPD OD2 OD2 O 0 1 N N N 10.028 29.680 25.456 -4.165 1.568 -0.113 OD2 PPD 21 PPD C C C 0 1 N N N 10.201 27.142 24.063 -1.632 -0.551 -3.784 C PPD 22 PPD O O O 0 1 N N N 10.033 26.455 25.096 -2.202 -1.457 -4.344 O PPD 23 PPD OXT OXT O 0 1 N N N 11.307 27.229 23.444 -0.839 0.276 -4.482 OXT PPD 24 PPD H2A1 1H2A H 0 0 N N N 5.515 23.902 26.657 5.643 -0.165 -1.885 H2A1 PPD 25 PPD H2A2 2H2A H 0 0 N N N 4.618 24.673 28.035 4.688 0.998 -2.834 H2A2 PPD 26 PPD H2A3 3H2A H 0 0 N N N 3.711 24.106 26.687 5.584 1.545 -1.397 H2A3 PPD 27 PPD HO3 HO3 H 0 1 N N N 7.325 25.968 24.553 2.282 0.523 -3.305 HO3 PPD 28 PPD H4A1 1H4A H 0 0 N N N 6.296 28.175 22.990 0.511 -1.477 -2.212 H4A1 PPD 29 PPD H4A2 2H4A H 0 0 N N N 6.588 29.435 24.062 -0.234 -1.481 -0.596 H4A2 PPD 30 PPD H6 H6 H 0 1 N N N 2.699 28.699 26.515 2.923 0.628 2.174 H6 PPD 31 PPD H5A1 1H5A H 0 0 N N N 3.788 30.660 25.531 -0.366 0.267 1.210 H5A1 PPD 32 PPD H5A2 2H5A H 0 0 N N N 5.405 30.564 25.038 0.219 -1.391 1.477 H5A2 PPD 33 PPD HOP2 2HOP H 0 0 N N N 5.075 32.513 21.536 -0.905 -0.134 5.828 HOP2 PPD 34 PPD HOP3 3HOP H 0 0 N N N 3.500 33.414 23.168 -1.419 1.515 3.360 HOP3 PPD 35 PPD HN HN H 0 1 N N N 7.742 26.743 24.596 -0.867 0.717 -0.888 HN PPD 36 PPD HA HA H 0 1 N N N 8.760 27.367 22.519 -1.999 -1.313 -1.825 HA PPD 37 PPD HB1 1HB H 0 1 N N N 10.229 29.316 22.443 -2.810 1.543 -2.529 HB1 PPD 38 PPD HB2 2HB H 0 1 N N N 8.571 29.721 22.519 -3.902 0.139 -2.471 HB2 PPD 39 PPD HOD HOD H 0 1 N N N 10.198 30.237 26.206 -4.280 1.697 0.837 HOD PPD 40 PPD HXT HXT H 0 1 N N N 12.054 26.774 23.814 -0.724 0.147 -5.434 HXT PPD 41 # # 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 PPD N1 C2 DOUB Y N 1 PPD N1 C6 SING Y N 2 PPD C2 C2A SING N N 3 PPD C2 C3 SING Y N 4 PPD C2A H2A1 SING N N 5 PPD C2A H2A2 SING N N 6 PPD C2A H2A3 SING N N 7 PPD C3 O3 SING N N 8 PPD C3 C4 DOUB Y N 9 PPD O3 HO3 SING N N 10 PPD C4 C4A SING N N 11 PPD C4 C5 SING Y N 12 PPD C4A N SING N N 13 PPD C4A H4A1 SING N N 14 PPD C4A H4A2 SING N N 15 PPD C5 C6 DOUB Y N 16 PPD C5 C5A SING N N 17 PPD C6 H6 SING N N 18 PPD C5A O4P SING N N 19 PPD C5A H5A1 SING N N 20 PPD C5A H5A2 SING N N 21 PPD O4P P SING N N 22 PPD P O1P DOUB N N 23 PPD P O2P SING N N 24 PPD P O3P SING N N 25 PPD O2P HOP2 SING N N 26 PPD O3P HOP3 SING N N 27 PPD N CA SING N N 28 PPD N HN SING N N 29 PPD CA CB SING N N 30 PPD CA C SING N N 31 PPD CA HA SING N N 32 PPD CB CG SING N N 33 PPD CB HB1 SING N N 34 PPD CB HB2 SING N N 35 PPD CG OD1 DOUB N N 36 PPD CG OD2 SING N N 37 PPD OD2 HOD SING N N 38 PPD C O DOUB N N 39 PPD C OXT SING N N 40 PPD OXT HXT SING N N 41 # # 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 PPD SMILES ACDLabs 10.04 "O=C(O)CC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O" PPD SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CC(O)=O)C(O)=O)c1O" PPD SMILES CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CC(O)=O)C(O)=O)c1O" PPD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CC(=O)O)C(=O)O)O" PPD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CC(=O)O)C(=O)O)O" PPD InChI InChI 1.03 "InChI=1S/C12H17N2O9P/c1-6-11(17)8(4-14-9(12(18)19)2-10(15)16)7(3-13-6)5-23-24(20,21)22/h3,9,14,17H,2,4-5H2,1H3,(H,15,16)(H,18,19)(H2,20,21,22)/t9-/m0/s1" PPD InChIKey InChI 1.03 UKHLSCZNRCHWTM-VIFPVBQESA-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 PPD "SYSTEMATIC NAME" ACDLabs 10.04 "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-aspartic acid" PPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]butanedioic 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 PPD "Create component" 1999-07-08 RCSB PPD "Modify descriptor" 2011-06-04 RCSB PPD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PPD _pdbx_chem_comp_synonyms.name "PYRIDOXYL-ASPARTIC ACID-5-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##