data_PGU
#
_chem_comp.id PGU
_chem_comp.name "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-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 ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag ?
_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 PGU
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1X28
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
PGU N1 N1 N 0 1 Y N N N N N 40.731 104.333 -11.118 6.214 2.558 2.479 N1 PGU 1
PGU C2 C2 C 0 1 Y N N N N N 40.242 105.493 -11.721 6.175 3.699 1.756 C2 PGU 2
PGU C2A C2A C 0 1 N N N N N N 41.283 106.590 -11.596 7.361 4.597 1.891 C2A PGU 3
PGU C3 C3 C 0 1 Y N N N N N 38.901 105.443 -12.326 5.123 4.057 0.928 C3 PGU 4
PGU O3 O3 O 0 1 N N N N N N 38.556 106.644 -12.876 5.147 5.221 0.227 O3 PGU 5
PGU C4 C4 C 0 1 Y N N N N N 38.086 104.271 -12.322 4.047 3.186 0.840 C4 PGU 6
PGU C4A C4A C 0 1 N N N N N N 36.683 104.244 -12.964 2.882 3.528 -0.044 C4A PGU 7
PGU C5 C5 C 0 1 Y N N N N N 38.741 103.150 -11.655 4.046 2.004 1.565 C5 PGU 8
PGU C6 C6 C 0 1 Y N N N N N 40.011 103.167 -11.072 5.145 1.737 2.364 C6 PGU 9
PGU C5A C5A C 0 1 N N N N N N 38.095 101.772 -11.508 2.915 1.036 1.505 C5A PGU 10
PGU O4P O4P O 0 1 N N N N N N 37.799 101.094 -12.670 3.148 0.098 0.460 O4P PGU 11
PGU P P P 0 1 N N N N N N 36.969 99.721 -12.760 2.046 -1.056 0.206 P PGU 12
PGU O1P O1P O 0 1 N N N N N N 37.618 98.762 -13.614 2.364 -2.005 -0.912 O1P PGU 13
PGU O2P O2P O 0 1 N N N N N N 35.569 100.183 -13.094 0.661 -0.237 0.045 O2P PGU 14
PGU O3P O3P O 0 1 N N N N N N 37.030 99.116 -11.368 1.905 -1.741 1.664 O3P PGU 15
PGU N N N 0 1 N N N N N N 36.060 105.601 -12.592 1.864 4.285 0.667 N PGU 16
PGU CA CA C 0 1 N N S N N N 34.870 105.976 -13.483 0.742 4.599 -0.215 CA PGU 17
PGU CB CB C 0 1 N N N N N N 33.764 104.897 -13.426 -0.406 5.300 0.532 CB PGU 18
PGU CG CG C 0 1 N N N N N N 32.839 104.865 -12.185 -0.935 4.587 1.780 CG PGU 19
PGU CD CD C 0 1 N N N N N N 33.589 104.682 -10.863 -1.572 3.250 1.496 CD PGU 20
PGU OE1 OE1 O 0 1 N N N N N N 33.554 105.624 -10.117 -1.520 2.409 2.559 OE1 PGU 21
PGU OE2 OE2 O 0 1 N N N N N N 34.144 103.578 -10.729 -2.073 2.946 0.421 OE2 PGU 22
PGU C C C 0 1 N N N N N N 34.317 107.367 -13.058 1.268 5.434 -1.368 C PGU 23
PGU O O O 0 1 N N N N N N 35.153 107.982 -12.186 0.611 5.169 -2.529 O PGU 24
PGU OXT OXT O 0 1 N N N N N N 33.188 107.879 -13.464 2.172 6.257 -1.295 OXT PGU 25
PGU H2A1 1H2A H 0 0 N N N N N N 41.535 106.738 -10.536 7.164 5.376 2.637 H2A1 PGU 26
PGU H2A2 2H2A H 0 0 N N N N N N 42.188 106.301 -12.151 8.251 4.035 2.200 H2A2 PGU 27
PGU H2A3 3H2A H 0 0 N N N N N N 40.881 107.526 -12.011 7.603 5.080 0.937 H2A3 PGU 28
PGU HO3 HO3 H 0 1 N N N N N N 38.476 107.296 -12.190 5.788 5.838 0.617 HO3 PGU 29
PGU H4A1 1H4A H 0 0 N N N N N N 36.083 103.411 -12.570 3.210 4.126 -0.901 H4A1 PGU 30
PGU H4A2 2H4A H 0 0 N N N N N N 36.727 104.092 -14.053 2.411 2.622 -0.440 H4A2 PGU 31
PGU H6 H6 H 0 1 N N N N N N 40.415 102.285 -10.598 5.205 0.829 2.956 H6 PGU 32
PGU H5A1 1H5A H 0 0 N N N N N N 37.147 101.916 -10.968 2.805 0.486 2.450 H5A1 PGU 33
PGU H5A2 2H5A H 0 0 N N N N N N 38.845 101.153 -10.993 1.962 1.548 1.311 H5A2 PGU 34
PGU HO2P HO2P H 0 0 N N N N N N 35.067 100.280 -12.293 -0.157 -0.728 -0.185 HO2P PGU 35
PGU HO3P HO3P H 0 0 N N N N N N 37.043 98.168 -11.434 1.351 -2.545 1.760 HO3P PGU 36
PGU HN HN H 0 1 N N N N N N 36.762 106.307 -12.690 2.267 5.153 1.013 HN PGU 37
PGU HA HA H 0 1 N N N N N N 35.215 106.033 -14.526 0.378 3.651 -0.627 HA PGU 38
PGU HB1 1HB H 0 1 N N N N N N 33.116 105.063 -14.299 -1.229 5.479 -0.171 HB1 PGU 39
PGU HB2 2HB H 0 1 N N N N N N 34.308 103.942 -13.393 -0.057 6.292 0.847 HB2 PGU 40
PGU HG1 1HG H 0 1 N N N N N N 32.295 105.820 -12.140 -0.142 4.444 2.522 HG1 PGU 41
PGU HG2 2HG H 0 1 N N N N N N 32.171 103.999 -12.301 -1.691 5.212 2.272 HG2 PGU 42
PGU HOE1 HOE1 H 0 0 N N N N N N 34.045 105.423 -9.329 -1.917 1.524 2.410 HOE1 PGU 43
PGU HO HO H 0 1 N N N N N N 34.786 108.820 -11.932 0.912 5.684 -3.307 HO PGU 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
PGU O1P P DOUB N N 1
PGU CA CB SING N N 2
PGU CA C SING N N 3
PGU CA N SING N N 4
PGU OXT C DOUB N N 5
PGU CB CG SING N N 6
PGU O2P P SING N N 7
PGU C O SING N N 8
PGU C4A N SING N N 9
PGU C4A C4 SING N N 10
PGU O3 C3 SING N N 11
PGU P O4P SING N N 12
PGU P O3P SING N N 13
PGU O4P C5A SING N N 14
PGU C3 C4 DOUB Y N 15
PGU C3 C2 SING Y N 16
PGU C4 C5 SING Y N 17
PGU CG CD SING N N 18
PGU C2 C2A SING N N 19
PGU C2 N1 DOUB Y N 20
PGU C5 C5A SING N N 21
PGU C5 C6 DOUB Y N 22
PGU N1 C6 SING Y N 23
PGU CD OE2 DOUB N N 24
PGU CD OE1 SING N N 25
PGU C2A H2A1 SING N N 26
PGU C2A H2A2 SING N N 27
PGU C2A H2A3 SING N N 28
PGU O3 HO3 SING N N 29
PGU C4A H4A1 SING N N 30
PGU C4A H4A2 SING N N 31
PGU C6 H6 SING N N 32
PGU C5A H5A1 SING N N 33
PGU C5A H5A2 SING N N 34
PGU O2P HO2P SING N N 35
PGU O3P HO3P SING N N 36
PGU N HN SING N N 37
PGU CA HA SING N N 38
PGU CB HB1 SING N N 39
PGU CB HB2 SING N N 40
PGU CG HG1 SING N N 41
PGU CG HG2 SING N N 42
PGU OE1 HOE1 SING N N 43
PGU O HO 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
PGU SMILES ACDLabs 10.04 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCC(=O)O"
PGU SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CCC(O)=O)C(O)=O)c1O"
PGU SMILES CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCC(O)=O)C(O)=O)c1O"
PGU 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"
PGU SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCC(=O)O)C(=O)O)O"
PGU 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-/m0/s1"
PGU InChIKey InChI 1.03 JMRKOGDJNHPMHS-JTQLQIEISA-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
PGU "SYSTEMATIC NAME" ACDLabs 10.04 "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid"
PGU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-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
PGU "Create component" 1999-07-08 RCSB
PGU "Modify descriptor" 2011-06-04 RCSB
PGU "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PGU
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical modification"
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom C4A
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#