data_PY4
#
_chem_comp.id PY4
_chem_comp.name "2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H19 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "VITAMIN B6 COMPLEXED WITH 2-AMINO-BUTYRIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-08-18
_chem_comp.pdbx_modified_date 2024-09-27
_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 334.262
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PY4
_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 1CQ6
_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
PY4 N1 N1 N 0 1 Y N N N N N 26.666 4.870 -14.793 -3.607 0.472 0.356 N1 PY4 1
PY4 C2 C2 C 0 1 Y N N N N N 26.345 6.074 -15.381 -3.544 0.240 -0.939 C2 PY4 2
PY4 C2A C2A C 0 1 N N N N N N 27.100 6.197 -16.695 -4.775 0.417 -1.790 C2A PY4 3
PY4 C3 C3 C 0 1 Y N N N N N 25.405 6.953 -14.694 -2.355 -0.164 -1.528 C3 PY4 4
PY4 O3 O3 O 0 1 N N N N N N 25.183 8.093 -15.396 -2.295 -0.403 -2.865 O3 PY4 5
PY4 C4 C4 C 0 1 Y N N N N N 24.817 6.633 -13.473 -1.226 -0.323 -0.731 C4 PY4 6
PY4 C4A C4A C 0 1 N N N N N N 23.828 7.560 -12.750 0.085 -0.762 -1.330 C4A PY4 7
PY4 C5 C5 C 0 1 Y N N N N N 25.259 5.353 -12.998 -1.338 -0.074 0.626 C5 PY4 8
PY4 C6 C6 C 0 1 Y N N N N N 26.147 4.498 -13.611 -2.556 0.331 1.139 C6 PY4 9
PY4 C5A C5A C 0 1 N N N N N N 24.780 4.772 -11.693 -0.144 -0.232 1.531 C5A PY4 10
PY4 O4P O4P O 0 1 N N N N N N 23.856 5.491 -10.988 -0.516 0.093 2.872 O4P PY4 11
PY4 P P P 0 1 N N N N N N 22.842 4.778 -10.038 0.799 -0.095 3.780 P PY4 12
PY4 O1P O1P O 0 1 N N N N N N 22.345 3.581 -10.642 1.866 0.808 3.296 O1P PY4 13
PY4 O2P O2P O 0 1 N N N N N N 21.946 5.861 -9.499 0.450 0.256 5.311 O2P PY4 14
PY4 O3P O3P O 0 1 N N N N N N 23.712 4.265 -8.943 1.304 -1.621 3.682 O3P PY4 15
PY4 N N N 0 1 N N N N N N 23.774 8.846 -13.578 0.853 0.418 -1.744 N PY4 16
PY4 CA CA C 0 1 N N R N N N 24.036 10.050 -12.707 2.113 -0.076 -2.316 CA PY4 17
PY4 C C C 0 1 N N N N N N 23.982 11.339 -13.527 1.938 -0.303 -3.795 C PY4 18
PY4 O O O 0 1 N N N N N N 24.182 11.085 -14.837 2.579 -1.162 -4.354 O PY4 19
PY4 CB CB C 0 1 N N N N N N 23.102 10.104 -11.505 3.218 0.956 -2.085 CB PY4 20
PY4 CG CG C 0 1 N N N N N N 23.687 9.453 -10.254 3.395 1.186 -0.583 CG PY4 21
PY4 OXT OXT O 0 1 N N N N N N 23.781 12.528 -13.032 1.072 0.448 -4.492 OXT PY4 22
PY4 H2A1 1H2A H 0 0 N N N N N N 26.840 7.171 -17.170 -5.326 -0.522 -1.831 H2A1 PY4 23
PY4 H2A2 2H2A H 0 0 N N N N N N 28.199 6.065 -16.567 -5.409 1.191 -1.356 H2A2 PY4 24
PY4 H2A3 3H2A H 0 0 N N N N N N 26.917 5.330 -17.372 -4.482 0.711 -2.798 H2A3 PY4 25
PY4 HO3 HO3 H 0 1 N N N N N N 24.570 8.665 -14.948 -2.511 -1.337 -2.992 HO3 PY4 26
PY4 H4A1 1H4A H 0 0 N N N N N N 22.827 7.097 -12.580 -0.104 -1.395 -2.196 H4A1 PY4 27
PY4 H4A2 2H4A H 0 0 N N N N N N 24.081 7.731 -11.677 0.653 -1.323 -0.588 H4A2 PY4 28
PY4 H6 H6 H 0 1 N N N N N N 26.437 3.532 -13.163 -2.649 0.531 2.197 H6 PY4 29
PY4 H5A1 1H5A H 0 0 N N N N N N 24.392 3.741 -11.867 0.207 -1.263 1.493 H5A1 PY4 30
PY4 H5A2 2H5A H 0 0 N N N N N N 25.657 4.556 -11.039 0.651 0.435 1.203 H5A2 PY4 31
PY4 HOP2 2HOP H 0 0 N N N N N N 21.329 5.427 -8.921 1.263 0.130 5.819 HOP2 PY4 32
PY4 HOP3 3HOP H 0 0 N N N N N N 23.095 3.831 -8.365 0.581 -2.176 4.005 HOP3 PY4 33
PY4 HN2 HN2 H 0 1 N N N N N N 22.894 8.931 -14.087 1.094 0.918 -0.902 HN2 PY4 34
PY4 HA HA H 0 1 N N N N N N 25.068 9.948 -12.299 2.386 -1.015 -1.834 HA PY4 35
PY4 HB1 1HB H 0 1 N N N N N N 22.787 11.153 -11.295 2.945 1.894 -2.567 HB1 PY4 36
PY4 HB2 2HB H 0 1 N N N N N N 22.109 9.660 -11.754 4.153 0.588 -2.509 HB2 PY4 37
PY4 HG1 HG1 H 0 1 N N N N N N 23.003 9.492 -9.374 4.183 1.921 -0.418 HG1 PY4 38
PY4 HG2 HG2 H 0 1 N N N N N N 24.001 8.404 -10.464 2.461 1.553 -0.159 HG2 PY4 39
PY4 HG3 HG3 H 0 1 N N N N N N 24.679 9.896 -10.004 3.668 0.247 -0.101 HG3 PY4 40
PY4 HXT HXT H 0 1 N N N N N N 23.747 13.329 -13.541 0.960 0.303 -5.441 HXT PY4 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
PY4 N1 C2 DOUB Y N 1
PY4 N1 C6 SING Y N 2
PY4 C2 C2A SING N N 3
PY4 C2 C3 SING Y N 4
PY4 C2A H2A1 SING N N 5
PY4 C2A H2A2 SING N N 6
PY4 C2A H2A3 SING N N 7
PY4 C3 O3 SING N N 8
PY4 C3 C4 DOUB Y N 9
PY4 O3 HO3 SING N N 10
PY4 C4 C4A SING N N 11
PY4 C4 C5 SING Y N 12
PY4 C4A N SING N N 13
PY4 C4A H4A1 SING N N 14
PY4 C4A H4A2 SING N N 15
PY4 C5 C6 DOUB Y N 16
PY4 C5 C5A SING N N 17
PY4 C6 H6 SING N N 18
PY4 C5A O4P SING N N 19
PY4 C5A H5A1 SING N N 20
PY4 C5A H5A2 SING N N 21
PY4 O4P P SING N N 22
PY4 P O1P DOUB N N 23
PY4 P O2P SING N N 24
PY4 P O3P SING N N 25
PY4 O2P HOP2 SING N N 26
PY4 O3P HOP3 SING N N 27
PY4 N CA SING N N 28
PY4 N HN2 SING N N 29
PY4 CA C SING N N 30
PY4 CA CB SING N N 31
PY4 CA HA SING N N 32
PY4 C O DOUB N N 33
PY4 C OXT SING N N 34
PY4 CB CG SING N N 35
PY4 CB HB1 SING N N 36
PY4 CB HB2 SING N N 37
PY4 CG HG1 SING N N 38
PY4 CG HG2 SING N N 39
PY4 CG HG3 SING N N 40
PY4 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
PY4 SMILES ACDLabs 10.04 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CC"
PY4 SMILES_CANONICAL CACTVS 3.341 "CC[C@@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"
PY4 SMILES CACTVS 3.341 "CC[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"
PY4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC[C@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"
PY4 SMILES "OpenEye OEToolkits" 1.5.0 "CCC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"
PY4 InChI InChI 1.03 "InChI=1S/C12H19N2O7P/c1-3-10(12(16)17)14-5-9-8(6-21-22(18,19)20)4-13-7(2)11(9)15/h4,10,14-15H,3,5-6H2,1-2H3,(H,16,17)(H2,18,19,20)/t10-/m1/s1"
PY4 InChIKey InChI 1.03 VRMPGTOTVVJQMU-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
PY4 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]butanoic acid"
PY4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]butanoic 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
PY4 "Create component" 1999-08-18 RCSB
PY4 "Modify descriptor" 2011-06-04 RCSB
PY4 "Modify synonyms" 2021-03-01 PDBE
PY4 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PY4
_pdbx_chem_comp_synonyms.name "VITAMIN B6 COMPLEXED WITH 2-AMINO-BUTYRIC ACID"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PY4
_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 CG
_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 ?
#