data_PY5
#
_chem_comp.id PY5
_chem_comp.name "2-[O-PHOSPHONOPYRIDOXYL]-AMINO-PENTANOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H21 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "VITAMIN B6 COMPLEXED WITH 2-AMINO-PENTANOIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-08-18
_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 348.289
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PY5
_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 1CQ7
_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
PY5 N1 N1 N 0 1 Y N N 26.691 3.739 -15.103 3.767 0.432 -0.541 N1 PY5 1
PY5 C2 C2 C 0 1 Y N N 26.404 4.867 -15.834 3.777 0.071 0.726 C2 PY5 2
PY5 C2A C2A C 0 1 N N N 27.113 4.794 -17.170 5.056 0.167 1.518 C2A PY5 3
PY5 C3 C3 C 0 1 Y N N 25.541 5.872 -15.247 2.624 -0.396 1.338 C3 PY5 4
PY5 O3 O3 O 0 1 N N N 25.357 6.912 -16.096 2.640 -0.769 2.645 O3 PY5 5
PY5 C4 C4 C 0 1 Y N N 24.965 5.755 -13.974 1.451 -0.480 0.594 C4 PY5 6
PY5 C4A C4A C 0 1 N N N 24.054 6.846 -13.383 0.175 -0.983 1.219 C4A PY5 7
PY5 C5 C5 C 0 1 Y N N 25.356 4.524 -13.325 1.486 -0.095 -0.735 C5 PY5 8
PY5 C6 C6 C 0 1 Y N N 26.176 3.538 -13.861 2.673 0.366 -1.273 C6 PY5 9
PY5 C5A C5A C 0 1 N N N 24.867 4.126 -11.927 0.241 -0.166 -1.582 C5A PY5 10
PY5 O4P O4P O 0 1 N N N 23.666 4.635 -11.506 0.537 0.294 -2.902 O4P PY5 11
PY5 P P P 0 1 N N N 22.770 3.977 -10.396 -0.829 0.190 -3.748 P PY5 12
PY5 O1P O1P O 0 1 N N N 22.283 2.704 -10.802 -1.865 1.037 -3.116 O1P PY5 13
PY5 O2P O2P O 0 1 N N N 21.850 5.084 -9.948 -0.568 0.697 -5.254 O2P PY5 14
PY5 O3P O3P O 0 1 N N N 23.728 3.656 -9.286 -1.329 -1.339 -3.775 O3P PY5 15
PY5 N N N 0 1 N N N 24.522 8.151 -14.048 -0.566 0.146 1.794 N PY5 16
PY5 CA CA C 0 1 N N S 23.447 9.221 -13.968 -1.792 -0.409 2.384 CA PY5 17
PY5 C C C 0 1 N N N 23.937 10.505 -14.638 -2.888 -0.415 1.350 C PY5 18
PY5 O O O 0 1 N N N 24.577 10.243 -15.795 -3.751 -1.260 1.390 O PY5 19
PY5 CB CB C 0 1 N N N 23.061 9.487 -12.518 -2.219 0.449 3.575 CB PY5 20
PY5 CG CG C 0 1 N N N 24.200 9.965 -11.631 -1.106 0.456 4.625 CG PY5 21
PY5 CD CD C 0 1 N N N 23.875 9.871 -10.152 -1.534 1.315 5.817 CD PY5 22
PY5 OXT OXT O 0 1 N N N 23.760 11.699 -14.155 -2.906 0.516 0.384 OXT PY5 23
PY5 H2A1 1H2A H 0 0 N N N 26.880 5.709 -17.763 5.607 -0.769 1.433 H2A1 PY5 24
PY5 H2A2 2H2A H 0 0 N N N 28.210 4.632 -17.057 5.664 0.983 1.129 H2A2 PY5 25
PY5 H2A3 3H2A H 0 0 N N N 26.870 3.858 -17.725 4.820 0.357 2.566 H2A3 PY5 26
PY5 HO3 HO3 H 0 1 N N N 24.791 7.570 -15.711 2.862 -1.709 2.665 HO3 PY5 27
PY5 H4A1 1H4A H 0 0 N N N 22.964 6.641 -13.504 0.413 -1.699 2.006 H4A1 PY5 28
PY5 H4A2 2H4A H 0 0 N N N 24.052 6.880 -12.268 -0.435 -1.469 0.458 H4A2 PY5 29
PY5 H6 H6 H 0 1 N N N 26.413 2.612 -13.310 2.705 0.671 -2.309 H6 PY5 30
PY5 H5A1 1H5A H 0 0 N N N 24.843 3.014 -11.847 -0.108 -1.198 -1.627 H5A1 PY5 31
PY5 H5A2 2H5A H 0 0 N N N 25.654 4.372 -11.177 -0.533 0.461 -1.143 H5A2 PY5 32
PY5 HOP2 2HOP H 0 0 N N N 21.308 4.686 -9.276 -1.409 0.619 -5.724 HOP2 PY5 33
PY5 HOP3 3HOP H 0 0 N N N 23.186 3.258 -8.614 -0.626 -1.855 -4.194 HOP3 PY5 34
PY5 HN2 HN2 H 0 1 N N N 24.826 7.994 -15.009 -0.854 0.728 1.021 HN2 PY5 35
PY5 HA HA H 0 1 N N N 22.540 8.858 -14.506 -1.603 -1.428 2.720 HA PY5 36
PY5 HB1 1HB H 0 1 N N N 22.208 10.203 -12.470 -3.129 0.037 4.013 HB1 PY5 37
PY5 HB2 2HB H 0 1 N N N 22.579 8.584 -12.074 -2.408 1.469 3.239 HB2 PY5 38
PY5 HG1 HG1 H 0 1 N N N 25.144 9.421 -11.867 -0.197 0.869 4.187 HG1 PY5 39
PY5 HG2 HG2 H 0 1 N N N 24.512 10.999 -11.905 -0.918 -0.563 4.961 HG2 PY5 40
PY5 HD1 HD1 H 0 1 N N N 24.710 10.221 -9.501 -0.741 1.320 6.564 HD1 PY5 41
PY5 HD2 HD2 H 0 1 N N N 22.930 10.414 -9.915 -1.723 2.335 5.480 HD2 PY5 42
PY5 HD3 HD3 H 0 1 N N N 23.562 8.836 -9.877 -2.443 0.903 6.254 HD3 PY5 43
PY5 HXT HXT H 0 1 N N N 24.064 12.496 -14.571 -3.609 0.512 -0.278 HXT PY5 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
PY5 N1 C2 DOUB Y N 1
PY5 N1 C6 SING Y N 2
PY5 C2 C2A SING N N 3
PY5 C2 C3 SING Y N 4
PY5 C2A H2A1 SING N N 5
PY5 C2A H2A2 SING N N 6
PY5 C2A H2A3 SING N N 7
PY5 C3 O3 SING N N 8
PY5 C3 C4 DOUB Y N 9
PY5 O3 HO3 SING N N 10
PY5 C4 C4A SING N N 11
PY5 C4 C5 SING Y N 12
PY5 C4A N SING N N 13
PY5 C4A H4A1 SING N N 14
PY5 C4A H4A2 SING N N 15
PY5 C5 C6 DOUB Y N 16
PY5 C5 C5A SING N N 17
PY5 C6 H6 SING N N 18
PY5 C5A O4P SING N N 19
PY5 C5A H5A1 SING N N 20
PY5 C5A H5A2 SING N N 21
PY5 O4P P SING N N 22
PY5 P O1P DOUB N N 23
PY5 P O2P SING N N 24
PY5 P O3P SING N N 25
PY5 O2P HOP2 SING N N 26
PY5 O3P HOP3 SING N N 27
PY5 N CA SING N N 28
PY5 N HN2 SING N N 29
PY5 CA C SING N N 30
PY5 CA CB SING N N 31
PY5 CA HA SING N N 32
PY5 C O DOUB N N 33
PY5 C OXT SING N N 34
PY5 CB CG SING N N 35
PY5 CB HB1 SING N N 36
PY5 CB HB2 SING N N 37
PY5 CG CD SING N N 38
PY5 CG HG1 SING N N 39
PY5 CG HG2 SING N N 40
PY5 CD HD1 SING N N 41
PY5 CD HD2 SING N N 42
PY5 CD HD3 SING N N 43
PY5 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
PY5 SMILES ACDLabs 10.04 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCC"
PY5 SMILES_CANONICAL CACTVS 3.341 "CCC[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"
PY5 SMILES CACTVS 3.341 "CCC[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"
PY5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCC[C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"
PY5 SMILES "OpenEye OEToolkits" 1.5.0 "CCCC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"
PY5 InChI InChI 1.03 "InChI=1S/C13H21N2O7P/c1-3-4-11(13(17)18)15-6-10-9(7-22-23(19,20)21)5-14-8(2)12(10)16/h5,11,15-16H,3-4,6-7H2,1-2H3,(H,17,18)(H2,19,20,21)/t11-/m0/s1"
PY5 InChIKey InChI 1.03 YYAMSLLSQINIQO-NSHDSACASA-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
PY5 "SYSTEMATIC NAME" ACDLabs 10.04 "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-norvaline"
PY5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic 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
PY5 "Create component" 1999-08-18 RCSB
PY5 "Modify descriptor" 2011-06-04 RCSB
PY5 "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PY5
_pdbx_chem_comp_synonyms.name "VITAMIN B6 COMPLEXED WITH 2-AMINO-PENTANOIC ACID"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##