data_PYX
#
_chem_comp.id PYX
_chem_comp.name "S-[S-THIOPYRIDOXAMINYL]CYSTEINE"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C11 H17 N3 O3 S2"
_chem_comp.mon_nstd_parent_comp_id CYS
_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 N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 303.401
_chem_comp.one_letter_code C
_chem_comp.three_letter_code PYX
_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 1A2D
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
PYX N N N 0 1 N N N N N N 3.069 33.648 25.745 -0.675 -1.471 -4.953 N PYX 1
PYX CA CA C 0 1 N N R N N N 2.803 34.299 24.467 -0.426 -0.477 -3.900 CA PYX 2
PYX C C C 0 1 N N N N N N 1.373 34.809 24.377 0.280 0.714 -4.491 C PYX 3
PYX O O O 0 1 N N N N N N 0.415 34.035 24.307 1.013 0.572 -5.441 O PYX 4
PYX OXT OXT O 0 1 N Y N N N N 1.242 36.128 24.349 0.096 1.934 -3.962 OXT PYX 5
PYX CB CB C 0 1 N N N N N N 3.058 33.331 23.333 0.446 -1.100 -2.809 CB PYX 6
PYX SG SG S 0 1 N N N N N N 4.667 32.540 23.338 0.806 0.145 -1.539 SG PYX 7
PYX SD SD S 0 1 N N N N N N 5.031 31.479 21.659 -1.063 0.382 -0.734 SD PYX 8
PYX CE CE C 0 1 N N N N N N 6.668 31.666 20.963 -1.071 -0.987 0.454 CE PYX 9
PYX C1 C1 C 0 1 Y N N N N N 6.951 30.839 19.748 -0.164 -0.655 1.610 C1 PYX 10
PYX C2 C2 C 0 1 Y N N N N N 6.114 30.970 18.631 1.149 -1.086 1.616 C2 PYX 11
PYX C6 C6 C 0 1 Y N N N N N 8.031 29.943 19.737 -0.637 0.086 2.681 C6 PYX 12
PYX N3 N3 N 0 1 Y N N N N N 6.348 30.206 17.489 1.951 -0.800 2.623 N3 PYX 13
PYX C5 C5 C 0 1 Y N N N N N 8.271 29.168 18.586 0.234 0.364 3.729 C5 PYX 14
PYX CM6 CM6 C 0 1 N N N N N N 8.952 29.807 20.985 -2.062 0.574 2.712 CM6 PYX 15
PYX C4 C4 C 0 1 Y N N N N N 7.423 29.303 17.456 1.540 -0.098 3.660 C4 PYX 16
PYX O5 O5 O 0 1 N N N N N N 9.371 28.249 18.565 -0.184 1.087 4.801 O5 PYX 17
PYX N6 N6 N 0 1 N N N N N N 8.318 28.941 22.009 -2.895 -0.391 3.441 N6 PYX 18
PYX CM4 CM4 C 0 1 N N N N N N 7.668 28.463 16.183 2.497 0.200 4.785 CM4 PYX 19
PYX H 1HN H 0 1 N N N N N N 4.028 33.306 25.805 -1.156 -2.243 -4.516 H PYX 20
PYX H2 2HN H 0 1 N Y N N N N 2.397 32.902 25.928 0.226 -1.818 -5.244 H2 PYX 21
PYX HA HA H 0 1 N N N N N N 3.489 35.174 24.388 -1.376 -0.160 -3.469 HA PYX 22
PYX HXT HXT H 0 1 N Y N N N N 0.348 36.446 24.292 0.550 2.699 -4.341 HXT PYX 23
PYX HB2 1HB H 0 1 N N N N N N 2.253 32.559 23.302 1.380 -1.452 -3.247 HB2 PYX 24
PYX HB3 2HB H 0 1 N N N N N N 2.884 33.836 22.354 -0.081 -1.939 -2.355 HB3 PYX 25
PYX HE2 1HE H 0 1 N N N N N N 6.870 32.741 20.748 -0.717 -1.895 -0.035 HE2 PYX 26
PYX HE3 2HE H 0 1 N N N N N N 7.439 31.471 21.744 -2.085 -1.144 0.821 HE3 PYX 27
PYX HC2 H2 H 0 1 N N N N N N 5.267 31.677 18.650 1.523 -1.664 0.784 HC2 PYX 28
PYX HM61 1HM6 H 0 0 N N N N N N 9.970 29.446 20.710 -2.104 1.541 3.214 HM61 PYX 29
PYX HM62 2HM6 H 0 0 N N N N N N 9.234 30.802 21.401 -2.433 0.677 1.692 HM62 PYX 30
PYX HO5 HO5 H 0 1 N N N N N N 9.532 27.726 17.788 -0.531 0.456 5.445 HO5 PYX 31
PYX HN61 1HN6 H 0 0 N N N N N N 8.921 28.851 22.826 -3.845 -0.057 3.383 HN61 PYX 32
PYX HN62 2HN6 H 0 0 N N N N N N 8.059 28.030 21.628 -2.860 -1.255 2.920 HN62 PYX 33
PYX HM41 1HM4 H 0 0 N N N N N N 8.521 27.746 16.156 3.015 1.138 4.583 HM41 PYX 34
PYX HM42 2HM4 H 0 0 N N N N N N 6.731 27.911 15.933 1.944 0.284 5.720 HM42 PYX 35
PYX HM43 3HM4 H 0 0 N N N N N N 7.755 29.153 15.311 3.226 -0.606 4.865 HM43 PYX 36
#
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
PYX N CA SING N N 1
PYX N H SING N N 2
PYX N H2 SING N N 3
PYX CA C SING N N 4
PYX CA CB SING N N 5
PYX CA HA SING N N 6
PYX C O DOUB N N 7
PYX C OXT SING N N 8
PYX OXT HXT SING N N 9
PYX CB SG SING N N 10
PYX CB HB2 SING N N 11
PYX CB HB3 SING N N 12
PYX SG SD SING N N 13
PYX SD CE SING N N 14
PYX CE C1 SING N N 15
PYX CE HE2 SING N N 16
PYX CE HE3 SING N N 17
PYX C1 C2 SING Y N 18
PYX C1 C6 DOUB Y N 19
PYX C2 N3 DOUB Y N 20
PYX C2 HC2 SING N N 21
PYX C6 C5 SING Y N 22
PYX C6 CM6 SING N N 23
PYX N3 C4 SING Y N 24
PYX C5 C4 DOUB Y N 25
PYX C5 O5 SING N N 26
PYX CM6 N6 SING N N 27
PYX CM6 HM61 SING N N 28
PYX CM6 HM62 SING N N 29
PYX C4 CM4 SING N N 30
PYX O5 HO5 SING N N 31
PYX N6 HN61 SING N N 32
PYX N6 HN62 SING N N 33
PYX CM4 HM41 SING N N 34
PYX CM4 HM42 SING N N 35
PYX CM4 HM43 SING N N 36
#
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
PYX SMILES ACDLabs 10.04 "O=C(O)C(N)CSSCc1cnc(c(O)c1CN)C"
PYX SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(CSSC[C@H](N)C(O)=O)c(CN)c1O"
PYX SMILES CACTVS 3.341 "Cc1ncc(CSSC[CH](N)C(O)=O)c(CN)c1O"
PYX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)CSSC[C@@H](C(=O)O)N)CN)O"
PYX SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)CSSCC(C(=O)O)N)CN)O"
PYX InChI InChI 1.03 "InChI=1S/C11H17N3O3S2/c1-6-10(15)8(2-12)7(3-14-6)4-18-19-5-9(13)11(16)17/h3,9,15H,2,4-5,12-13H2,1H3,(H,16,17)/t9-/m0/s1"
PYX InChIKey InChI 1.03 GNMYVMXAEUCEOO-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
PYX "SYSTEMATIC NAME" ACDLabs 10.04 "3-({[4-(aminomethyl)-5-hydroxy-6-methylpyridin-3-yl]methyl}disulfanyl)-L-alanine"
PYX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-amino-3-[[4-(aminomethyl)-5-hydroxy-6-methyl-pyridin-3-yl]methyldisulfanyl]propanoic 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
PYX "Create component" 1999-07-08 RCSB
PYX "Modify descriptor" 2011-06-04 RCSB
PYX "Modify PCM" 2024-09-27 PDBE
#