data_TYO
#
_chem_comp.id TYO
_chem_comp.name '(4Z,6E)-2-AMINO-7-HYDROPEROXY-4-[(E)-2-HYDROXYVINYL]HEPTA-4,6-DIENOIC ACID'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C9 H13 N O5'
_chem_comp.mon_nstd_parent_comp_id TYR
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-09-22
_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 215.203
_chem_comp.one_letter_code Y
_chem_comp.three_letter_code TYO
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details 'Corina V3.40'
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2HHF
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
TYO N N N 0 1 N N N Y Y N 29.983 -6.178 22.560 1.340 1.763 1.021 N TYO 1
TYO CA CA C 0 1 N N S Y N N 28.872 -6.228 21.615 2.060 0.637 0.413 CA TYO 2
TYO CB CB C 0 1 N N N N N N 27.919 -5.064 21.873 1.320 0.177 -0.844 CB TYO 3
TYO CG CG C 0 1 N N N N N N 26.503 -5.270 21.346 -0.030 -0.373 -0.460 CG TYO 4
TYO CD1 CD1 C 0 1 N N N N N N 25.658 -6.420 21.978 -0.159 -1.770 -0.043 CD1 TYO 5
TYO CE1 CE1 C 0 1 N N N N N N 24.332 -6.339 22.064 0.923 -2.560 -0.004 CE1 TYO 6
TYO OE1 OE1 O 0 1 N N N N N N 23.736 -6.032 23.326 0.804 -3.854 0.382 OE1 TYO 7
TYO CD2 CD2 C 0 1 N N N N N N 26.115 -4.552 20.211 -1.120 0.423 -0.500 CD2 TYO 8
TYO CE2 CE2 C 0 1 N N N N N N 25.049 -5.041 19.140 -2.430 -0.111 -0.126 CE2 TYO 9
TYO CZ CZ C 0 1 N N N N N N 23.735 -4.955 19.403 -3.512 0.679 -0.166 CZ TYO 10
TYO OH OH O 0 1 N N N N N N 22.813 -5.613 18.530 -4.725 0.185 0.180 OH TYO 11
TYO OH1 OH1 O 0 1 N N N N N N 21.579 -6.230 19.112 -5.817 1.163 0.089 OH1 TYO 12
TYO C C C 0 1 N N N Y N Y 29.443 -6.186 20.198 3.455 1.072 0.044 C TYO 13
TYO O O O 0 1 N N N Y N Y 30.245 -5.314 19.859 3.708 2.247 -0.081 O TYO 14
TYO OXT OXT O 0 1 N Y N Y N Y 29.070 -7.189 19.381 4.416 0.155 -0.146 OXT TYO 15
TYO H HN1 H 0 1 N N N Y Y N 30.848 -6.167 22.058 1.277 2.540 0.380 HN1 TYO 16
TYO H2 HN2 H 0 1 N Y N Y Y N 29.910 -5.351 23.117 0.425 1.480 1.336 HN2 TYO 17
TYO HA HA H 0 1 N N N Y N N 28.297 -7.157 21.740 2.114 -0.187 1.125 HA TYO 18
TYO HB1 HB1 H 0 1 N N N N N N 27.854 -4.919 22.961 1.189 1.023 -1.518 HB1 TYO 19
TYO HB2 HB2 H 0 1 N N N N N N 28.330 -4.197 21.335 1.900 -0.599 -1.344 HB2 TYO 20
TYO HD1 HD1 H 0 1 N N N N N N 26.159 -7.300 22.353 -1.125 -2.164 0.232 HD1 TYO 21
TYO HE1 HE1 H 0 1 N N N N N N 23.716 -6.503 21.193 1.890 -2.166 -0.279 HE1 TYO 22
TYO HOE1 HOE1 H 0 0 N N N N N N 24.413 -5.964 23.988 1.638 -4.344 0.379 HOE1 TYO 23
TYO HD21 HD21 H 0 0 N N N N N N 26.576 -3.589 20.050 -1.025 1.454 -0.807 HD21 TYO 24
TYO HE2 HE2 H 0 1 N N N N N N 25.383 -5.445 18.195 -2.525 -1.142 0.181 HE2 TYO 25
TYO HZ HZ H 0 1 N N N N N N 23.381 -4.399 20.258 -3.417 1.710 -0.474 HZ TYO 26
TYO HOH1 HOH1 H 0 0 N N N N N N 21.700 -6.361 20.045 -6.683 0.810 0.335 HOH1 TYO 27
TYO HXT HXT H 0 1 N Y N Y N Y 29.515 -7.101 18.547 5.295 0.482 -0.382 HXT TYO 28
#
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
TYO N CA SING N N 1
TYO N H SING N N 2
TYO N H2 SING N N 3
TYO CA C SING N N 4
TYO CA CB SING N N 5
TYO CA HA SING N N 6
TYO CB CG SING N N 7
TYO CB HB1 SING N N 8
TYO CB HB2 SING N N 9
TYO CG CD2 DOUB N Z 10
TYO CG CD1 SING N N 11
TYO CD1 CE1 DOUB N E 12
TYO CD1 HD1 SING N N 13
TYO CE1 OE1 SING N N 14
TYO CE1 HE1 SING N N 15
TYO OE1 HOE1 SING N N 16
TYO CD2 CE2 SING N N 17
TYO CD2 HD21 SING N N 18
TYO CE2 CZ DOUB N E 19
TYO CE2 HE2 SING N N 20
TYO CZ OH SING N N 21
TYO CZ HZ SING N N 22
TYO OH OH1 SING N N 23
TYO OH1 HOH1 SING N N 24
TYO C O DOUB N N 25
TYO C OXT SING N N 26
TYO OXT HXT SING N N 27
#
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
TYO SMILES ACDLabs 10.04 'O=C(O)C(N)CC(\C=C\O)=C\C=C\OO'
TYO SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CC(/C=C/O)=C/C=C/OO)C(O)=O'
TYO SMILES CACTVS 3.341 'N[CH](CC(C=CO)=CC=COO)C(O)=O'
TYO SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@@H](C(=O)O)N)C(=C\C=C\OO)C=CO'
TYO SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(=O)O)N)C(=CC=COO)C=CO'
TYO InChI InChI 1.03 'InChI=1S/C9H13NO5/c10-8(9(12)13)6-7(3-4-11)2-1-5-15-14/h1-5,8,11,14H,6,10H2,(H,12,13)/b4-3?,5-1+,7-2+/t8-/m0/s1'
TYO InChIKey InChI 1.03 AMEKAKFJYGGFTQ-BFJUJRPPSA-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
TYO 'SYSTEMATIC NAME' ACDLabs 10.04 '(2S,4Z,6E)-2-amino-7-hydroperoxy-4-[(E)-2-hydroxyethenyl]hepta-4,6-dienoic acid'
TYO 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S,6E)-2-amino-7-hydroperoxy-4-(2-hydroxyethenyl)hepta-4,6-dienoic 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
TYO 'Create component' 2006-09-22 EBI
TYO 'Modify descriptor' 2011-06-04 RCSB
TYO 'Modify backbone' 2023-11-03 PDBE
TYO 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id TYO
_pdbx_chem_comp_pcm.modified_residue_id TYR
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_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 ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
TYO N N 0.262 -3.050 1
TYO CA C 1.561 -2.299 2
TYO CB C 1.559 -0.799 3
TYO CG C 0.260 -0.050 4
TYO CD1 C -1.039 -0.801 5
TYO CE1 C -2.338 -0.052 6
TYO OE1 O -3.637 -0.803 7
TYO CD2 C 0.259 1.450 8
TYO CE2 C -1.041 2.199 9
TYO CZ C -1.042 3.699 10
TYO OH O -2.342 4.448 11
TYO OH1 O -2.343 5.948 12
TYO C C 2.860 -3.048 13
TYO O O 4.159 -2.297 14
TYO OXT O 2.861 -4.548 15
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
TYO CA N SINGLE BEGINWEDGE 1
TYO CA C SINGLE NONE 2
TYO CA CB SINGLE NONE 3
TYO CB CG SINGLE ENDUPRIGHT 4
TYO CG CD2 DOUBLE NONE 5
TYO CG CD1 SINGLE ENDUPRIGHT 6
TYO CD1 CE1 DOUBLE NONE 7
TYO CE1 OE1 SINGLE ENDUPRIGHT 8
TYO CD2 CE2 SINGLE ENDUPRIGHT 9
TYO CE2 CZ DOUBLE NONE 10
TYO CZ OH SINGLE ENDUPRIGHT 11
TYO OH OH1 SINGLE NONE 12
TYO C O DOUBLE NONE 13
TYO C OXT SINGLE NONE 14
#
_pdbe_chem_comp_substructure.comp_id TYO
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
TYO O F1 1
TYO C F1 1
TYO CA F1 1
TYO N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id TYO
_pdbe_chem_comp_rdkit_properties.exactmw 215.079
_pdbe_chem_comp_rdkit_properties.amw 215.205
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 105.158
_pdbe_chem_comp_rdkit_properties.tpsa 113.010
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.790
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.934
_pdbe_chem_comp_rdkit_properties.chi0v 6.988
_pdbe_chem_comp_rdkit_properties.chi1v 3.207
_pdbe_chem_comp_rdkit_properties.chi2v 0.893
_pdbe_chem_comp_rdkit_properties.chi3v 0.893
_pdbe_chem_comp_rdkit_properties.chi4v 0.423
_pdbe_chem_comp_rdkit_properties.chi0n 19.988
_pdbe_chem_comp_rdkit_properties.chi1n 9.326
_pdbe_chem_comp_rdkit_properties.chi2n 0.893
_pdbe_chem_comp_rdkit_properties.chi3n 0.893
_pdbe_chem_comp_rdkit_properties.chi4n 0.423
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.790
_pdbe_chem_comp_rdkit_properties.kappa1 3.099
_pdbe_chem_comp_rdkit_properties.kappa2 7.599
_pdbe_chem_comp_rdkit_properties.kappa3 6.303
_pdbe_chem_comp_rdkit_properties.Phi 1.570
#
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
TYO N -2.162 -1.506 0.237 ETKDGv3 1
TYO CA -1.744 -0.545 1.260 ETKDGv3 2
TYO CB -1.178 0.732 0.606 ETKDGv3 3
TYO CG 0.132 0.468 -0.113 ETKDGv3 4
TYO CD1 0.140 0.257 -1.583 ETKDGv3 5
TYO CE1 -0.550 1.025 -2.425 ETKDGv3 6
TYO OE1 -0.505 0.768 -3.790 ETKDGv3 7
TYO CD2 1.251 0.317 0.623 ETKDGv3 8
TYO CE2 2.592 0.069 0.051 ETKDGv3 9
TYO CZ 3.643 -0.151 0.848 ETKDGv3 10
TYO OH 4.928 -0.377 0.342 ETKDGv3 11
TYO OH1 5.182 -0.447 -0.974 ETKDGv3 12
TYO C -2.921 -0.182 2.121 ETKDGv3 13
TYO O -2.809 -0.184 3.376 ETKDGv3 14
TYO OXT -4.128 0.186 1.533 ETKDGv3 15
TYO H -1.310 -1.861 -0.254 ETKDGv3 16
TYO H2 -2.574 -2.340 0.717 ETKDGv3 17
TYO HA -0.962 -1.010 1.903 ETKDGv3 18
TYO HB1 -1.939 1.150 -0.084 ETKDGv3 19
TYO HB2 -1.006 1.505 1.389 ETKDGv3 20
TYO HD1 0.749 -0.539 -1.994 ETKDGv3 21
TYO HE1 -1.138 1.861 -2.068 ETKDGv3 22
TYO HOE1 -1.021 1.350 -4.438 ETKDGv3 23
TYO HD21 1.176 0.409 1.701 ETKDGv3 24
TYO HE2 2.736 0.084 -1.020 ETKDGv3 25
TYO HZ 3.514 -0.153 1.923 ETKDGv3 26
TYO HOH1 4.829 -1.328 -1.261 ETKDGv3 27
TYO HXT -4.926 0.443 2.102 ETKDGv3 28
#