data_ZT9
#
_chem_comp.id ZT9
_chem_comp.name '(2R)-amino(4-methoxyphenyl)ethanethioic O-acid'
_chem_comp.type 'D-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C9 H11 N O2 S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-03-30
_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 197.254
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ZT9
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 8GJV
_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
ZT9 N N N 0 1 N N N Y Y N 15.504 9.256 5.756 2.027 1.232 -1.434 N ZT9 1
ZT9 CA CA C 0 1 N N R Y N N 14.378 8.350 5.587 1.512 -0.083 -1.028 CA ZT9 2
ZT9 C C C 0 1 N N N Y N Y 13.214 8.679 6.506 2.339 -0.616 0.112 C ZT9 3
ZT9 C1 C1 C 0 1 Y N N N N N 13.863 8.287 4.151 0.077 0.054 -0.588 C1 ZT9 4
ZT9 C2 C2 C 0 1 Y N N N N N 12.645 7.626 3.894 -0.847 -0.915 -0.934 C2 ZT9 5
ZT9 C3 C3 C 0 1 Y N N N N N 12.141 7.605 2.618 -2.162 -0.791 -0.531 C3 ZT9 6
ZT9 C4 C4 C 0 1 Y N N N N N 12.846 8.166 1.555 -2.556 0.306 0.222 C4 ZT9 7
ZT9 C5 C5 C 0 1 Y N N N N N 14.062 8.751 1.808 -1.628 1.276 0.568 C5 ZT9 8
ZT9 C6 C6 C 0 1 Y N N N N N 14.566 8.866 3.110 -0.312 1.146 0.167 C6 ZT9 9
ZT9 O4 O4 O 0 1 N N N N N N 12.324 8.135 0.274 -3.852 0.432 0.614 O4 ZT9 10
ZT9 S S S 0 1 N N N Y N Y 12.592 10.207 6.568 3.402 0.331 0.840 S ZT9 11
ZT9 C7 C7 C 0 1 N N N N N N 11.653 9.531 -0.053 -4.752 -0.606 0.222 C7 ZT9 12
ZT9 H H H 0 1 N N N Y Y N 15.794 9.253 6.713 1.984 1.889 -0.669 H ZT9 13
ZT9 H2 H2 H 0 1 N Y N Y Y N 16.262 8.957 5.177 2.966 1.157 -1.795 H2 ZT9 14
ZT9 HA HA1 H 0 1 N N N Y N N 14.719 7.338 5.849 1.568 -0.771 -1.872 HA1 ZT9 15
ZT9 H21 H21 H 0 1 N N N N N N 12.111 7.139 4.697 -0.540 -1.768 -1.520 H21 ZT9 16
ZT9 H5 H5 H 0 1 N Y N N N N 11.181 7.146 2.434 -2.884 -1.548 -0.802 H5 ZT9 17
ZT9 H6 H6 H 0 1 N Y N N N N 14.645 9.132 0.982 -1.932 2.131 1.153 H6 ZT9 18
ZT9 H61 H61 H 0 1 N N N N N N 15.487 9.397 3.298 0.411 1.901 0.436 H61 ZT9 19
ZT9 H73 H73 H 0 1 N N N N N N 11.237 9.509 -1.071 -4.781 -0.670 -0.866 H73 ZT9 20
ZT9 H71 H71 H 0 1 N N N N N N 10.846 9.728 0.668 -4.413 -1.556 0.633 H71 ZT9 21
ZT9 H72 H72 H 0 1 N N N N N N 12.409 10.327 0.017 -5.750 -0.382 0.599 H72 ZT9 22
ZT9 OXT OXT O 0 1 N Y N Y N Y 12.721 7.618 7.147 2.183 -1.889 0.518 OXT ZT9 23
ZT9 HXT HXT H 0 1 N Y N Y N Y 11.955 7.877 7.646 2.736 -2.186 1.254 HXT ZT9 24
#
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
ZT9 C7 O4 SING N N 1
ZT9 O4 C4 SING N N 2
ZT9 C4 C5 DOUB Y N 3
ZT9 C4 C3 SING Y N 4
ZT9 C5 C6 SING Y N 5
ZT9 C3 C2 DOUB Y N 6
ZT9 C6 C1 DOUB Y N 7
ZT9 C2 C1 SING Y N 8
ZT9 C1 CA SING N N 9
ZT9 CA N SING N N 10
ZT9 CA C SING N N 11
ZT9 C S DOUB N N 12
ZT9 N H SING N N 13
ZT9 N H2 SING N N 14
ZT9 CA HA SING N N 15
ZT9 C2 H21 SING N N 16
ZT9 C3 H5 SING N N 17
ZT9 C5 H6 SING N N 18
ZT9 C6 H61 SING N N 19
ZT9 C7 H73 SING N N 20
ZT9 C7 H71 SING N N 21
ZT9 C7 H72 SING N N 22
ZT9 C OXT SING N N 23
ZT9 OXT HXT SING N N 24
#
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
ZT9 SMILES ACDLabs 12.01 'COc1ccc(cc1)C(N)C(O)=S'
ZT9 InChI InChI 1.06 'InChI=1S/C9H11NO2S/c1-12-7-4-2-6(3-5-7)8(10)9(11)13/h2-5,8H,10H2,1H3,(H,11,13)/t8-/m1/s1'
ZT9 InChIKey InChI 1.06 INSVIGJTBISSTF-MRVPVSSYSA-N
ZT9 SMILES_CANONICAL CACTVS 3.385 'COc1ccc(cc1)[C@@H](N)C(O)=S'
ZT9 SMILES CACTVS 3.385 'COc1ccc(cc1)[CH](N)C(O)=S'
ZT9 SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'COc1ccc(cc1)[C@H](C(=S)O)N'
ZT9 SMILES 'OpenEye OEToolkits' 2.0.7 'COc1ccc(cc1)C(C(=S)O)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
ZT9 'SYSTEMATIC NAME' ACDLabs 12.01 '(2R)-amino(4-methoxyphenyl)ethanethioic O-acid'
ZT9 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 '(2~{R})-2-azanyl-2-(4-methoxyphenyl)ethanethioic O-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
ZT9 'Create component' 2023-03-30 RCSB
ZT9 'Initial release' 2023-06-21 RCSB
ZT9 'Modify backbone' 2023-11-03 PDBE
ZT9 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id ZT9
_pdbx_chem_comp_pcm.modified_residue_id ?
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain and backbone'
_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 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
ZT9 N N 3.805 2.768 1
ZT9 CA C 5.104 2.018 2
ZT9 C C 6.404 2.768 3
ZT9 C1 C 5.104 0.517 4
ZT9 C2 C 6.404 -0.233 5
ZT9 C3 C 6.404 -1.732 6
ZT9 C4 C 5.104 -2.482 7
ZT9 C5 C 3.805 -1.732 8
ZT9 C6 C 3.805 -0.233 9
ZT9 O4 O 5.104 -3.982 10
ZT9 S S 6.404 4.268 11
ZT9 C7 C 3.805 -4.732 12
ZT9 OXT O 7.702 2.018 13
#
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
ZT9 C7 O4 SINGLE NONE 1
ZT9 O4 C4 SINGLE NONE 2
ZT9 C4 C5 DOUBLE NONE 3
ZT9 C4 C3 SINGLE NONE 4
ZT9 C5 C6 SINGLE NONE 5
ZT9 C3 C2 DOUBLE NONE 6
ZT9 C6 C1 DOUBLE NONE 7
ZT9 C2 C1 SINGLE NONE 8
ZT9 C1 CA SINGLE NONE 9
ZT9 CA N SINGLE BEGINWEDGE 10
ZT9 CA C SINGLE NONE 11
ZT9 C S DOUBLE NONE 12
ZT9 C OXT SINGLE NONE 13
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
ZT9 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
ZT9 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
ZT9 C1 S1 1
ZT9 C2 S1 1
ZT9 C3 S1 1
ZT9 C4 S1 1
ZT9 C5 S1 1
ZT9 C6 S1 1
ZT9 C1 F1 1
ZT9 C6 F1 1
ZT9 C5 F1 1
ZT9 C4 F1 1
ZT9 C3 F1 1
ZT9 C2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ZT9
_pdbe_chem_comp_rdkit_properties.exactmw 197.051
_pdbe_chem_comp_rdkit_properties.amw 197.259
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 97.790
_pdbe_chem_comp_rdkit_properties.tpsa 55.480
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.063
_pdbe_chem_comp_rdkit_properties.CrippenMR 54.273
_pdbe_chem_comp_rdkit_properties.chi0v 6.988
_pdbe_chem_comp_rdkit_properties.chi1v 3.448
_pdbe_chem_comp_rdkit_properties.chi2v 1.328
_pdbe_chem_comp_rdkit_properties.chi3v 1.328
_pdbe_chem_comp_rdkit_properties.chi4v 0.675
_pdbe_chem_comp_rdkit_properties.chi0n 17.172
_pdbe_chem_comp_rdkit_properties.chi1n 8.343
_pdbe_chem_comp_rdkit_properties.chi2n 1.134
_pdbe_chem_comp_rdkit_properties.chi3n 1.134
_pdbe_chem_comp_rdkit_properties.chi4n 0.573
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.130
_pdbe_chem_comp_rdkit_properties.kappa1 2.681
_pdbe_chem_comp_rdkit_properties.kappa2 4.204
_pdbe_chem_comp_rdkit_properties.kappa3 2.402
_pdbe_chem_comp_rdkit_properties.Phi 0.867
#
_pdbe_chem_comp_external_mappings.comp_id ZT9
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 168451767
#
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
ZT9 N -2.411 -1.746 -1.223 ETKDGv3 1
ZT9 CA -2.327 -0.378 -0.707 ETKDGv3 2
ZT9 C -3.081 -0.255 0.590 ETKDGv3 3
ZT9 C1 -0.881 0.048 -0.531 ETKDGv3 4
ZT9 C2 -0.031 -0.579 0.516 ETKDGv3 5
ZT9 C3 1.248 -0.214 0.661 ETKDGv3 6
ZT9 C4 1.838 0.822 -0.228 ETKDGv3 7
ZT9 C5 1.073 1.381 -1.175 ETKDGv3 8
ZT9 C6 -0.339 0.978 -1.338 ETKDGv3 9
ZT9 O4 3.172 1.235 -0.110 ETKDGv3 10
ZT9 S -3.680 1.199 1.054 ETKDGv3 11
ZT9 C7 4.081 0.717 0.854 ETKDGv3 12
ZT9 H -1.963 -1.771 -2.169 ETKDGv3 13
ZT9 H2 -1.866 -2.394 -0.608 ETKDGv3 14
ZT9 HA -2.831 0.287 -1.445 ETKDGv3 15
ZT9 H21 -0.444 -1.336 1.170 ETKDGv3 16
ZT9 H5 1.844 -0.685 1.431 ETKDGv3 17
ZT9 H6 1.487 2.136 -1.832 ETKDGv3 18
ZT9 H61 -0.925 1.446 -2.119 ETKDGv3 19
ZT9 H73 4.214 -0.375 0.706 ETKDGv3 20
ZT9 H71 5.065 1.215 0.730 ETKDGv3 21
ZT9 H72 3.707 0.921 1.880 ETKDGv3 22
ZT9 OXT -3.231 -1.362 1.424 ETKDGv3 23
ZT9 HXT -3.719 -1.292 2.309 ETKDGv3 24
#