data_PSW
#
_chem_comp.id PSW
_chem_comp.name 3-(SULFANYLSELANYL)-L-ALANINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C3 H7 N O2 S Se"
_chem_comp.mon_nstd_parent_comp_id SEC
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-08-07
_chem_comp.pdbx_modified_date 2023-11-03
_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 200.118
_chem_comp.one_letter_code U
_chem_comp.three_letter_code PSW
_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 2WPN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
PSW N N N 0 1 N N N Y Y N 3.870 2.883 16.877 1.567 1.673 -0.425 N PSW 1
PSW C C C 0 1 N N N Y N Y 4.303 0.643 17.468 2.833 -0.357 0.002 C PSW 2
PSW O O O 0 1 N N N Y N Y 3.627 0.535 18.509 3.501 -0.067 -0.962 O PSW 3
PSW CA CA C 0 1 N N R Y N N 4.976 1.905 17.071 1.552 0.386 0.283 CA PSW 4
PSW CB CB C 0 1 N N N N N N 6.175 2.088 18.015 0.363 -0.448 -0.200 CB PSW 5
PSW SE SE SE 0 0 N N N N N N 5.734 3.083 19.639 -1.308 0.442 0.307 SE PSW 6
PSW SD SD S 0 1 N N N N N N 7.583 4.027 20.100 -2.801 -0.967 -0.509 SD PSW 7
PSW OXT OXT O 0 1 N Y N Y N Y 4.457 -0.333 16.587 3.232 -1.341 0.823 OXT PSW 8
PSW H HN1 H 0 1 N N N Y Y N 3.459 3.102 17.762 2.305 2.267 -0.078 HN1 PSW 9
PSW H2 HN2 H 0 1 N Y N Y Y N 4.232 3.718 16.462 1.651 1.537 -1.421 HN2 PSW 10
PSW HA HA H 0 1 N N N Y N N 5.507 2.000 16.112 1.461 0.561 1.355 HA PSW 11
PSW HXT HXT H 0 1 N Y N Y N Y 3.979 -1.101 16.878 4.060 -1.788 0.602 HXT PSW 12
PSW HB1C HB1C H 0 0 N N N N N N 6.536 1.092 18.309 0.407 -0.548 -1.285 HB1C PSW 13
PSW HB2C HB2C H 0 0 N N N N N N 6.936 2.667 17.471 0.402 -1.436 0.258 HB2C PSW 14
PSW HD HD H 0 1 N N N N N N 8.257 4.220 19.005 -3.972 -0.391 -0.181 HD PSW 15
#
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
PSW N CA SING N N 1
PSW C O DOUB N N 2
PSW C CA SING N N 3
PSW C OXT SING N N 4
PSW CA CB SING N N 5
PSW CB SE SING N N 6
PSW SE SD SING N N 7
PSW N H SING N N 8
PSW N H2 SING N N 9
PSW CA HA SING N N 10
PSW OXT HXT SING N N 11
PSW CB HB1C SING N N 12
PSW CB HB2C SING N N 13
PSW SD HD SING N N 14
#
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
PSW SMILES ACDLabs 10.04 O=C(O)C(N)C[Se]S
PSW SMILES_CANONICAL CACTVS 3.352 N[C@@H](C[Se]S)C(O)=O
PSW SMILES CACTVS 3.352 N[CH](C[Se]S)C(O)=O
PSW SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 C([C@@H](C(=O)O)N)[Se]S
PSW SMILES "OpenEye OEToolkits" 1.6.1 C(C(C(=O)O)N)[Se]S
PSW InChI InChI 1.03 InChI=1S/C3H7NO2SSe/c4-2(1-8-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
PSW InChIKey InChI 1.03 SPXWFQKISDCWEH-REOHCLBHSA-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
PSW "SYSTEMATIC NAME" ACDLabs 10.04 3-(sulfanylselanyl)-L-alanine
PSW "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(2R)-2-amino-3-sulfanylselanyl-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
PSW 'Create component' 2009-08-07 EBI
PSW 'Modify descriptor' 2011-06-04 RCSB
PSW 'Modify parent residue' 2014-01-20 EBI
PSW 'Modify one letter code' 2014-01-20 EBI
PSW 'Modify one letter code' 2014-01-31 EBI
PSW 'Modify one letter code' 2019-04-15 EBI
PSW 'Modify backbone' 2023-11-03 PDBE
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
PSW N N 3.805 1.732 1
PSW C C 6.404 1.732 2
PSW O O 7.702 0.983 3
PSW CA C 5.104 0.983 4
PSW CB C 5.104 -0.517 5
PSW SE Se 3.805 -1.268 6
PSW SD S 3.805 -2.768 7
PSW OXT O 6.404 3.232 8
#
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
PSW CA N SINGLE BEGINDASH 1
PSW C O DOUBLE NONE 2
PSW C CA SINGLE NONE 3
PSW C OXT SINGLE NONE 4
PSW CA CB SINGLE NONE 5
PSW CB SE SINGLE NONE 6
PSW SE SD SINGLE NONE 7
#
_pdbe_chem_comp_substructure.comp_id PSW
_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
PSW O F1 1
PSW C F1 1
PSW CA F1 1
PSW N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PSW
_pdbe_chem_comp_rdkit_properties.exactmw 200.936
_pdbe_chem_comp_rdkit_properties.amw 200.121
_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 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 67.986
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.634
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.158
_pdbe_chem_comp_rdkit_properties.chi0v 6.110
_pdbe_chem_comp_rdkit_properties.chi1v 4.791
_pdbe_chem_comp_rdkit_properties.chi2v 1.345
_pdbe_chem_comp_rdkit_properties.chi3v 1.345
_pdbe_chem_comp_rdkit_properties.chi4v 0.832
_pdbe_chem_comp_rdkit_properties.chi0n 10.580
_pdbe_chem_comp_rdkit_properties.chi1n 4.714
_pdbe_chem_comp_rdkit_properties.chi2n 0.332
_pdbe_chem_comp_rdkit_properties.chi3n 0.332
_pdbe_chem_comp_rdkit_properties.chi4n 0.081
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.299
_pdbe_chem_comp_rdkit_properties.kappa1 2.163
_pdbe_chem_comp_rdkit_properties.kappa2 4.205
_pdbe_chem_comp_rdkit_properties.kappa3 3.320
_pdbe_chem_comp_rdkit_properties.Phi 1.137
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
PSW UniChem PDBe PSW
PSW UniChem PubChem 49867530
#
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
PSW N -0.551 -1.460 0.906 ETKDGv3 1
PSW C -1.630 0.415 -0.234 ETKDGv3 2
PSW O -2.095 -0.165 -1.252 ETKDGv3 3
PSW CA -0.372 -0.088 0.423 ETKDGv3 4
PSW CB 0.811 -0.011 -0.548 ETKDGv3 5
PSW SE 2.478 -0.476 0.356 ETKDGv3 6
PSW SD 3.654 -0.160 -1.542 ETKDGv3 7
PSW OXT -2.283 1.529 0.286 ETKDGv3 8
PSW H -1.333 -1.471 1.601 ETKDGv3 9
PSW H2 -0.830 -2.079 0.110 ETKDGv3 10
PSW HA -0.146 0.566 1.294 ETKDGv3 11
PSW HXT -3.130 1.882 -0.143 ETKDGv3 12
PSW HB1C 0.656 -0.704 -1.403 ETKDGv3 13
PSW HB2C 0.906 1.025 -0.941 ETKDGv3 14
PSW HD 3.864 1.199 -1.246 ETKDGv3 15
#