data_VGT
#
_chem_comp.id VGT
_chem_comp.name 4-((2-hydroxy-3-(phenylselanyl)propyl)thio)benzenesulfonamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H17 N O3 S2 Se"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-05-18
_chem_comp.pdbx_modified_date 2022-05-27
_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 402.390
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VGT
_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 7OK8
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
VGT C7 C1 C 0 1 Y N N N N N -1.813 11.007 13.443 -5.672 -1.356 1.196 C7 VGT 1
VGT C8 C2 C 0 1 N N N N N N -2.133 5.486 13.249 -0.013 0.709 -0.029 C8 VGT 2
VGT C9 C3 C 0 1 Y N N N N N -4.423 4.329 14.376 2.750 1.131 0.107 C9 VGT 3
VGT O1 O1 O 0 1 N N N N N N -5.464 1.019 18.135 7.654 -0.187 -0.509 O1 VGT 4
VGT C1 C4 C 0 1 N N N N N N -2.055 7.948 12.796 -2.461 0.208 -0.042 C1 VGT 5
VGT C5 C5 C 0 1 Y N N N N N -0.532 12.951 14.018 -6.951 -2.887 -0.129 C5 VGT 6
VGT C6 C6 C 0 1 Y N N N N N -1.588 12.368 13.338 -6.464 -2.485 1.101 C6 VGT 7
VGT C4 C7 C 0 1 Y N N N N N 0.310 12.163 14.802 -6.646 -2.160 -1.264 C4 VGT 8
VGT C3 C8 C 0 1 Y N N N N N 0.087 10.800 14.919 -5.848 -1.034 -1.170 C3 VGT 9
VGT C2 C9 C 0 1 Y N N N N N -0.982 10.232 14.250 -5.366 -0.629 0.060 C2 VGT 10
VGT O2 O2 O 0 1 N N N N N N -7.478 0.939 16.708 6.399 -2.318 -0.868 O2 VGT 11
VGT S1 S1 S 0 1 N N N N N N -6.037 0.853 16.821 6.665 -1.134 -0.130 S1 VGT 12
VGT N N1 N 0 1 N N N N N N -5.526 -0.500 16.162 7.045 -1.617 1.408 N VGT 13
VGT C12 C10 C 0 1 Y N N N N N -5.423 2.192 15.863 5.142 -0.253 -0.038 C12 VGT 14
VGT C11 C11 C 0 1 Y N N N N N -6.262 3.254 15.496 5.147 1.115 0.171 C11 VGT 15
VGT C10 C12 C 0 1 Y N N N N N -5.757 4.304 14.747 3.956 1.809 0.243 C10 VGT 16
VGT C13 C13 C 0 1 Y N N N N N -4.084 2.217 15.481 3.944 -0.930 -0.174 C13 VGT 17
VGT C14 C14 C 0 1 Y N N N N N -3.585 3.293 14.755 2.748 -0.243 -0.102 C14 VGT 18
VGT S S2 S 0 1 N N N N N N -3.915 5.677 13.337 1.227 2.011 0.206 S VGT 19
VGT C C15 C 0 1 N N R N N N -1.527 6.586 12.394 -1.414 1.321 0.031 C VGT 20
VGT O O3 O 0 1 N N N N N N -1.961 6.397 11.034 -1.591 2.215 -1.070 O VGT 21
VGT SE SE1 SE 0 0 N N N N N N -1.391 8.403 14.585 -4.249 0.975 0.195 SE VGT 22
VGT H1 H1 H 0 1 N N N N N N -2.628 10.548 12.903 -5.295 -1.040 2.157 H1 VGT 23
VGT H2 H2 H 0 1 N N N N N N -1.894 4.508 12.805 0.135 0.237 -1.000 H2 VGT 24
VGT H3 H3 H 0 1 N N N N N N -1.711 5.541 14.264 0.091 -0.038 0.758 H3 VGT 25
VGT H4 H4 H 0 1 N N N N N N -1.710 8.703 12.074 -2.402 -0.283 -1.014 H4 VGT 26
VGT H5 H5 H 0 1 N N N N N N -3.155 7.926 12.807 -2.272 -0.522 0.745 H5 VGT 27
VGT H6 H6 H 0 1 N N N N N N -0.361 14.015 13.941 -7.574 -3.766 -0.202 H6 VGT 28
VGT H7 H7 H 0 1 N N N N N N -2.237 12.976 12.725 -6.703 -3.053 1.988 H7 VGT 29
VGT H8 H8 H 0 1 N N N N N N 1.141 12.617 15.321 -7.030 -2.471 -2.224 H8 VGT 30
VGT H9 H9 H 0 1 N N N N N N 0.740 10.189 15.525 -5.610 -0.466 -2.057 H9 VGT 31
VGT H10 H10 H 0 1 N N N N N N -5.864 -1.278 16.692 7.578 -1.042 1.979 H10 VGT 32
VGT H11 H11 H 0 1 N N N N N N -5.866 -0.563 15.224 6.735 -2.475 1.737 H11 VGT 33
VGT H12 H12 H 0 1 N N N N N N -7.299 3.253 15.797 6.085 1.640 0.277 H12 VGT 34
VGT H13 H13 H 0 1 N N N N N N -6.410 5.111 14.449 3.961 2.876 0.406 H13 VGT 35
VGT H14 H14 H 0 1 N N N N N N -3.432 1.399 15.749 3.943 -1.997 -0.337 H14 VGT 36
VGT H15 H15 H 0 1 N N N N N N -2.540 3.321 14.485 1.813 -0.772 -0.209 H15 VGT 37
VGT H16 H16 H 0 1 N N N N N N -0.430 6.565 12.471 -1.531 1.869 0.966 H16 VGT 38
VGT H17 H17 H 0 1 N N N N N N -1.659 5.553 10.719 -1.501 1.795 -1.936 H17 VGT 39
#
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
VGT O C SING N N 1
VGT C C1 SING N N 2
VGT C C8 SING N N 3
VGT C1 SE SING N N 4
VGT C8 S SING N N 5
VGT S C9 SING N N 6
VGT C6 C7 DOUB Y N 7
VGT C6 C5 SING Y N 8
VGT C7 C2 SING Y N 9
VGT C5 C4 DOUB Y N 10
VGT C2 SE SING N N 11
VGT C2 C3 DOUB Y N 12
VGT C9 C10 DOUB Y N 13
VGT C9 C14 SING Y N 14
VGT C10 C11 SING Y N 15
VGT C14 C13 DOUB Y N 16
VGT C4 C3 SING Y N 17
VGT C13 C12 SING Y N 18
VGT C11 C12 DOUB Y N 19
VGT C12 S1 SING N N 20
VGT N S1 SING N N 21
VGT O2 S1 DOUB N N 22
VGT S1 O1 DOUB N N 23
VGT C7 H1 SING N N 24
VGT C8 H2 SING N N 25
VGT C8 H3 SING N N 26
VGT C1 H4 SING N N 27
VGT C1 H5 SING N N 28
VGT C5 H6 SING N N 29
VGT C6 H7 SING N N 30
VGT C4 H8 SING N N 31
VGT C3 H9 SING N N 32
VGT N H10 SING N N 33
VGT N H11 SING N N 34
VGT C11 H12 SING N N 35
VGT C10 H13 SING N N 36
VGT C13 H14 SING N N 37
VGT C14 H15 SING N N 38
VGT C H16 SING N N 39
VGT O H17 SING N N 40
#
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
VGT InChI InChI 1.03 InChI=1S/C15H17NO3S2Se/c16-21(18,19)14-8-6-13(7-9-14)20-10-12(17)11-22-15-4-2-1-3-5-15/h1-9,12,17H,10-11H2,(H2,16,18,19)/t12-/m1/s1
VGT InChIKey InChI 1.03 QKCBBWIKTLMXPY-GFCCVEGCSA-N
VGT SMILES_CANONICAL CACTVS 3.385 N[S](=O)(=O)c1ccc(SC[C@@H](O)C[Se]c2ccccc2)cc1
VGT SMILES CACTVS 3.385 N[S](=O)(=O)c1ccc(SC[CH](O)C[Se]c2ccccc2)cc1
VGT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)[Se]C[C@@H](CSc2ccc(cc2)S(=O)(=O)N)O
VGT SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)[Se]CC(CSc2ccc(cc2)S(=O)(=O)N)O
#
_pdbx_chem_comp_identifier.comp_id VGT
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier 4-[(2~{R})-2-oxidanyl-3-phenylselanyl-propyl]sulfanylbenzenesulfonamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VGT 'Create component' 2021-05-18 PDBE
VGT 'Initial release' 2022-06-01 RCSB
#
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
VGT C7 C 5.598 -6.982 1
VGT C8 C 8.196 -0.983 2
VGT C9 C 9.495 1.268 3
VGT O1 O 9.495 7.268 4
VGT C1 C 6.897 -3.232 5
VGT C5 C 3.000 -6.982 6
VGT C6 C 4.299 -7.732 7
VGT C4 C 3.000 -5.482 8
VGT C3 C 4.299 -4.732 9
VGT C2 C 5.598 -5.482 10
VGT O2 O 7.995 5.768 11
VGT S1 S 9.495 5.768 12
VGT N N 10.995 5.768 13
VGT C12 C 9.495 4.268 14
VGT C11 C 8.196 3.518 15
VGT C10 C 8.196 2.018 16
VGT C13 C 10.794 3.518 17
VGT C14 C 10.794 2.018 18
VGT S S 9.495 -0.233 19
VGT C C 8.196 -2.482 20
VGT O O 9.495 -3.232 21
VGT SE Se 6.897 -4.732 22
#
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
VGT C O SINGLE BEGINWEDGE 1
VGT C C1 SINGLE NONE 2
VGT C C8 SINGLE NONE 3
VGT C1 SE SINGLE NONE 4
VGT C8 S SINGLE NONE 5
VGT S C9 SINGLE NONE 6
VGT C6 C7 DOUBLE NONE 7
VGT C6 C5 SINGLE NONE 8
VGT C7 C2 SINGLE NONE 9
VGT C5 C4 DOUBLE NONE 10
VGT C2 SE SINGLE NONE 11
VGT C2 C3 DOUBLE NONE 12
VGT C9 C10 SINGLE NONE 13
VGT C9 C14 DOUBLE NONE 14
VGT C10 C11 DOUBLE NONE 15
VGT C14 C13 SINGLE NONE 16
VGT C4 C3 SINGLE NONE 17
VGT C13 C12 DOUBLE NONE 18
VGT C11 C12 SINGLE NONE 19
VGT C12 S1 SINGLE NONE 20
VGT N S1 SINGLE NONE 21
VGT O2 S1 DOUBLE NONE 22
VGT S1 O1 DOUBLE NONE 23
#
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
VGT MurckoScaffold S1 scaffold 'c1ccc(SCCC[Se]c2ccccc2)cc1' InChI=1S/C15H16SSe/c1-3-8-14(9-4-1)16-12-7-13-17-15-10-5-2-6-11-15/h1-6,8-11H,7,12-13H2 ZPCWISPXVHPOLF-UHFFFAOYSA-N
VGT 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
VGT C7 S1 1
VGT C8 S1 1
VGT C9 S1 1
VGT C1 S1 1
VGT C5 S1 1
VGT C6 S1 1
VGT C4 S1 1
VGT C3 S1 1
VGT C2 S1 1
VGT C12 S1 1
VGT C11 S1 1
VGT C10 S1 1
VGT C13 S1 1
VGT C14 S1 1
VGT S S1 1
VGT C S1 1
VGT SE S1 1
VGT C7 F1 1
VGT C6 F1 1
VGT C5 F1 1
VGT C4 F1 1
VGT C3 F1 1
VGT C2 F1 1
VGT C9 F1 2
VGT C10 F1 2
VGT C11 F1 2
VGT C12 F1 2
VGT C13 F1 2
VGT C14 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id VGT
_pdbe_chem_comp_rdkit_properties.exactmw 402.982
_pdbe_chem_comp_rdkit_properties.amw 402.399
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 164.969
_pdbe_chem_comp_rdkit_properties.tpsa 80.390
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.019
_pdbe_chem_comp_rdkit_properties.CrippenMR 92.323
_pdbe_chem_comp_rdkit_properties.chi0v 13.743
_pdbe_chem_comp_rdkit_properties.chi1v 9.210
_pdbe_chem_comp_rdkit_properties.chi2v 4.681
_pdbe_chem_comp_rdkit_properties.chi3v 4.681
_pdbe_chem_comp_rdkit_properties.chi4v 2.874
_pdbe_chem_comp_rdkit_properties.chi0n 27.397
_pdbe_chem_comp_rdkit_properties.chi1n 13.543
_pdbe_chem_comp_rdkit_properties.chi2n 1.806
_pdbe_chem_comp_rdkit_properties.chi3n 1.806
_pdbe_chem_comp_rdkit_properties.chi4n 0.975
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.821
_pdbe_chem_comp_rdkit_properties.kappa1 5.618
_pdbe_chem_comp_rdkit_properties.kappa2 8.150
_pdbe_chem_comp_rdkit_properties.kappa3 5.758
_pdbe_chem_comp_rdkit_properties.Phi 2.081
#
_pdbe_chem_comp_external_mappings.comp_id VGT
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 163321836
#
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
VGT C7 4.523 -0.980 -0.381 ETKDGv3 1
VGT C8 0.387 -0.746 1.172 ETKDGv3 2
VGT C9 -2.024 -1.243 0.082 ETKDGv3 3
VGT O1 -6.562 1.193 1.288 ETKDGv3 4
VGT C1 1.987 1.225 1.180 ETKDGv3 5
VGT C5 6.068 0.126 -1.914 ETKDGv3 6
VGT C6 5.251 -1.036 -1.503 ETKDGv3 7
VGT C4 6.082 1.234 -1.162 ETKDGv3 8
VGT C3 5.279 1.297 0.078 ETKDGv3 9
VGT C2 4.531 0.247 0.447 ETKDGv3 10
VGT O2 -6.133 1.903 -1.010 ETKDGv3 11
VGT S1 -6.166 0.720 -0.083 ETKDGv3 12
VGT N -7.324 -0.426 -0.657 ETKDGv3 13
VGT C12 -4.574 -0.029 -0.015 ETKDGv3 14
VGT C11 -3.612 0.169 -1.124 ETKDGv3 15
VGT C10 -2.405 -0.409 -1.079 ETKDGv3 16
VGT C13 -4.235 -0.806 1.026 ETKDGv3 17
VGT C14 -2.903 -1.443 1.074 ETKDGv3 18
VGT S -0.409 -2.026 0.132 ETKDGv3 19
VGT C 1.147 0.273 0.311 ETKDGv3 20
VGT O 0.224 1.026 -0.431 ETKDGv3 21
VGT SE 3.487 0.320 2.060 ETKDGv3 22
VGT H1 3.927 -1.831 -0.080 ETKDGv3 23
VGT H2 -0.355 -0.231 1.820 ETKDGv3 24
VGT H3 1.097 -1.277 1.839 ETKDGv3 25
VGT H4 1.346 1.687 1.960 ETKDGv3 26
VGT H5 2.393 2.046 0.551 ETKDGv3 27
VGT H6 6.654 0.077 -2.822 ETKDGv3 28
VGT H7 5.244 -1.931 -2.111 ETKDGv3 29
VGT H8 6.681 2.085 -1.460 ETKDGv3 30
VGT H9 5.297 2.196 0.680 ETKDGv3 31
VGT H10 -7.295 -1.243 -0.006 ETKDGv3 32
VGT H11 -6.982 -0.768 -1.583 ETKDGv3 33
VGT H12 -3.883 0.774 -1.980 ETKDGv3 34
VGT H13 -1.710 -0.270 -1.897 ETKDGv3 35
VGT H14 -4.931 -0.975 1.837 ETKDGv3 36
VGT H15 -2.641 -2.065 1.921 ETKDGv3 37
VGT H16 1.819 -0.282 -0.382 ETKDGv3 38
VGT H17 0.720 1.419 -1.196 ETKDGv3 39
#