data_VDD
#
_chem_comp.id VDD
_chem_comp.name "(2S)-2-[(pyridin-2-yl)sulfanyl]propanoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H9 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 2022-08-29
_chem_comp.pdbx_modified_date 2022-10-28
_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 183.228
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VDD
_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 7FLI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
VDD C7 C1 C 0 1 Y N N N N N 26.947 15.319 38.818 2.646 1.445 0.211 C7 VDD 1
VDD O1 O1 O 0 1 N N N N N N 31.989 16.036 42.976 -3.773 0.880 0.655 O1 VDD 2
VDD C1 C2 C 0 1 N N S N N N 29.864 16.377 41.845 -1.413 0.432 0.088 C1 VDD 3
VDD C5 C3 C 0 1 Y N N N N N 28.441 14.693 37.127 3.630 -0.725 0.024 C5 VDD 4
VDD C6 C4 C 0 1 Y N N N N N 27.173 14.709 37.596 3.773 0.651 0.146 C6 VDD 5
VDD C4 C5 C 0 1 Y N N N N N 29.458 15.241 37.873 2.353 -1.254 -0.030 C4 VDD 6
VDD C3 C6 C 0 1 Y N N N N N 29.138 15.793 39.099 1.261 -0.393 0.036 C3 VDD 7
VDD C2 C7 C 0 1 N N N N N N 31.108 16.857 42.670 -2.861 0.024 0.168 C2 VDD 8
VDD O O2 O 0 1 N N N N N N 31.141 18.064 42.917 -3.201 -1.073 -0.206 O VDD 9
VDD C C8 C 0 1 N N N N N N 29.433 14.967 42.154 -1.197 1.307 -1.149 C VDD 10
VDD S S1 S 0 1 N N N N N N 30.446 16.351 40.130 -0.373 -1.050 -0.031 S VDD 11
VDD N N1 N 0 1 Y N N N N N 27.894 15.862 39.560 1.439 0.914 0.157 N VDD 12
VDD H1 H1 H 0 1 N N N N N N 25.933 15.353 39.187 2.753 2.516 0.311 H1 VDD 13
VDD H2 H2 H 0 1 N N N N N N 32.694 16.482 43.431 -4.690 0.573 0.687 H2 VDD 14
VDD H3 H3 H 0 1 N N N N N N 29.033 17.094 41.919 -1.143 0.994 0.982 H3 VDD 15
VDD H4 H4 H 0 1 N N N N N N 28.655 14.250 36.166 4.496 -1.367 -0.029 H4 VDD 16
VDD H5 H5 H 0 1 N N N N N N 26.365 14.261 37.037 4.757 1.095 0.190 H5 VDD 17
VDD H6 H6 H 0 1 N N N N N N 30.476 15.240 37.512 2.205 -2.319 -0.125 H6 VDD 18
VDD H7 H7 H 0 1 N N N N N N 29.066 14.914 43.190 -0.149 1.602 -1.207 H7 VDD 19
VDD H8 H8 H 0 1 N N N N N N 28.629 14.670 41.464 -1.466 0.744 -2.043 H8 VDD 20
VDD H9 H9 H 0 1 N N N N N N 30.289 14.287 42.034 -1.822 2.197 -1.078 H9 VDD 21
#
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
VDD C5 C6 DOUB Y N 1
VDD C5 C4 SING Y N 2
VDD C6 C7 SING Y N 3
VDD C4 C3 DOUB Y N 4
VDD C7 N DOUB Y N 5
VDD C3 N SING Y N 6
VDD C3 S SING N N 7
VDD S C1 SING N N 8
VDD C1 C SING N N 9
VDD C1 C2 SING N N 10
VDD C2 O DOUB N N 11
VDD C2 O1 SING N N 12
VDD C7 H1 SING N N 13
VDD O1 H2 SING N N 14
VDD C1 H3 SING N N 15
VDD C5 H4 SING N N 16
VDD C6 H5 SING N N 17
VDD C4 H6 SING N N 18
VDD C H7 SING N N 19
VDD C H8 SING N N 20
VDD C H9 SING N N 21
#
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
VDD SMILES ACDLabs 12.01 CC(Sc1ccccn1)C(=O)O
VDD InChI InChI 1.06 InChI=1S/C8H9NO2S/c1-6(8(10)11)12-7-4-2-3-5-9-7/h2-6H,1H3,(H,10,11)/t6-/m0/s1
VDD InChIKey InChI 1.06 FAAIBCMHMKYUAH-LURJTMIESA-N
VDD SMILES_CANONICAL CACTVS 3.385 C[C@H](Sc1ccccn1)C(O)=O
VDD SMILES CACTVS 3.385 C[CH](Sc1ccccn1)C(O)=O
VDD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@H](C(=O)O)Sc1ccccn1
VDD SMILES "OpenEye OEToolkits" 2.0.7 CC(C(=O)O)Sc1ccccn1
#
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
VDD "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-[(pyridin-2-yl)sulfanyl]propanoic acid"
VDD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-pyridin-2-ylsulfanylpropanoic 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
VDD 'Create component' 2022-08-29 RCSB
VDD 'Initial release' 2022-11-02 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
VDD C7 C 10.301 2.250 1
VDD O1 O 5.104 -2.250 2
VDD C1 C 6.404 0.000 3
VDD C5 C 11.600 0.000 4
VDD C6 C 11.600 1.500 5
VDD C4 C 10.301 -0.750 6
VDD C3 C 9.002 0.000 7
VDD C2 C 5.104 -0.750 8
VDD O O 3.805 0.000 9
VDD C C 6.404 1.500 10
VDD S S 7.702 -0.750 11
VDD N N 9.002 1.500 12
#
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
VDD C5 C6 SINGLE NONE 1
VDD C5 C4 DOUBLE NONE 2
VDD C6 C7 DOUBLE NONE 3
VDD C4 C3 SINGLE NONE 4
VDD C7 N SINGLE NONE 5
VDD C3 N DOUBLE NONE 6
VDD C3 S SINGLE NONE 7
VDD S C1 SINGLE NONE 8
VDD C1 C SINGLE BEGINDASH 9
VDD C1 C2 SINGLE NONE 10
VDD C2 O DOUBLE NONE 11
VDD C2 O1 SINGLE NONE 12
#
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
VDD MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
VDD pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
VDD C7 S1 1
VDD C5 S1 1
VDD C6 S1 1
VDD C4 S1 1
VDD C3 S1 1
VDD N S1 1
VDD C7 F1 1
VDD C6 F1 1
VDD C5 F1 1
VDD C4 F1 1
VDD C3 F1 1
VDD N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VDD
_pdbe_chem_comp_rdkit_properties.exactmw 183.035
_pdbe_chem_comp_rdkit_properties.amw 183.232
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 87.556
_pdbe_chem_comp_rdkit_properties.tpsa 50.190
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.539
_pdbe_chem_comp_rdkit_properties.CrippenMR 47.762
_pdbe_chem_comp_rdkit_properties.chi0v 6.488
_pdbe_chem_comp_rdkit_properties.chi1v 3.580
_pdbe_chem_comp_rdkit_properties.chi2v 1.587
_pdbe_chem_comp_rdkit_properties.chi3v 1.587
_pdbe_chem_comp_rdkit_properties.chi4v 0.876
_pdbe_chem_comp_rdkit_properties.chi0n 14.672
_pdbe_chem_comp_rdkit_properties.chi1n 7.172
_pdbe_chem_comp_rdkit_properties.chi2n 0.829
_pdbe_chem_comp_rdkit_properties.chi3n 0.829
_pdbe_chem_comp_rdkit_properties.chi4n 0.406
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.030
_pdbe_chem_comp_rdkit_properties.kappa1 2.734
_pdbe_chem_comp_rdkit_properties.kappa2 4.110
_pdbe_chem_comp_rdkit_properties.kappa3 2.543
_pdbe_chem_comp_rdkit_properties.Phi 0.937
#
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
VDD UniChem ZINC ZINC000005739057
VDD UniChem PubChem 40560276
#
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
VDD C7 2.518 -0.684 1.216 ETKDGv3 1
VDD O1 -1.319 0.982 1.886 ETKDGv3 2
VDD C1 -1.722 0.030 -0.393 ETKDGv3 3
VDD C5 2.803 0.570 -0.846 ETKDGv3 4
VDD C6 3.276 0.143 0.486 ETKDGv3 5
VDD C4 1.627 0.129 -1.306 ETKDGv3 6
VDD C3 0.818 -0.778 -0.466 ETKDGv3 7
VDD C2 -1.814 -0.057 1.103 ETKDGv3 8
VDD O -2.332 -1.066 1.654 ETKDGv3 9
VDD C -3.117 0.039 -1.014 ETKDGv3 10
VDD S -0.764 -1.381 -1.056 ETKDGv3 11
VDD N 1.256 -1.146 0.705 ETKDGv3 12
VDD H1 2.852 -1.006 2.194 ETKDGv3 13
VDD H2 -1.368 0.939 2.897 ETKDGv3 14
VDD H3 -1.216 0.979 -0.676 ETKDGv3 15
VDD H4 3.408 1.237 -1.446 ETKDGv3 16
VDD H5 4.226 0.495 0.865 ETKDGv3 17
VDD H6 1.271 0.438 -2.280 ETKDGv3 18
VDD H7 -3.658 -0.904 -0.783 ETKDGv3 19
VDD H8 -3.705 0.898 -0.623 ETKDGv3 20
VDD H9 -3.038 0.144 -2.117 ETKDGv3 21
#