data_VCW
#
_chem_comp.id VCW
_chem_comp.name "[(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H18 O10 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "sulfoquinovosyl glycerol; SQGro"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-05-05
_chem_comp.pdbx_modified_date 2022-01-14
_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 318.298
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VCW
_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 7OFX
_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
VCW C4 C1 C 0 1 N N N N N N 19.733 54.606 2.641 -2.046 -0.067 -0.666 C4 VCW 1
VCW C5 C2 C 0 1 N N R N N N 18.824 55.782 2.387 -3.152 0.061 0.383 C5 VCW 2
VCW C6 C3 C 0 1 N N N N N N 17.623 55.392 1.547 -4.008 1.291 0.074 C6 VCW 3
VCW C7 C4 C 0 1 N N R N N N 22.694 54.596 4.879 0.607 -2.667 -0.903 C7 VCW 4
VCW C8 C5 C 0 1 N N S N N N 23.786 54.368 3.799 1.212 -2.573 0.501 C8 VCW 5
VCW C1 C6 C 0 1 N N N N N N 22.351 50.997 2.562 2.340 1.092 0.169 C1 VCW 6
VCW C2 C7 C 0 1 N N S N N N 22.424 52.485 2.894 1.387 -0.105 0.172 C2 VCW 7
VCW C3 C8 C 0 1 N N S N N N 21.338 54.124 4.357 -0.104 -1.352 -1.234 C3 VCW 8
VCW C9 C9 C 0 1 N N S N N N 23.789 52.895 3.411 2.158 -1.370 0.558 C9 VCW 9
VCW O1 O1 O 0 1 N N N N N N 21.249 51.004 0.222 0.555 2.910 0.959 O1 VCW 10
VCW S1 S1 S 0 1 N N N N N N 21.010 50.483 1.531 1.401 2.612 -0.143 S1 VCW 11
VCW O2 O2 O 0 1 N N N N N N 19.762 50.877 2.126 2.447 3.717 -0.123 O2 VCW 12
VCW O3 O3 O 0 1 N N N N N N 21.124 49.007 1.606 0.902 2.626 -1.474 O3 VCW 13
VCW O4 O4 O 0 1 N N N N N N 21.390 52.793 3.854 0.825 -0.271 -1.133 O4 VCW 14
VCW O5 O5 O 0 1 N N N N N N 20.941 54.988 3.326 -1.178 -1.145 -0.314 O5 VCW 15
VCW O6 O6 O 0 1 N N N N N N 18.401 56.260 3.659 -3.972 -1.109 0.356 O6 VCW 16
VCW O7 O7 O 0 1 N N N N N N 16.608 56.387 1.614 -4.967 1.478 1.117 O7 VCW 17
VCW O8 O8 O 0 1 N N N N N N 22.569 55.952 5.300 -0.333 -3.742 -0.947 O8 VCW 18
VCW O9 O9 O 0 1 N N N N N N 25.117 54.705 4.231 1.940 -3.769 0.789 O9 VCW 19
VCW O10 O10 O 0 1 N N N N N N 24.740 52.682 2.391 2.672 -1.230 1.884 O10 VCW 20
VCW H1 H1 H 0 1 N N N N N N 19.195 53.869 3.256 -2.492 -0.263 -1.642 H1 VCW 21
VCW H2 H2 H 0 1 N N N N N N 20.002 54.152 1.676 -1.475 0.861 -0.708 H2 VCW 22
VCW H3 H3 H 0 1 N N N N N N 19.389 56.563 1.858 -2.705 0.169 1.371 H3 VCW 23
VCW H4 H4 H 0 1 N N N N N N 17.218 54.439 1.919 -3.369 2.171 0.007 H4 VCW 24
VCW H5 H5 H 0 1 N N N N N N 17.940 55.272 0.501 -4.526 1.145 -0.874 H5 VCW 25
VCW H6 H6 H 0 1 N N N N N N 22.954 53.973 5.747 1.399 -2.845 -1.630 H6 VCW 26
VCW H7 H7 H 0 1 N N N N N N 23.522 54.963 2.912 0.414 -2.447 1.234 H7 VCW 27
VCW H8 H8 H 0 1 N N N N N N 22.273 50.446 3.511 2.837 1.164 1.136 H8 VCW 28
VCW H9 H9 H 0 1 N N N N N N 23.287 50.722 2.054 3.087 0.959 -0.614 H9 VCW 29
VCW H10 H10 H 0 1 N N N N N N 22.229 53.047 1.968 0.589 0.068 0.894 H10 VCW 30
VCW H11 H11 H 0 1 N N N N N N 20.616 54.175 5.185 -0.499 -1.397 -2.249 H11 VCW 31
VCW H12 H12 H 0 1 N N N N N N 24.033 52.292 4.298 2.983 -1.521 -0.139 H12 VCW 32
VCW H13 H13 H 0 1 N N N N N N 19.161 56.501 4.176 -4.403 -1.267 -0.495 H13 VCW 33
VCW H14 H14 H 0 1 N N N N N N 15.868 56.121 1.081 -5.546 2.242 0.987 H14 VCW 34
VCW H15 H15 H 0 1 N N N N N N 21.887 56.018 5.958 -0.758 -3.858 -1.809 H15 VCW 35
VCW H16 H16 H 0 1 N N N N N N 25.147 55.621 4.481 1.402 -4.572 0.763 H16 VCW 36
VCW H17 H17 H 0 1 N N N N N N 25.601 52.935 2.702 3.173 -1.997 2.195 H17 VCW 37
VCW H18 H18 H 0 1 N N N N N N 19.298 50.106 2.430 2.089 4.601 -0.278 H18 VCW 38
#
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
VCW O1 S1 DOUB N N 1
VCW S1 O3 DOUB N N 2
VCW S1 O2 SING N N 3
VCW S1 C1 SING N N 4
VCW C6 O7 SING N N 5
VCW C6 C5 SING N N 6
VCW C5 C4 SING N N 7
VCW C5 O6 SING N N 8
VCW O10 C9 SING N N 9
VCW C1 C2 SING N N 10
VCW C4 O5 SING N N 11
VCW C2 C9 SING N N 12
VCW C2 O4 SING N N 13
VCW O5 C3 SING N N 14
VCW C9 C8 SING N N 15
VCW C8 O9 SING N N 16
VCW C8 C7 SING N N 17
VCW O4 C3 SING N N 18
VCW C3 C7 SING N N 19
VCW C7 O8 SING N N 20
VCW C4 H1 SING N N 21
VCW C4 H2 SING N N 22
VCW C5 H3 SING N N 23
VCW C6 H4 SING N N 24
VCW C6 H5 SING N N 25
VCW C7 H6 SING N N 26
VCW C8 H7 SING N N 27
VCW C1 H8 SING N N 28
VCW C1 H9 SING N N 29
VCW C2 H10 SING N N 30
VCW C3 H11 SING N N 31
VCW C9 H12 SING N N 32
VCW O6 H13 SING N N 33
VCW O7 H14 SING N N 34
VCW O8 H15 SING N N 35
VCW O9 H16 SING N N 36
VCW O10 H17 SING N N 37
VCW O2 H18 SING N N 38
#
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
VCW InChI InChI 1.03 InChI=1S/C9H18O10S/c10-1-4(11)2-18-9-8(14)7(13)6(12)5(19-9)3-20(15,16)17/h4-14H,1-3H2,(H,15,16,17)/t4-,5-,6-,7+,8-,9+/m1/s1
VCW InChIKey InChI 1.03 JTXHNMDHGMNPEG-NZJLWHDDSA-N
VCW SMILES_CANONICAL CACTVS 3.385 OC[C@@H](O)CO[C@H]1O[C@H](C[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1O
VCW SMILES CACTVS 3.385 OC[CH](O)CO[CH]1O[CH](C[S](O)(=O)=O)[CH](O)[CH](O)[CH]1O
VCW SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OC[C@@H](CO)O)O)O)O)S(=O)(=O)O
VCW SMILES "OpenEye OEToolkits" 2.0.7 C(C1C(C(C(C(O1)OCC(CO)O)O)O)O)S(=O)(=O)O
#
_pdbx_chem_comp_identifier.comp_id VCW
_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
"[(2~{S},3~{S},4~{S},5~{R},6~{S})-6-[(2~{R})-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid"
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 VCW "sulfoquinovosyl glycerol" AUTHOR ?
2 VCW SQGro AUTHOR ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VCW 'Create component' 2021-05-05 PDBE
VCW 'Initial release' 2022-01-19 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
VCW 'sulfoquinovosyl glycerol' wwPDB ?
VCW SQGro wwPDB ?
#
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
VCW C4 C 9.696 1.268 1
VCW C5 C 10.995 2.018 2
VCW C6 C 10.995 3.518 3
VCW C7 C 8.397 -2.482 4
VCW C8 C 7.098 -3.232 5
VCW C1 C 4.500 -0.233 6
VCW C2 C 5.799 -0.983 7
VCW C3 C 8.397 -0.983 8
VCW C9 C 5.799 -2.482 9
VCW O1 O 4.500 2.768 10
VCW S1 S 4.500 1.268 11
VCW O2 O 6.000 1.268 12
VCW O3 O 3.000 1.268 13
VCW O4 O 7.098 -0.233 14
VCW O5 O 9.696 -0.233 15
VCW O6 O 12.294 1.268 16
VCW O7 O 12.294 4.268 17
VCW O8 O 9.696 -3.232 18
VCW O9 O 7.098 -4.732 19
VCW O10 O 4.500 -3.232 20
#
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
VCW O1 S1 DOUBLE NONE 1
VCW S1 O3 DOUBLE NONE 2
VCW S1 O2 SINGLE NONE 3
VCW S1 C1 SINGLE NONE 4
VCW C6 O7 SINGLE NONE 5
VCW C6 C5 SINGLE NONE 6
VCW C5 C4 SINGLE NONE 7
VCW C5 O6 SINGLE BEGINWEDGE 8
VCW C9 O10 SINGLE BEGINDASH 9
VCW C2 C1 SINGLE BEGINWEDGE 10
VCW C4 O5 SINGLE NONE 11
VCW C2 C9 SINGLE NONE 12
VCW C2 O4 SINGLE NONE 13
VCW C3 O5 SINGLE BEGINDASH 14
VCW C9 C8 SINGLE NONE 15
VCW C8 O9 SINGLE BEGINWEDGE 16
VCW C8 C7 SINGLE NONE 17
VCW O4 C3 SINGLE NONE 18
VCW C3 C7 SINGLE NONE 19
VCW C7 O8 SINGLE BEGINDASH 20
#
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
VCW MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
VCW pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-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
VCW C7 S1 1
VCW C8 S1 1
VCW C2 S1 1
VCW C3 S1 1
VCW C9 S1 1
VCW O4 S1 1
VCW C9 F1 1
VCW C2 F1 1
VCW O4 F1 1
VCW C3 F1 1
VCW C7 F1 1
VCW C8 F1 1
VCW O5 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VCW
_pdbe_chem_comp_rdkit_properties.exactmw 318.062
_pdbe_chem_comp_rdkit_properties.amw 318.300
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 140.289
_pdbe_chem_comp_rdkit_properties.tpsa 173.980
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.948
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.142
_pdbe_chem_comp_rdkit_properties.chi0v 9.807
_pdbe_chem_comp_rdkit_properties.chi1v 5.699
_pdbe_chem_comp_rdkit_properties.chi2v 1.981
_pdbe_chem_comp_rdkit_properties.chi3v 1.981
_pdbe_chem_comp_rdkit_properties.chi4v 1.207
_pdbe_chem_comp_rdkit_properties.chi0n 26.991
_pdbe_chem_comp_rdkit_properties.chi1n 12.741
_pdbe_chem_comp_rdkit_properties.chi2n 1.546
_pdbe_chem_comp_rdkit_properties.chi3n 1.546
_pdbe_chem_comp_rdkit_properties.chi4n 0.846
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.370
_pdbe_chem_comp_rdkit_properties.kappa1 4.811
_pdbe_chem_comp_rdkit_properties.kappa2 7.064
_pdbe_chem_comp_rdkit_properties.kappa3 4.873
_pdbe_chem_comp_rdkit_properties.Phi 1.700
#
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
VCW UniChem ChEMBL CHEMBL1207986
VCW UniChem PDBe VCW
VCW UniChem PubChem 44575488
#
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
VCW C4 1.872 1.277 0.358 ETKDGv3 1
VCW C5 3.382 1.511 0.256 ETKDGv3 2
VCW C6 3.969 0.798 -0.974 ETKDGv3 3
VCW C7 -0.014 -1.736 1.199 ETKDGv3 4
VCW C8 -1.527 -2.086 1.230 ETKDGv3 5
VCW C1 -2.352 0.152 -1.886 ETKDGv3 6
VCW C2 -1.578 -0.795 -0.947 ETKDGv3 7
VCW C3 0.225 -0.349 0.575 ETKDGv3 8
VCW C9 -2.358 -1.127 0.358 ETKDGv3 9
VCW O1 -1.351 2.314 -0.585 ETKDGv3 10
VCW S1 -2.611 1.797 -1.218 ETKDGv3 11
VCW O2 -3.838 1.776 -0.068 ETKDGv3 12
VCW O3 -3.005 2.721 -2.335 ETKDGv3 13
VCW O4 -0.254 -0.293 -0.763 ETKDGv3 14
VCW O5 1.618 -0.096 0.582 ETKDGv3 15
VCW O6 3.620 2.892 0.165 ETKDGv3 16
VCW O7 5.356 0.994 -1.042 ETKDGv3 17
VCW O8 0.688 -2.699 0.454 ETKDGv3 18
VCW O9 -2.011 -2.035 2.548 ETKDGv3 19
VCW O10 -3.585 -1.741 0.052 ETKDGv3 20
VCW H1 1.484 1.879 1.212 ETKDGv3 21
VCW H2 1.389 1.632 -0.582 ETKDGv3 22
VCW H3 3.857 1.103 1.180 ETKDGv3 23
VCW H4 3.743 -0.292 -0.939 ETKDGv3 24
VCW H5 3.509 1.209 -1.898 ETKDGv3 25
VCW H6 0.391 -1.711 2.238 ETKDGv3 26
VCW H7 -1.670 -3.119 0.831 ETKDGv3 27
VCW H8 -1.779 0.254 -2.832 ETKDGv3 28
VCW H9 -3.336 -0.288 -2.149 ETKDGv3 29
VCW H10 -1.476 -1.754 -1.502 ETKDGv3 30
VCW H11 -0.305 0.407 1.203 ETKDGv3 31
VCW H12 -2.529 -0.191 0.939 ETKDGv3 32
VCW H13 4.552 3.046 0.470 ETKDGv3 33
VCW H14 5.760 0.411 -0.347 ETKDGv3 34
VCW H15 0.767 -3.504 1.029 ETKDGv3 35
VCW H16 -1.677 -2.849 3.007 ETKDGv3 36
VCW H17 -4.271 -1.024 0.009 ETKDGv3 37
VCW H18 -4.653 1.517 -0.569 ETKDGv3 38
#