data_VTB
#
_chem_comp.id VTB
_chem_comp.name 7-O-phosphono-alpha-L-galacto-hept-2-ulopyranose
_chem_comp.type "L-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C7 H15 O10 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;[(2~{S},3~{S},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate;
7-O-phosphono-alpha-L-galacto-hept-2-ulose; 7-O-phosphono-L-galacto-hept-2-ulose; 7-O-phosphono-galacto-hept-2-ulose
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-06-19
_chem_comp.pdbx_modified_date 2020-07-17
_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 290.162
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VTB
_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 5A5L
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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 VTB "[(2~{S},3~{S},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate" PDB ?
2 VTB 7-O-phosphono-alpha-L-galacto-hept-2-ulose PDB ?
3 VTB 7-O-phosphono-L-galacto-hept-2-ulose PDB ?
4 VTB 7-O-phosphono-galacto-hept-2-ulose PDB ?
#
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
VTB C1 C1 C 0 1 N N S N N N 11.312 -28.079 30.641 -1.218 -1.748 -0.128 C1 VTB 1
VTB C2 C2 C 0 1 N N R N N N 9.885 -27.471 30.731 -2.641 -1.327 -0.510 C2 VTB 2
VTB C3 C3 C 0 1 N N S N N N 9.239 -27.398 32.130 -3.009 -0.055 0.259 C3 VTB 3
VTB O4 O4 O 0 1 N N N N N N 10.654 -29.151 32.720 -0.674 0.567 0.300 O4 VTB 4
VTB O6 O6 O 0 1 N N N N N N 11.686 -28.695 29.405 -1.171 -2.066 1.264 O6 VTB 5
VTB C7 C7 C 0 1 N N S N N N 11.717 -29.032 31.749 -0.257 -0.593 -0.422 C7 VTB 6
VTB O8 O8 O 0 1 N N N N N N 8.970 -28.089 29.829 -3.555 -2.372 -0.171 O8 VTB 7
VTB C10 C10 C 0 1 N N N N N N 12.230 -30.338 31.103 1.158 -0.984 0.012 C10 VTB 8
VTB O12 O12 O 0 1 N N N N N N 13.621 -30.278 30.712 2.073 0.045 -0.367 O12 VTB 9
VTB O15 O15 O 0 1 N N N N N N 8.788 -26.060 32.421 -4.306 0.388 -0.143 O15 VTB 10
VTB P15 P15 P 0 1 N N N N N N 14.710 -31.115 31.571 3.653 -0.032 -0.067 P15 VTB 11
VTB O16 O16 O 0 1 N N N N N N 16.224 -30.957 31.091 4.201 -1.287 -0.630 O16 VTB 12
VTB O17 O17 O 0 1 N N N N N N 14.340 -32.683 31.544 4.391 1.228 -0.746 O17 VTB 13
VTB O18 O18 O 0 1 N N N N N N 14.599 -30.612 33.104 3.899 -0.005 1.524 O18 VTB 14
VTB C20 C20 C 0 1 N N R N N N 10.196 -27.876 33.204 -1.978 1.035 -0.049 C20 VTB 15
VTB O20 O20 O 0 1 N N N N N N 11.239 -26.905 33.357 -2.016 1.344 -1.444 O20 VTB 16
VTB C21 C21 C 0 1 N N N N N N 9.581 -27.912 34.609 -2.305 2.290 0.761 C21 VTB 17
VTB O22 O22 O 0 1 N N N N N N 8.679 -28.992 34.827 -1.343 3.307 0.473 O22 VTB 18
VTB H1 H1 H 0 1 N N N N N N 11.984 -27.216 30.756 -0.927 -2.621 -0.712 H1 VTB 19
VTB H2 H2 H 0 1 N N N N N N 9.994 -26.426 30.405 -2.688 -1.133 -1.581 H2 VTB 20
VTB H3 H3 H 0 1 N N N N N N 8.370 -28.072 32.129 -3.010 -0.263 1.329 H3 VTB 21
VTB H4 H4 H 0 1 N N N N N N 12.574 -29.027 29.472 -1.761 -2.787 1.523 H4 VTB 22
VTB H5 H5 H 0 1 N N N N N N 12.580 -28.577 32.257 -0.263 -0.378 -1.491 H5 VTB 23
VTB H6 H6 H 0 1 N N N N N N 8.114 -27.686 29.920 -3.377 -3.211 -0.617 H6 VTB 24
VTB H7 H7 H 0 1 N N N N N N 11.625 -30.545 30.208 1.183 -1.112 1.094 H7 VTB 25
VTB H8 H8 H 0 1 N N N N N N 12.106 -31.157 31.827 1.441 -1.919 -0.471 H8 VTB 26
VTB H9 H9 H 0 1 N N N N N N 8.395 -26.039 33.285 -5.009 -0.256 0.019 H9 VTB 27
VTB H10 H10 H 0 1 N N N N N N 15.094 -33.182 31.251 5.348 1.246 -0.605 H10 VTB 28
VTB H11 H11 H 0 1 N N N N N N 15.453 -30.326 33.407 3.565 0.790 1.960 H11 VTB 29
VTB H12 H12 H 0 1 N N N N N N 11.846 -27.194 34.028 -1.387 2.029 -1.712 H12 VTB 30
VTB H13 H13 H 0 1 N N N N N N 10.398 -27.993 35.341 -3.300 2.646 0.495 H13 VTB 31
VTB H14 H14 H 0 1 N N N N N N 9.036 -26.970 34.771 -2.275 2.054 1.825 H14 VTB 32
VTB H15 H15 H 0 1 N N N N N N 8.341 -28.949 35.714 -1.488 4.134 0.953 H15 VTB 33
#
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
VTB O6 C1 SING N N 1
VTB O8 C2 SING N N 2
VTB C1 C2 SING N N 3
VTB C1 C7 SING N N 4
VTB O12 C10 SING N N 5
VTB O12 P15 SING N N 6
VTB C2 C3 SING N N 7
VTB O16 P15 DOUB N N 8
VTB C10 C7 SING N N 9
VTB O17 P15 SING N N 10
VTB P15 O18 SING N N 11
VTB C7 O4 SING N N 12
VTB C3 O15 SING N N 13
VTB C3 C20 SING N N 14
VTB O4 C20 SING N N 15
VTB C20 O20 SING N N 16
VTB C20 C21 SING N N 17
VTB C21 O22 SING N N 18
VTB C1 H1 SING N N 19
VTB C2 H2 SING N N 20
VTB C3 H3 SING N N 21
VTB O6 H4 SING N N 22
VTB C7 H5 SING N N 23
VTB O8 H6 SING N N 24
VTB C10 H7 SING N N 25
VTB C10 H8 SING N N 26
VTB O15 H9 SING N N 27
VTB O17 H10 SING N N 28
VTB O18 H11 SING N N 29
VTB O20 H12 SING N N 30
VTB C21 H13 SING N N 31
VTB C21 H14 SING N N 32
VTB O22 H15 SING N N 33
#
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
VTB InChI InChI 1.03 InChI=1S/C7H15O10P/c8-2-7(12)6(11)5(10)4(9)3(17-7)1-16-18(13,14)15/h3-6,8-12H,1-2H2,(H2,13,14,15)/t3-,4+,5+,6-,7+/m0/s1
VTB InChIKey InChI 1.03 CBIDVWSRUUODHL-CXNFULCWSA-N
VTB SMILES_CANONICAL CACTVS 3.385 OC[C@@]1(O)O[C@@H](CO[P](O)(O)=O)[C@@H](O)[C@@H](O)[C@@H]1O
VTB SMILES CACTVS 3.385 OC[C]1(O)O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
VTB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C([C@H]1[C@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O)OP(=O)(O)O
VTB SMILES "OpenEye OEToolkits" 2.0.6 C(C1C(C(C(C(O1)(CO)O)O)O)O)OP(=O)(O)O
#
_pdbx_chem_comp_identifier.comp_id VTB
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier
"[(2~{S},3~{S},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate"
#
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
VTB "CARBOHYDRATE ISOMER" L PDB ?
VTB "CARBOHYDRATE RING" pyranose PDB ?
VTB "CARBOHYDRATE ANOMER" alpha PDB ?
VTB "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose PDB ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VTB 'Create component' 2015-06-19 EBI
VTB 'Initial release' 2015-10-14 RCSB
VTB 'Modify name' 2018-11-12 EBI
VTB 'Other modification' 2020-07-03 RCSB
VTB 'Modify name' 2020-07-17 RCSB
VTB 'Modify synonyms' 2020-07-17 RCSB
VTB 'Modify internal type' 2020-07-17 RCSB
VTB 'Modify linking type' 2020-07-17 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
VTB '[(2~{S},3~{S},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate' wwPDB ?
VTB 7-O-phosphono-alpha-L-galacto-hept-2-ulose wwPDB ?
VTB 7-O-phosphono-L-galacto-hept-2-ulose wwPDB ?
VTB 7-O-phosphono-galacto-hept-2-ulose 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
VTB C1 C 6.404 2.219 1
VTB C2 C 5.104 1.469 2
VTB C3 C 5.104 -0.031 3
VTB O4 O 7.702 -0.031 4
VTB O6 O 6.404 3.719 5
VTB C7 C 7.702 1.469 6
VTB O8 O 3.805 2.219 7
VTB C10 C 9.002 2.219 8
VTB O12 O 10.301 1.469 9
VTB O15 O 3.805 -0.781 10
VTB P15 P 11.600 2.219 11
VTB O16 O 12.899 2.969 12
VTB O17 O 12.350 0.920 13
VTB O18 O 10.850 3.518 14
VTB C20 C 6.404 -0.781 15
VTB O20 O 7.154 -2.080 16
VTB C21 C 5.654 -2.080 17
VTB O22 O 6.404 -3.379 18
#
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
VTB C1 O6 SINGLE BEGINDASH 1
VTB C2 O8 SINGLE BEGINDASH 2
VTB C1 C2 SINGLE NONE 3
VTB C1 C7 SINGLE NONE 4
VTB O12 C10 SINGLE NONE 5
VTB O12 P15 SINGLE NONE 6
VTB C2 C3 SINGLE NONE 7
VTB O16 P15 DOUBLE NONE 8
VTB C7 C10 SINGLE BEGINDASH 9
VTB O17 P15 SINGLE NONE 10
VTB P15 O18 SINGLE NONE 11
VTB C7 O4 SINGLE NONE 12
VTB C3 O15 SINGLE BEGINWEDGE 13
VTB C3 C20 SINGLE NONE 14
VTB O4 C20 SINGLE NONE 15
VTB C20 O20 SINGLE BEGINWEDGE 16
VTB C20 C21 SINGLE NONE 17
VTB C21 O22 SINGLE NONE 18
#
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
VTB MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
VTB phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
VTB pyranose F2 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
VTB C1 S1 1
VTB C2 S1 1
VTB C3 S1 1
VTB O4 S1 1
VTB C7 S1 1
VTB C20 S1 1
VTB O12 F1 1
VTB P15 F1 1
VTB O16 F1 1
VTB O17 F1 1
VTB O18 F1 1
VTB C1 F2 1
VTB C7 F2 1
VTB O4 F2 1
VTB C20 F2 1
VTB C3 F2 1
VTB C2 F2 1
VTB O20 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VTB
_pdbe_chem_comp_rdkit_properties.exactmw 290.040
_pdbe_chem_comp_rdkit_properties.amw 290.161
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 122.941
_pdbe_chem_comp_rdkit_properties.tpsa 177.140
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.742
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.925
_pdbe_chem_comp_rdkit_properties.chi0v 8.924
_pdbe_chem_comp_rdkit_properties.chi1v 5.324
_pdbe_chem_comp_rdkit_properties.chi2v 1.863
_pdbe_chem_comp_rdkit_properties.chi3v 1.863
_pdbe_chem_comp_rdkit_properties.chi4v 1.019
_pdbe_chem_comp_rdkit_properties.chi0n 23.030
_pdbe_chem_comp_rdkit_properties.chi1n 10.721
_pdbe_chem_comp_rdkit_properties.chi2n 1.548
_pdbe_chem_comp_rdkit_properties.chi3n 1.548
_pdbe_chem_comp_rdkit_properties.chi4n 0.824
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.130
_pdbe_chem_comp_rdkit_properties.kappa1 4.707
_pdbe_chem_comp_rdkit_properties.kappa2 5.470
_pdbe_chem_comp_rdkit_properties.kappa3 3.455
_pdbe_chem_comp_rdkit_properties.Phi 1.430
#
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
VTB UniChem PDBe VTB
VTB UniChem ZINC ZINC000015273183
VTB UniChem PubChem 91936961
#
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
VTB C1 -0.760 -1.541 -0.562 ETKDGv3 1
VTB C2 -1.688 -1.184 0.610 ETKDGv3 2
VTB C3 -2.301 0.227 0.402 ETKDGv3 3
VTB O4 0.000 0.799 -0.154 ETKDGv3 4
VTB O6 -0.205 -2.820 -0.374 ETKDGv3 5
VTB C7 0.346 -0.449 -0.749 ETKDGv3 6
VTB O8 -0.956 -1.225 1.810 ETKDGv3 7
VTB C10 1.708 -0.879 -0.179 ETKDGv3 8
VTB O12 2.639 0.161 -0.369 ETKDGv3 9
VTB O15 -3.573 0.146 -0.195 ETKDGv3 10
VTB P15 4.123 -0.307 0.330 ETKDGv3 11
VTB O16 3.969 -0.447 1.828 ETKDGv3 12
VTB O17 5.284 0.879 0.003 ETKDGv3 13
VTB O18 4.643 -1.780 -0.322 ETKDGv3 14
VTB C20 -1.346 1.177 -0.402 ETKDGv3 15
VTB O20 -1.600 1.124 -1.794 ETKDGv3 16
VTB C21 -1.495 2.634 0.088 ETKDGv3 17
VTB O22 -2.825 3.065 -0.018 ETKDGv3 18
VTB H1 -1.374 -1.556 -1.494 ETKDGv3 19
VTB H2 -2.506 -1.943 0.655 ETKDGv3 20
VTB H3 -2.461 0.659 1.415 ETKDGv3 21
VTB H4 -0.932 -3.477 -0.537 ETKDGv3 22
VTB H5 0.502 -0.294 -1.841 ETKDGv3 23
VTB H6 -1.616 -1.311 2.547 ETKDGv3 24
VTB H7 1.582 -1.104 0.904 ETKDGv3 25
VTB H8 2.048 -1.793 -0.718 ETKDGv3 26
VTB H9 -3.495 -0.420 -1.007 ETKDGv3 27
VTB H10 4.883 1.723 0.331 ETKDGv3 28
VTB H11 4.730 -1.608 -1.293 ETKDGv3 29
VTB H12 -2.481 1.543 -1.975 ETKDGv3 30
VTB H13 -0.839 3.294 -0.523 ETKDGv3 31
VTB H14 -1.165 2.706 1.150 ETKDGv3 32
VTB H15 -2.839 4.001 0.311 ETKDGv3 33
#