data_U9D
#
_chem_comp.id U9D
_chem_comp.name 4-deoxy-2,3,6-tri-O-methyl-alpha-D-xylo-hexopyranose
_chem_comp.type "D-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C9 H18 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-05-05
_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 206.236
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code U9D
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_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
U9D C4 C4 C 0 1 N N N N N N 31.759 7.524 38.679 -0.257 1.310 -0.302 C4 U9D 1
U9D C5 C5 C 0 1 N N S N N N 32.395 6.958 40.044 -1.286 0.272 0.154 C5 U9D 2
U9D O5 O5 O 0 1 N N N N N N 31.335 6.777 41.075 -0.936 -1.008 -0.377 O5 U9D 3
U9D C6 C6 C 0 1 N N N N N N 33.485 7.914 40.587 -2.673 0.672 -0.351 C6 U9D 4
U9D O6 O6 O 0 1 N N N N N N 34.113 7.253 41.686 -3.649 -0.232 0.171 O6 U9D 5
U9D C6M C6M C 0 1 N N N N N N ? ? ? -4.986 0.054 -0.243 C6M U9D 6
U9D C3 C3 C 0 1 N N S N N N 30.671 6.547 38.203 1.137 0.872 0.156 C3 U9D 7
U9D O3 O3 O 0 1 N N N N N N 30.108 7.021 37.007 2.112 1.797 -0.328 O3 U9D 8
U9D C3M C3M C 0 1 N N N N N N 29.818 5.913 35.868 2.375 2.884 0.563 C3M U9D 9
U9D C2 C2 C 0 1 N N R N N N 29.578 6.376 39.350 1.432 -0.523 -0.404 C2 U9D 10
U9D O2 O2 O 0 1 N N N N N N 28.565 5.520 38.969 2.700 -0.973 0.076 O2 U9D 11
U9D C2M C2M C 0 1 N N N N N N 27.194 6.096 38.534 3.383 -1.852 -0.820 C2M U9D 12
U9D C1 C1 C 0 1 N N S N N N 30.237 5.858 40.658 0.338 -1.490 0.056 C1 U9D 13
U9D O1 O1 O 0 1 N N N N N N 29.621 4.514 41.063 0.353 -1.584 1.482 O1 U9D 14
U9D H101 H101 H 0 0 N N N N N N 31.315 8.514 38.860 -0.276 1.388 -1.389 H101 U9D 15
U9D H102 H102 H 0 0 N N N N N N 32.543 7.608 37.912 -0.498 2.278 0.138 H102 U9D 16
U9D H11 H11 H 0 1 N N N N N N 32.859 5.986 39.823 -1.295 0.223 1.243 H11 U9D 17
U9D H131 H131 H 0 0 N N N N N N 34.225 8.127 39.802 -2.902 1.685 -0.020 H131 U9D 18
U9D H132 H132 H 0 0 N N N N N N 33.027 8.856 40.925 -2.688 0.633 -1.441 H132 U9D 19
U9D H151 H151 H 0 0 N N N N N N ? ? ? -5.049 0.003 -1.330 H151 U9D 20
U9D H152 H152 H 0 0 N N N N N N ? ? ? -5.667 -0.676 0.195 H152 U9D 21
U9D H153 H153 H 0 0 N N N N N N ? ? ? -5.264 1.054 0.090 H153 U9D 22
U9D H16 H16 H 0 1 N N N N N N 31.137 5.565 38.038 1.171 0.843 1.245 H16 U9D 23
U9D H181 H181 H 0 0 N N N N N N 29.380 6.401 34.984 1.456 3.445 0.733 H181 U9D 24
U9D H182 H182 H 0 0 N N N N N N 30.761 5.422 35.586 2.744 2.495 1.512 H182 U9D 25
U9D H183 H183 H 0 0 N N N N N N 29.115 5.162 36.258 3.125 3.541 0.123 H183 U9D 26
U9D H19 H19 H 0 1 N N N N N N 29.166 7.375 39.558 1.449 -0.482 -1.493 H19 U9D 27
U9D H1B1 H1B1 H 0 0 N N N N N N 26.517 5.271 38.268 2.772 -2.738 -0.995 H1B1 U9D 28
U9D H1B2 H1B2 H 0 0 N N N N N N 26.759 6.674 39.363 3.560 -1.340 -1.766 H1B2 U9D 29
U9D H1B3 H1B3 H 0 0 N N N N N N 27.332 6.753 37.662 4.336 -2.148 -0.382 H1B3 U9D 30
U9D H1C H1C H 0 1 N N N N N N 29.508 6.407 41.273 0.519 -2.475 -0.375 H1C U9D 31
U9D H2 H2 H 0 1 N Y N N N N 28.899 4.308 40.481 -0.316 -2.181 1.844 H2 U9D 32
#
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
U9D C4 C5 SING N N 1
U9D C4 C3 SING N N 2
U9D C4 H101 SING N N 3
U9D C4 H102 SING N N 4
U9D C5 O5 SING N N 5
U9D C5 C6 SING N N 6
U9D C5 H11 SING N N 7
U9D O5 C1 SING N N 8
U9D C6 O6 SING N N 9
U9D C6 H131 SING N N 10
U9D C6 H132 SING N N 11
U9D O6 C6M SING N N 12
U9D C6M H151 SING N N 13
U9D C6M H152 SING N N 14
U9D C6M H153 SING N N 15
U9D C3 O3 SING N N 16
U9D C3 C2 SING N N 17
U9D C3 H16 SING N N 18
U9D O3 C3M SING N N 19
U9D C3M H181 SING N N 20
U9D C3M H182 SING N N 21
U9D C3M H183 SING N N 22
U9D C2 O2 SING N N 23
U9D C2 C1 SING N N 24
U9D C2 H19 SING N N 25
U9D O2 C2M SING N N 26
U9D C2M H1B1 SING N N 27
U9D C2M H1B2 SING N N 28
U9D C2M H1B3 SING N N 29
U9D C1 O1 SING N N 30
U9D C1 H1C SING N N 31
U9D O1 H2 SING N N 32
#
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
U9D SMILES ACDLabs 12.01 C1C(OC(C(C1OC)OC)O)COC
U9D InChI InChI 1.03 InChI=1S/C9H18O5/c1-11-5-6-4-7(12-2)8(13-3)9(10)14-6/h6-10H,4-5H2,1-3H3/t6-,7-,8+,9?/m0/s1
U9D InChIKey InChI 1.03 VGIKFUPOZBZSKX-VTBDLZGYSA-N
U9D SMILES_CANONICAL CACTVS 3.385 COC[C@@H]1C[C@H](OC)[C@@H](OC)[C@@H](O)O1
U9D SMILES CACTVS 3.385 COC[CH]1C[CH](OC)[CH](OC)[CH](O)O1
U9D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 COC[C@@H]1C[C@@H]([C@H](C(O1)O)OC)OC
U9D SMILES "OpenEye OEToolkits" 2.0.7 COCC1CC(C(C(O1)O)OC)OC
#
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
U9D "SYSTEMATIC NAME" ACDLabs 12.01 4-deoxy-2,3,6-tri-O-methyl-alpha-D-xylo-hexopyranose
U9D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 (3~{R},4~{S},6~{S})-3,4-dimethoxy-6-(methoxymethyl)oxan-2-ol
#
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
U9D "CARBOHYDRATE ISOMER" D PDB ?
U9D "CARBOHYDRATE RING" pyranose PDB ?
U9D "CARBOHYDRATE ANOMER" alpha PDB ?
U9D "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose 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
U9D 'Create component' 2020-05-05 RCSB
U9D 'Initial release' 2020-07-29 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
U9D C4 C 5.598 -0.750 1
U9D C5 C 5.598 0.750 2
U9D O5 O 6.897 1.500 3
U9D C6 C 4.299 1.500 4
U9D O6 O 4.299 3.000 5
U9D C6M C 3.000 3.750 6
U9D C3 C 6.897 -1.500 7
U9D O3 O 6.897 -3.000 8
U9D C3M C 5.598 -3.750 9
U9D C2 C 8.196 -0.750 10
U9D O2 O 9.495 -1.500 11
U9D C2M C 9.495 -3.000 12
U9D C1 C 8.196 0.750 13
U9D O1 O 9.495 1.500 14
#
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
U9D C4 C5 SINGLE NONE 1
U9D C4 C3 SINGLE NONE 2
U9D C5 O5 SINGLE NONE 3
U9D C5 C6 SINGLE BEGINWEDGE 4
U9D O5 C1 SINGLE NONE 5
U9D C6 O6 SINGLE NONE 6
U9D O6 C6M SINGLE NONE 7
U9D C3 O3 SINGLE BEGINWEDGE 8
U9D C3 C2 SINGLE NONE 9
U9D O3 C3M SINGLE NONE 10
U9D C2 O2 SINGLE BEGINDASH 11
U9D C2 C1 SINGLE NONE 12
U9D O2 C2M SINGLE NONE 13
U9D C1 O1 SINGLE BEGINDASH 14
#
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
U9D MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
U9D 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
U9D C4 S1 1
U9D C5 S1 1
U9D O5 S1 1
U9D C3 S1 1
U9D C2 S1 1
U9D C1 S1 1
U9D C4 F1 1
U9D C5 F1 1
U9D O5 F1 1
U9D C1 F1 1
U9D C2 F1 1
U9D C3 F1 1
U9D O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id U9D
_pdbe_chem_comp_rdkit_properties.exactmw 206.115
_pdbe_chem_comp_rdkit_properties.amw 206.238
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 109.278
_pdbe_chem_comp_rdkit_properties.tpsa 57.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.230
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.967
_pdbe_chem_comp_rdkit_properties.chi0v 6.541
_pdbe_chem_comp_rdkit_properties.chi1v 3.087
_pdbe_chem_comp_rdkit_properties.chi2v 1.161
_pdbe_chem_comp_rdkit_properties.chi3v 1.161
_pdbe_chem_comp_rdkit_properties.chi4v 0.670
_pdbe_chem_comp_rdkit_properties.chi0n 24.541
_pdbe_chem_comp_rdkit_properties.chi1n 11.995
_pdbe_chem_comp_rdkit_properties.chi2n 1.161
_pdbe_chem_comp_rdkit_properties.chi3n 1.161
_pdbe_chem_comp_rdkit_properties.chi4n 0.670
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 2.236
_pdbe_chem_comp_rdkit_properties.kappa2 5.625
_pdbe_chem_comp_rdkit_properties.kappa3 2.648
_pdbe_chem_comp_rdkit_properties.Phi 0.898
#
_pdbe_chem_comp_external_mappings.comp_id U9D
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 146681152
#
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
U9D C4 -0.125 0.476 -1.228 ETKDGv3 1
U9D C5 1.178 -0.189 -0.728 ETKDGv3 2
U9D O5 0.946 -1.436 -0.085 ETKDGv3 3
U9D C6 2.077 0.755 0.102 ETKDGv3 4
U9D O6 3.191 0.049 0.617 ETKDGv3 5
U9D C6M 4.316 0.222 -0.217 ETKDGv3 6
U9D C3 -1.236 0.504 -0.164 ETKDGv3 7
U9D O3 -0.950 1.479 0.827 ETKDGv3 8
U9D C3M -1.610 2.694 0.543 ETKDGv3 9
U9D C2 -1.352 -0.875 0.507 ETKDGv3 10
U9D O2 -1.846 -1.826 -0.426 ETKDGv3 11
U9D C2M -3.225 -2.048 -0.231 ETKDGv3 12
U9D C1 0.035 -1.333 0.996 ETKDGv3 13
U9D O1 -0.078 -2.598 1.593 ETKDGv3 14
U9D H101 -0.497 -0.105 -2.101 ETKDGv3 15
U9D H102 0.085 1.503 -1.597 ETKDGv3 16
U9D H11 1.760 -0.420 -1.646 ETKDGv3 17
U9D H131 1.517 1.170 0.961 ETKDGv3 18
U9D H132 2.360 1.642 -0.514 ETKDGv3 19
U9D H151 4.660 1.279 -0.201 ETKDGv3 20
U9D H152 4.105 -0.102 -1.259 ETKDGv3 21
U9D H153 5.143 -0.407 0.170 ETKDGv3 22
U9D H16 -2.207 0.701 -0.681 ETKDGv3 23
U9D H181 -1.282 3.455 1.280 ETKDGv3 24
U9D H182 -1.354 3.072 -0.471 ETKDGv3 25
U9D H183 -2.711 2.574 0.646 ETKDGv3 26
U9D H19 -2.003 -0.772 1.411 ETKDGv3 27
U9D H1B1 -3.408 -2.549 0.745 ETKDGv3 28
U9D H1B2 -3.804 -1.101 -0.296 ETKDGv3 29
U9D H1B3 -3.591 -2.724 -1.031 ETKDGv3 30
U9D H1C 0.424 -0.624 1.763 ETKDGv3 31
U9D H2 -0.519 -2.466 2.473 ETKDGv3 32
#