data_TVD
#
_chem_comp.id TVD
_chem_comp.name N-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosylamine
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C10 H18 N2 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-04-01
_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 262.260
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TVD
_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 5NF7
_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
TVD O7 O7 O 0 1 N N N N N N 26.932 -9.654 1.444 2.721 -0.902 1.276 O7 TVD 1
TVD C7 C7 C 0 1 N N N N N N 26.243 -10.586 1.863 2.663 -1.438 0.189 C7 TVD 2
TVD C8 C8 C 0 1 N N N N N N 26.658 -11.473 3.032 3.911 -2.005 -0.438 C8 TVD 3
TVD N2 N2 N 0 1 N N N N N N 25.051 -10.966 1.341 1.483 -1.532 -0.454 N2 TVD 4
TVD C2 C2 C 0 1 N N R N N N 24.613 -10.287 0.093 0.269 -0.987 0.159 C2 TVD 5
TVD C1 C1 C 0 1 N N R N N N 25.019 -11.129 -1.155 0.154 0.503 -0.171 C1 TVD 6
TVD N1 N1 N 0 1 N N N N N N 26.440 -10.933 -1.431 1.296 1.220 0.404 N1 TVD 7
TVD C9 C9 C 0 1 N N N N N N 27.139 -12.047 -1.913 1.827 2.273 -0.247 C9 TVD 8
TVD C10 C10 C 0 1 N N N N N N 28.641 -12.037 -1.812 3.001 3.011 0.344 C10 TVD 9
TVD O9 O9 O 0 1 N N N N N N 26.536 -12.989 -2.435 1.361 2.628 -1.309 O9 TVD 10
TVD C3 C3 C 0 1 N N R N N N 23.095 -10.236 0.213 -0.957 -1.720 -0.394 C3 TVD 11
TVD O3 O3 O 0 1 N N N N N N 22.828 -9.365 1.357 -0.895 -3.100 -0.027 O3 TVD 12
TVD C4 C4 C 0 1 N N S N N N 22.521 -9.687 -1.048 -2.223 -1.090 0.195 C4 TVD 13
TVD C5 C5 C 0 1 N N R N N N 22.988 -10.560 -2.239 -2.241 0.405 -0.137 C5 TVD 14
TVD C6 C6 C 0 1 N N N N N N 22.514 -9.993 -3.581 -3.473 1.053 0.499 C6 TVD 15
TVD O6 O6 O 0 1 N N N N N N 22.658 -8.563 -3.830 -3.552 2.421 0.095 O6 TVD 16
TVD O5 O5 O 0 1 N N N N N N 24.382 -10.527 -2.229 -1.059 1.020 0.379 O5 TVD 17
TVD O4 O4 O 0 1 N N N N N N 21.135 -9.810 -0.899 -3.376 -1.718 -0.370 O4 TVD 18
TVD H81 H81 H 0 1 N N N N N N 27.636 -11.144 3.413 4.759 -1.840 0.226 H81 TVD 19
TVD H82 H82 H 0 1 N N N N N N 25.908 -11.398 3.833 3.781 -3.074 -0.603 H82 TVD 20
TVD H83 H83 H 0 1 N N N N N N 26.729 -12.517 2.693 4.095 -1.510 -1.392 H83 TVD 21
TVD HN2 HN2 H 0 1 N N N N N N 24.491 -11.671 1.776 1.437 -1.961 -1.323 HN2 TVD 22
TVD H2 H2 H 0 1 N N N N N N 25.033 -9.273 0.021 0.316 -1.119 1.240 H2 TVD 23
TVD H1 H1 H 0 1 N N N N N N 24.757 -12.189 -1.019 0.149 0.637 -1.253 H1 TVD 24
TVD HN1 HN1 H 0 1 N N N N N N 26.889 -10.052 -1.284 1.668 0.937 1.253 HN1 TVD 25
TVD H11 H11 H 0 1 N N N N N N 29.045 -12.957 -2.259 3.839 2.324 0.463 H11 TVD 26
TVD H12 H12 H 0 1 N N N N N N 29.039 -11.164 -2.349 3.290 3.826 -0.319 H12 TVD 27
TVD H13 H13 H 0 1 N N N N N N 28.937 -11.982 -0.754 2.723 3.416 1.317 H13 TVD 28
TVD H3 H3 H 0 1 N N N N N N 22.704 -11.247 0.398 -0.976 -1.632 -1.480 H3 TVD 29
TVD HO3 HO3 H 0 1 N Y N N N N 23.207 -9.745 2.141 -1.642 -3.625 -0.345 HO3 TVD 30
TVD H4 H4 H 0 1 N N N N N N 22.834 -8.643 -1.200 -2.228 -1.224 1.276 H4 TVD 31
TVD H5 H5 H 0 1 N N N N N N 22.605 -11.584 -2.114 -2.278 0.537 -1.218 H5 TVD 32
TVD H61 H61 H 0 1 N N N N N N 21.444 -10.231 -3.673 -4.370 0.526 0.174 H61 TVD 33
TVD H62 H62 H 0 1 N N N N N N 23.075 -10.516 -4.369 -3.393 0.998 1.585 H62 TVD 34
TVD HO6 HO6 H 0 1 N Y N N N N 22.325 -8.357 -4.695 -4.311 2.896 0.462 HO6 TVD 35
TVD HO4 HO4 H 0 1 N Y N N N N 20.846 -9.275 -0.169 -4.215 -1.368 -0.041 HO4 TVD 36
#
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
TVD O6 C6 SING N N 1
TVD C6 C5 SING N N 2
TVD O9 C9 DOUB N N 3
TVD C5 O5 SING N N 4
TVD C5 C4 SING N N 5
TVD O5 C1 SING N N 6
TVD C9 C10 SING N N 7
TVD C9 N1 SING N N 8
TVD N1 C1 SING N N 9
TVD C1 C2 SING N N 10
TVD C4 O4 SING N N 11
TVD C4 C3 SING N N 12
TVD C2 C3 SING N N 13
TVD C2 N2 SING N N 14
TVD C3 O3 SING N N 15
TVD N2 C7 SING N N 16
TVD O7 C7 DOUB N N 17
TVD C7 C8 SING N N 18
TVD C8 H81 SING N N 19
TVD C8 H82 SING N N 20
TVD C8 H83 SING N N 21
TVD N2 HN2 SING N N 22
TVD C2 H2 SING N N 23
TVD C1 H1 SING N N 24
TVD N1 HN1 SING N N 25
TVD C10 H11 SING N N 26
TVD C10 H12 SING N N 27
TVD C10 H13 SING N N 28
TVD C3 H3 SING N N 29
TVD O3 HO3 SING N N 30
TVD C4 H4 SING N N 31
TVD C5 H5 SING N N 32
TVD C6 H61 SING N N 33
TVD C6 H62 SING N N 34
TVD O6 HO6 SING N N 35
TVD O4 HO4 SING N N 36
#
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
TVD SMILES ACDLabs 12.01 O=C(C)NC1C(O)C(O)C(OC1NC(C)=O)CO
TVD InChI InChI 1.03 InChI=1S/C10H18N2O6/c1-4(14)11-7-9(17)8(16)6(3-13)18-10(7)12-5(2)15/h6-10,13,16-17H,3H2,1-2H3,(H,11,14)(H,12,15)/t6-,7-,8-,9-,10-/m1/s1
TVD InChIKey InChI 1.03 MVMHZICMHUYFIW-VVULQXIFSA-N
TVD SMILES_CANONICAL CACTVS 3.385 CC(=O)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=O
TVD SMILES CACTVS 3.385 CC(=O)N[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1NC(C)=O
TVD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1NC(=O)C)CO)O)O
TVD SMILES "OpenEye OEToolkits" 2.0.7 CC(=O)NC1C(C(C(OC1NC(=O)C)CO)O)O
#
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
TVD "SYSTEMATIC NAME" ACDLabs 12.01 N-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosylamine
TVD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide
#
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
TVD "CARBOHYDRATE ISOMER" D PDB ?
TVD "CARBOHYDRATE RING" pyranose PDB ?
TVD "CARBOHYDRATE ANOMER" beta PDB ?
TVD "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
TVD 'Create component' 2020-04-01 RCSB
TVD 'Initial release' 2020-07-29 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
TVD O7 O 7.702 -3.750 1
TVD C7 C 9.002 -3.000 2
TVD C8 C 10.301 -3.750 3
TVD N2 N 9.002 -1.500 4
TVD C2 C 7.702 -0.750 5
TVD C1 C 7.702 0.750 6
TVD N1 N 9.002 1.500 7
TVD C9 C 9.002 3.000 8
TVD C10 C 10.301 3.750 9
TVD O9 O 7.702 3.750 10
TVD C3 C 6.404 -1.500 11
TVD O3 O 6.404 -3.000 12
TVD C4 C 5.104 -0.750 13
TVD C5 C 5.104 0.750 14
TVD C6 C 3.805 1.500 15
TVD O6 O 3.805 3.000 16
TVD O5 O 6.404 1.500 17
TVD O4 O 3.805 -1.500 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
TVD O6 C6 SINGLE NONE 1
TVD C5 C6 SINGLE BEGINWEDGE 2
TVD O9 C9 DOUBLE NONE 3
TVD C5 O5 SINGLE NONE 4
TVD C5 C4 SINGLE NONE 5
TVD O5 C1 SINGLE NONE 6
TVD C9 C10 SINGLE NONE 7
TVD C9 N1 SINGLE NONE 8
TVD C1 N1 SINGLE BEGINWEDGE 9
TVD C1 C2 SINGLE NONE 10
TVD C4 O4 SINGLE BEGINDASH 11
TVD C4 C3 SINGLE NONE 12
TVD C2 C3 SINGLE NONE 13
TVD C2 N2 SINGLE BEGINDASH 14
TVD C3 O3 SINGLE BEGINWEDGE 15
TVD N2 C7 SINGLE NONE 16
TVD O7 C7 DOUBLE NONE 17
TVD C7 C8 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
TVD MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
TVD amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-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
TVD C2 S1 1
TVD C1 S1 1
TVD C3 S1 1
TVD C4 S1 1
TVD C5 S1 1
TVD O5 S1 1
TVD N2 F1 1
TVD C7 F1 1
TVD O7 F1 1
TVD C8 F1 1
TVD N1 F1 2
TVD C9 F1 2
TVD O9 F1 2
TVD C10 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id TVD
_pdbe_chem_comp_rdkit_properties.exactmw 262.116
_pdbe_chem_comp_rdkit_properties.amw 262.262
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 129.603
_pdbe_chem_comp_rdkit_properties.tpsa 128.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.934
_pdbe_chem_comp_rdkit_properties.CrippenMR 59.182
_pdbe_chem_comp_rdkit_properties.chi0v 8.344
_pdbe_chem_comp_rdkit_properties.chi1v 4.073
_pdbe_chem_comp_rdkit_properties.chi2v 1.538
_pdbe_chem_comp_rdkit_properties.chi3v 1.538
_pdbe_chem_comp_rdkit_properties.chi4v 0.934
_pdbe_chem_comp_rdkit_properties.chi0n 26.344
_pdbe_chem_comp_rdkit_properties.chi1n 12.692
_pdbe_chem_comp_rdkit_properties.chi2n 1.538
_pdbe_chem_comp_rdkit_properties.chi3n 1.538
_pdbe_chem_comp_rdkit_properties.chi4n 0.934
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.220
_pdbe_chem_comp_rdkit_properties.kappa1 3.454
_pdbe_chem_comp_rdkit_properties.kappa2 6.096
_pdbe_chem_comp_rdkit_properties.kappa3 3.388
_pdbe_chem_comp_rdkit_properties.Phi 1.170
#
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
TVD UniChem SureChEMBL SCHEMBL9302990
TVD UniChem 'PubChem TPHARMA' 16571488
TVD UniChem CCDC BUBTIB
TVD UniChem Nikkaji J1.972.807B
TVD UniChem PubChem 165420
TVD UniChem ACTor 6205-72-7
#
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
TVD O7 1.746 2.211 1.825 ETKDGv3 1
TVD C7 2.209 1.833 0.715 ETKDGv3 2
TVD C8 3.264 2.650 0.043 ETKDGv3 3
TVD N2 1.706 0.652 0.075 ETKDGv3 4
TVD C2 0.597 -0.142 0.618 ETKDGv3 5
TVD C1 -0.701 0.176 -0.165 ETKDGv3 6
TVD N1 -1.388 1.307 0.461 ETKDGv3 7
TVD C9 -1.163 2.668 0.069 ETKDGv3 8
TVD C10 -1.772 3.780 0.859 ETKDGv3 9
TVD O9 -0.431 2.938 -0.922 ETKDGv3 10
TVD C3 0.946 -1.657 0.564 ETKDGv3 11
TVD O3 0.483 -2.326 1.713 ETKDGv3 12
TVD C4 0.412 -2.346 -0.712 ETKDGv3 13
TVD C5 -1.073 -1.955 -1.016 ETKDGv3 14
TVD C6 -2.006 -3.170 -0.939 ETKDGv3 15
TVD O6 -2.039 -3.683 0.364 ETKDGv3 16
TVD O5 -1.564 -0.946 -0.147 ETKDGv3 17
TVD O4 1.228 -1.984 -1.797 ETKDGv3 18
TVD H81 4.074 1.987 -0.327 ETKDGv3 19
TVD H82 2.817 3.195 -0.814 ETKDGv3 20
TVD H83 3.700 3.384 0.753 ETKDGv3 21
TVD HN2 2.071 0.413 -0.875 ETKDGv3 22
TVD H2 0.447 0.120 1.689 ETKDGv3 23
TVD H1 -0.457 0.448 -1.220 ETKDGv3 24
TVD HN1 -1.967 1.124 1.312 ETKDGv3 25
TVD H11 -2.850 3.575 1.024 ETKDGv3 26
TVD H12 -1.670 4.745 0.318 ETKDGv3 27
TVD H13 -1.260 3.858 1.840 ETKDGv3 28
TVD H3 2.054 -1.767 0.572 ETKDGv3 29
TVD HO3 -0.484 -2.133 1.816 ETKDGv3 30
TVD H4 0.508 -3.448 -0.556 ETKDGv3 31
TVD H5 -1.150 -1.589 -2.067 ETKDGv3 32
TVD H61 -1.656 -3.955 -1.647 ETKDGv3 33
TVD H62 -3.032 -2.860 -1.242 ETKDGv3 34
TVD HO6 -2.650 -4.464 0.337 ETKDGv3 35
TVD HO4 1.051 -2.639 -2.521 ETKDGv3 36
#