data_RST
#
_chem_comp.id RST
_chem_comp.name 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose
_chem_comp.type "L-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H13 N O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;RISTOSAMINE; 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexose; 3-amino-2,3,6-trideoxy-L-ribo-hexose;
3-amino-2,3,6-trideoxy-ribo-hexose
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-09-02
_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 147.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RST
_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 ?
_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 RST RISTOSAMINE PDB ?
2 RST 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexose PDB ?
3 RST 3-amino-2,3,6-trideoxy-L-ribo-hexose PDB ?
4 RST 3-amino-2,3,6-trideoxy-ribo-hexose 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
RST C1 C1 C 0 1 N N R N N N 20.761 22.130 16.616 -1.410 0.495 -0.215 C1 RST 1
RST O1 O1 O 0 1 N Y N N N N 21.189 21.025 17.326 -2.514 1.242 0.299 O1 RST 2
RST C2 C2 C 0 1 N N N N N N 19.998 23.014 17.575 -0.152 1.368 -0.200 C2 RST 3
RST C3 C3 C 0 1 N N R N N N 20.889 23.524 18.698 1.039 0.542 -0.695 C3 RST 4
RST N3 N3 N 0 1 N N N N N N 21.276 22.414 19.596 2.265 1.348 -0.612 N3 RST 5
RST C4 C4 C 0 1 N N R N N N 22.134 24.193 18.097 1.185 -0.703 0.185 C4 RST 6
RST O4 O4 O 0 1 N N N N N N 23.018 24.567 19.171 1.472 -0.308 1.528 O4 RST 7
RST C5 C5 C 0 1 N N S N N N 22.807 23.400 17.022 -0.125 -1.496 0.155 C5 RST 8
RST O5 O5 O 0 1 N N N N N N 21.892 22.853 16.084 -1.196 -0.660 0.598 O5 RST 9
RST C6 C6 C 0 1 N N N N N N 23.848 24.255 16.279 -0.403 -1.967 -1.274 C6 RST 10
RST H1 H1 H 0 1 N N N N N N 20.091 21.831 15.797 -1.625 0.186 -1.238 H1 RST 11
RST HO1 HO1 H 0 1 N Y N N N N 21.674 20.446 16.750 -3.346 0.750 0.318 HO1 RST 12
RST H2 H21 H 0 1 N N N N N N 19.593 23.874 17.022 -0.297 2.227 -0.854 H2 RST 13
RST H22 H22 H 0 1 N N N N N N 19.170 22.436 18.011 0.041 1.711 0.817 H22 RST 14
RST H3 H3 H 0 1 N N N N N N 20.332 24.278 19.274 0.870 0.241 -1.729 H3 RST 15
RST HN31 HN31 H 0 0 N N N N N N 21.860 22.765 20.328 2.190 2.179 -1.180 HN31 RST 16
RST HN32 HN32 H 0 0 N N N N N N 20.455 22.005 19.993 2.480 1.582 0.345 HN32 RST 17
RST H4 H4 H 0 1 N N N N N N 21.783 25.123 17.626 1.996 -1.324 -0.194 H4 RST 18
RST HO4 HO4 H 0 1 N Y N N N N 23.794 24.983 18.813 1.577 -1.048 2.142 HO4 RST 19
RST H5 H5 H 0 1 N N N N N N 23.350 22.575 17.506 -0.042 -2.361 0.813 H5 RST 20
RST H61 H61 H 0 1 N N N N N N 24.328 23.650 15.495 0.415 -2.604 -1.612 H61 RST 21
RST H62 H62 H 0 1 N N N N N N 23.350 25.122 15.820 -1.335 -2.532 -1.296 H62 RST 22
RST H63 H63 H 0 1 N N N N N N 24.611 24.605 16.991 -0.486 -1.102 -1.932 H63 RST 23
#
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
RST C1 O1 SING N N 1
RST C1 C2 SING N N 2
RST C1 O5 SING N N 3
RST C1 H1 SING N N 4
RST O1 HO1 SING N N 5
RST C2 C3 SING N N 6
RST C2 H2 SING N N 7
RST C2 H22 SING N N 8
RST C3 N3 SING N N 9
RST C3 C4 SING N N 10
RST C3 H3 SING N N 11
RST N3 HN31 SING N N 12
RST N3 HN32 SING N N 13
RST C4 O4 SING N N 14
RST C4 C5 SING N N 15
RST C4 H4 SING N N 16
RST O4 HO4 SING N N 17
RST C5 O5 SING N N 18
RST C5 C6 SING N N 19
RST C5 H5 SING N N 20
RST C6 H61 SING N N 21
RST C6 H62 SING N N 22
RST C6 H63 SING N N 23
#
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
RST SMILES ACDLabs 12.01 OC1C(OC(O)CC1N)C
RST InChI InChI 1.03 InChI=1S/C6H13NO3/c1-3-6(9)4(7)2-5(8)10-3/h3-6,8-9H,2,7H2,1H3/t3-,4+,5+,6-/m0/s1
RST InChIKey InChI 1.03 BBMKQGIZNKEDOX-KCDKBNATSA-N
RST SMILES_CANONICAL CACTVS 3.370 C[C@@H]1O[C@@H](O)C[C@@H](N)[C@H]1O
RST SMILES CACTVS 3.370 C[CH]1O[CH](O)C[CH](N)[CH]1O
RST SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C[C@H]1[C@@H]([C@@H](C[C@@H](O1)O)N)O
RST SMILES "OpenEye OEToolkits" 1.7.6 CC1C(C(CC(O1)O)N)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
RST "SYSTEMATIC NAME" ACDLabs 12.01 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose
RST "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 (2R,4R,5R,6S)-4-azanyl-6-methyl-oxane-2,5-diol
#
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
RST "CARBOHYDRATE ISOMER" L PDB ?
RST "CARBOHYDRATE RING" pyranose PDB ?
RST "CARBOHYDRATE ANOMER" alpha PDB ?
RST "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
RST 'Create component' 2002-09-02 RCSB
RST 'Modify descriptor' 2011-06-04 RCSB
RST 'Modify leaving atom flag' 2012-06-22 RCSB
RST 'Other modification' 2020-07-03 RCSB
RST 'Modify name' 2020-07-17 RCSB
RST 'Modify synonyms' 2020-07-17 RCSB
RST 'Modify linking type' 2020-07-17 RCSB
RST 'Modify atom id' 2020-07-17 RCSB
RST 'Modify component atom id' 2020-07-17 RCSB
RST 'Modify leaving atom flag' 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
RST RISTOSAMINE wwPDB ?
RST 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexose wwPDB ?
RST 3-amino-2,3,6-trideoxy-L-ribo-hexose wwPDB ?
RST 3-amino-2,3,6-trideoxy-ribo-hexose 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
RST C1 C 7.702 1.268 1
RST O1 O 9.002 2.018 2
RST C2 C 6.404 2.018 3
RST C3 C 5.104 1.268 4
RST N3 N 3.805 2.018 5
RST C4 C 5.104 -0.233 6
RST O4 O 3.805 -0.983 7
RST C5 C 6.404 -0.983 8
RST O5 O 7.702 -0.233 9
RST C6 C 6.404 -2.482 10
#
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
RST C1 O1 SINGLE BEGINDASH 1
RST C1 C2 SINGLE NONE 2
RST C1 O5 SINGLE NONE 3
RST C2 C3 SINGLE NONE 4
RST C3 N3 SINGLE BEGINDASH 5
RST C3 C4 SINGLE NONE 6
RST C4 O4 SINGLE BEGINDASH 7
RST C4 C5 SINGLE NONE 8
RST C5 O5 SINGLE NONE 9
RST C5 C6 SINGLE BEGINWEDGE 10
#
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
RST MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
RST 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
RST C1 S1 1
RST C2 S1 1
RST C3 S1 1
RST C4 S1 1
RST C5 S1 1
RST O5 S1 1
RST C4 F1 1
RST C5 F1 1
RST O5 F1 1
RST C1 F1 1
RST C2 F1 1
RST C3 F1 1
RST O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RST
_pdbe_chem_comp_rdkit_properties.exactmw 147.090
_pdbe_chem_comp_rdkit_properties.amw 147.174
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 78.154
_pdbe_chem_comp_rdkit_properties.tpsa 75.710
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.198
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.153
_pdbe_chem_comp_rdkit_properties.chi0v 4.672
_pdbe_chem_comp_rdkit_properties.chi1v 2.290
_pdbe_chem_comp_rdkit_properties.chi2v 0.837
_pdbe_chem_comp_rdkit_properties.chi3v 0.837
_pdbe_chem_comp_rdkit_properties.chi4v 0.426
_pdbe_chem_comp_rdkit_properties.chi0n 17.672
_pdbe_chem_comp_rdkit_properties.chi1n 8.501
_pdbe_chem_comp_rdkit_properties.chi2n 0.837
_pdbe_chem_comp_rdkit_properties.chi3n 0.837
_pdbe_chem_comp_rdkit_properties.chi4n 0.426
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.160
_pdbe_chem_comp_rdkit_properties.kappa1 1.474
_pdbe_chem_comp_rdkit_properties.kappa2 2.837
_pdbe_chem_comp_rdkit_properties.kappa3 1.462
_pdbe_chem_comp_rdkit_properties.Phi 0.418
#
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
RST UniChem PDBe RST
RST UniChem fdasrs Y5T2AJP16N
RST UniChem PubChem 55289611
RST UniChem Nikkaji J2.673.746J
#
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
RST C1 -0.842 1.603 0.409 ETKDGv3 1
RST O1 -1.132 1.935 -0.925 ETKDGv3 2
RST C2 -1.642 0.369 0.857 ETKDGv3 3
RST C3 -1.128 -0.927 0.214 ETKDGv3 4
RST N3 -1.642 -1.064 -1.154 ETKDGv3 5
RST C4 0.418 -0.996 0.286 ETKDGv3 6
RST O4 0.902 -2.048 -0.510 ETKDGv3 7
RST C5 1.056 0.341 -0.159 ETKDGv3 8
RST O5 0.552 1.422 0.609 ETKDGv3 9
RST C6 2.575 0.298 0.026 ETKDGv3 10
RST H1 -1.167 2.449 1.055 ETKDGv3 11
RST HO1 -0.666 2.793 -1.107 ETKDGv3 12
RST H2 -2.721 0.511 0.626 ETKDGv3 13
RST H22 -1.549 0.277 1.962 ETKDGv3 14
RST H3 -1.535 -1.774 0.813 ETKDGv3 15
RST HN31 -1.097 -0.468 -1.816 ETKDGv3 16
RST HN32 -1.519 -2.055 -1.463 ETKDGv3 17
RST H4 0.705 -1.173 1.349 ETKDGv3 18
RST HO4 0.679 -2.891 -0.034 ETKDGv3 19
RST H5 0.878 0.515 -1.243 ETKDGv3 20
RST H61 3.023 -0.503 -0.600 ETKDGv3 21
RST H62 3.018 1.268 -0.285 ETKDGv3 22
RST H63 2.833 0.116 1.091 ETKDGv3 23
#