data_3LJ
#
_chem_comp.id 3LJ
_chem_comp.name 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
_chem_comp.type "D-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H13 N O8 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;N-acetyl-6-O-sulfo-alpha-D-glucosamine; 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucose;
2-amino-2-deoxy-6-O-sulfo-D-glucose; 2-amino-2-deoxy-6-O-sulfo-glucose
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-09-12
_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 259.234
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3LJ
_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 4R9J
_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 3LJ N-acetyl-6-O-sulfo-alpha-D-glucosamine PDB ?
2 3LJ 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucose PDB ?
3 3LJ 2-amino-2-deoxy-6-O-sulfo-D-glucose PDB ?
4 3LJ 2-amino-2-deoxy-6-O-sulfo-glucose 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
3LJ O1 O1 O 0 1 N Y N N N N 53.614 6.240 -15.462 2.167 1.904 -1.173 O1 3LJ 1
3LJ C1 C1 C 0 1 N N S N N N 54.917 5.745 -15.616 2.057 1.611 0.221 C1 3LJ 2
3LJ C2 C2 C 0 1 N N R N N N 55.774 6.448 -14.564 3.119 0.581 0.612 C2 3LJ 3
3LJ C3 C3 C 0 1 N N R N N N 56.628 7.602 -15.037 2.866 -0.719 -0.158 C3 3LJ 4
3LJ C4 C4 C 0 1 N N S N N N 57.310 7.210 -16.331 1.445 -1.208 0.140 C4 3LJ 5
3LJ C5 C5 C 0 1 N N R N N N 56.225 6.944 -17.423 0.447 -0.108 -0.232 C5 3LJ 6
3LJ C6 C6 C 0 1 N N N N N N 56.776 6.420 -18.763 -0.970 -0.565 0.119 C6 3LJ 7
3LJ O3 O3 O 0 1 N N N N N N 57.607 7.902 -14.005 3.809 -1.711 0.255 O3 3LJ 8
3LJ O4 O4 O 0 1 N N N N N N 58.275 8.265 -16.529 1.172 -2.381 -0.628 O4 3LJ 9
3LJ O5 O5 O 0 1 N N N N N N 55.326 5.865 -16.988 0.758 1.082 0.496 O5 3LJ 10
3LJ O6 O6 O 0 1 N N N N N N 57.644 5.305 -18.476 -1.911 0.412 -0.333 O6 3LJ 11
3LJ N2 N N 0 1 N N N N N N 55.008 6.916 -13.427 4.452 1.098 0.276 N2 3LJ 12
3LJ S S S 0 1 N N N N N N 58.087 4.367 -19.684 -3.361 0.058 -0.035 S 3LJ 13
3LJ O7 O7 O 0 1 N N N N N N 56.944 3.752 -20.152 -4.156 1.017 -0.719 O7 3LJ 14
3LJ O8 O8 O 0 1 N N N N N N 58.702 5.229 -20.670 -3.483 -1.342 -0.242 O8 3LJ 15
3LJ O9 O9 O 0 1 N N N N N N 59.100 3.410 -18.885 -3.586 0.294 1.451 O9 3LJ 16
3LJ HO1 H1 H 0 1 N N N N N N 53.349 6.158 -14.553 1.523 2.552 -1.491 HO1 3LJ 17
3LJ H1 H2 H 0 1 N N N N N N 54.913 4.676 -15.358 2.207 2.524 0.798 H1 3LJ 18
3LJ H2 H3 H 0 1 N N N N N N 56.472 5.687 -14.186 3.063 0.387 1.683 H2 3LJ 19
3LJ H3 H4 H 0 1 N N N N N N 55.988 8.478 -15.216 2.973 -0.537 -1.227 H3 3LJ 20
3LJ H4 H5 H 0 1 N N N N N N 57.845 6.264 -16.161 1.354 -1.438 1.202 H4 3LJ 21
3LJ H5 H6 H 0 1 N N N N N N 55.656 7.869 -17.599 0.510 0.093 -1.302 H5 3LJ 22
3LJ H61 H7 H 0 1 N N N N N N 57.343 7.214 -19.271 -1.175 -1.519 -0.367 H61 3LJ 23
3LJ H62 H8 H 0 1 N N N N N N 55.946 6.092 -19.407 -1.058 -0.681 1.199 H62 3LJ 24
3LJ HO3 H9 H 0 1 N Y N N N N 57.159 8.145 -13.204 4.731 -1.465 0.101 HO3 3LJ 25
3LJ HO4 H10 H 0 1 N Y N N N N 58.863 8.301 -15.783 1.771 -3.119 -0.445 HO4 3LJ 26
3LJ HN2 H11 H 0 1 N N N N N N 55.619 7.365 -12.775 4.641 1.959 0.768 HN2 3LJ 27
3LJ H12 H12 H 0 1 N N N N N N 54.315 7.567 -13.737 5.166 0.410 0.465 H12 3LJ 28
3LJ H13 H13 H 0 1 N N N N N N 58.746 2.529 -18.853 -4.485 0.098 1.749 H13 3LJ 29
#
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
3LJ O8 S DOUB N N 1
3LJ O7 S DOUB N N 2
3LJ S O9 SING N N 3
3LJ S O6 SING N N 4
3LJ C6 O6 SING N N 5
3LJ C6 C5 SING N N 6
3LJ C5 O5 SING N N 7
3LJ C5 C4 SING N N 8
3LJ O5 C1 SING N N 9
3LJ O4 C4 SING N N 10
3LJ C4 C3 SING N N 11
3LJ C1 O1 SING N N 12
3LJ C1 C2 SING N N 13
3LJ C3 C2 SING N N 14
3LJ C3 O3 SING N N 15
3LJ C2 N2 SING N N 16
3LJ O1 HO1 SING N N 17
3LJ C1 H1 SING N N 18
3LJ C2 H2 SING N N 19
3LJ C3 H3 SING N N 20
3LJ C4 H4 SING N N 21
3LJ C5 H5 SING N N 22
3LJ C6 H61 SING N N 23
3LJ C6 H62 SING N N 24
3LJ O3 HO3 SING N N 25
3LJ O4 HO4 SING N N 26
3LJ N2 HN2 SING N N 27
3LJ N2 H12 SING N N 28
3LJ O9 H13 SING N N 29
#
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
3LJ SMILES ACDLabs 12.01 O=S(=O)(O)OCC1OC(O)C(N)C(O)C1O
3LJ InChI InChI 1.03 InChI=1S/C6H13NO8S/c7-3-5(9)4(8)2(15-6(3)10)1-14-16(11,12)13/h2-6,8-10H,1,7H2,(H,11,12,13)/t2-,3-,4-,5-,6+/m1/s1
3LJ InChIKey InChI 1.03 MTDHILKWIRSIHB-UKFBFLRUSA-N
3LJ SMILES_CANONICAL CACTVS 3.385 N[C@H]1[C@@H](O)O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@@H]1O
3LJ SMILES CACTVS 3.385 N[CH]1[CH](O)O[CH](CO[S](O)(=O)=O)[CH](O)[CH]1O
3LJ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)N)O)O)OS(=O)(=O)O
3LJ SMILES "OpenEye OEToolkits" 1.7.6 C(C1C(C(C(C(O1)O)N)O)O)OS(=O)(=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
3LJ "SYSTEMATIC NAME" ACDLabs 12.01 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
3LJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R,6S)-5-azanyl-3,4,6-tris(oxidanyl)oxan-2-yl]methyl hydrogen sulfate"
3LJ "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGlcpN[6S]a
3LJ "COMMON NAME" GMML 1.0 6-sulfo-a-D-glucopyranose-osamine
3LJ "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-GlcpN6SO3
#
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
3LJ "CARBOHYDRATE ISOMER" D PDB ?
3LJ "CARBOHYDRATE RING" pyranose PDB ?
3LJ "CARBOHYDRATE ANOMER" alpha PDB ?
3LJ "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
3LJ 'Create component' 2014-09-12 RCSB
3LJ 'Initial release' 2014-11-05 RCSB
3LJ 'Other modification' 2020-07-03 RCSB
3LJ 'Modify synonyms' 2020-07-17 RCSB
3LJ 'Modify internal type' 2020-07-17 RCSB
3LJ 'Modify linking type' 2020-07-17 RCSB
3LJ 'Modify atom id' 2020-07-17 RCSB
3LJ 'Modify component atom id' 2020-07-17 RCSB
3LJ '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
3LJ N-acetyl-6-O-sulfo-alpha-D-glucosamine wwPDB ?
3LJ 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucose wwPDB ?
3LJ 2-amino-2-deoxy-6-O-sulfo-D-glucose wwPDB ?
3LJ 2-amino-2-deoxy-6-O-sulfo-glucose 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
3LJ O1 O 10.794 0.517 1
3LJ C1 C 9.495 -0.233 2
3LJ C2 C 9.495 -1.732 3
3LJ C3 C 8.196 -2.482 4
3LJ C4 C 6.897 -1.732 5
3LJ C5 C 6.897 -0.233 6
3LJ C6 C 5.598 0.517 7
3LJ O3 O 8.196 -3.982 8
3LJ O4 O 5.598 -2.482 9
3LJ O5 O 8.196 0.517 10
3LJ O6 O 5.598 2.018 11
3LJ N2 N 10.794 -2.482 12
3LJ S S 4.299 2.768 13
3LJ O7 O 5.049 4.066 14
3LJ O8 O 3.000 3.518 15
3LJ O9 O 3.549 1.468 16
#
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
3LJ O8 S DOUBLE NONE 1
3LJ O7 S DOUBLE NONE 2
3LJ S O9 SINGLE NONE 3
3LJ S O6 SINGLE NONE 4
3LJ C6 O6 SINGLE NONE 5
3LJ C5 C6 SINGLE BEGINWEDGE 6
3LJ C5 O5 SINGLE NONE 7
3LJ C5 C4 SINGLE NONE 8
3LJ O5 C1 SINGLE NONE 9
3LJ C4 O4 SINGLE BEGINDASH 10
3LJ C4 C3 SINGLE NONE 11
3LJ C1 O1 SINGLE BEGINDASH 12
3LJ C1 C2 SINGLE NONE 13
3LJ C3 C2 SINGLE NONE 14
3LJ C3 O3 SINGLE BEGINWEDGE 15
3LJ C2 N2 SINGLE BEGINDASH 16
#
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
3LJ MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
3LJ 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
3LJ C1 S1 1
3LJ C2 S1 1
3LJ C3 S1 1
3LJ C4 S1 1
3LJ C5 S1 1
3LJ O5 S1 1
3LJ C4 F1 1
3LJ C5 F1 1
3LJ O5 F1 1
3LJ C1 F1 1
3LJ C2 F1 1
3LJ C3 F1 1
3LJ O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 3LJ
_pdbe_chem_comp_rdkit_properties.exactmw 259.036
_pdbe_chem_comp_rdkit_properties.amw 259.236
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_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 110.073
_pdbe_chem_comp_rdkit_properties.tpsa 159.540
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.428
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.369
_pdbe_chem_comp_rdkit_properties.chi0v 7.938
_pdbe_chem_comp_rdkit_properties.chi1v 4.698
_pdbe_chem_comp_rdkit_properties.chi2v 1.540
_pdbe_chem_comp_rdkit_properties.chi3v 1.540
_pdbe_chem_comp_rdkit_properties.chi4v 0.825
_pdbe_chem_comp_rdkit_properties.chi0n 20.121
_pdbe_chem_comp_rdkit_properties.chi1n 9.392
_pdbe_chem_comp_rdkit_properties.chi2n 1.252
_pdbe_chem_comp_rdkit_properties.chi3n 1.252
_pdbe_chem_comp_rdkit_properties.chi4n 0.647
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.330
_pdbe_chem_comp_rdkit_properties.kappa1 4.103
_pdbe_chem_comp_rdkit_properties.kappa2 4.893
_pdbe_chem_comp_rdkit_properties.kappa3 3.330
_pdbe_chem_comp_rdkit_properties.Phi 1.255
#
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
3LJ UniChem PDBe 3LJ
3LJ UniChem ZINC ZINC000013543969
3LJ UniChem PubChem 46926129
3LJ UniChem PubChem 46926130
#
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
3LJ O1 -1.368 2.474 1.284 ETKDGv3 1
3LJ C1 -1.015 1.326 0.557 ETKDGv3 2
3LJ C2 -2.276 0.517 0.138 ETKDGv3 3
3LJ C3 -1.905 -0.958 -0.188 ETKDGv3 4
3LJ C4 -0.414 -1.082 -0.548 ETKDGv3 5
3LJ C5 0.464 -0.511 0.610 ETKDGv3 6
3LJ C6 1.840 -0.040 0.115 ETKDGv3 7
3LJ O3 -2.681 -1.429 -1.260 ETKDGv3 8
3LJ O4 -0.071 -2.416 -0.836 ETKDGv3 9
3LJ O5 -0.168 0.525 1.359 ETKDGv3 10
3LJ O6 2.546 -1.131 -0.425 ETKDGv3 11
3LJ N2 -3.293 0.550 1.195 ETKDGv3 12
3LJ S 4.025 -0.566 -1.027 ETKDGv3 13
3LJ O7 3.786 0.352 -2.194 ETKDGv3 14
3LJ O8 4.844 -1.737 -1.492 ETKDGv3 15
3LJ O9 4.875 0.256 0.169 ETKDGv3 16
3LJ HO1 -1.770 3.111 0.636 ETKDGv3 17
3LJ H1 -0.469 1.657 -0.360 ETKDGv3 18
3LJ H2 -2.693 0.998 -0.777 ETKDGv3 19
3LJ H3 -2.084 -1.594 0.713 ETKDGv3 20
3LJ H4 -0.239 -0.486 -1.472 ETKDGv3 21
3LJ H5 0.649 -1.336 1.333 ETKDGv3 22
3LJ H61 1.701 0.759 -0.647 ETKDGv3 23
3LJ H62 2.393 0.380 0.984 ETKDGv3 24
3LJ HO3 -3.582 -1.630 -0.896 ETKDGv3 25
3LJ HO4 -0.284 -2.964 -0.037 ETKDGv3 26
3LJ HN2 -4.099 -0.048 0.902 ETKDGv3 27
3LJ H12 -3.681 1.519 1.256 ETKDGv3 28
3LJ H13 4.969 -0.398 0.908 ETKDGv3 29
#