data_15L
#
_chem_comp.id 15L
_chem_comp.name D-galactaro-1,5-lactone
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H8 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"galactaro-1,5-lactone; (2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-oxidotetrahydro-2H-pyran-2-carboxylate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-04-11
_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 192.124
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 15L
_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 3RFV
_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 15L galactaro-1,5-lactone PDB ?
2 15L (2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-oxidotetrahydro-2H-pyran-2-carboxylate 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
15L C1 C1 C 0 1 N N N N N N 80.281 94.193 -23.686 1.049 -1.340 -0.062 C1 15L 1
15L O1 O1 O 0 1 N N N N N N 79.327 93.257 -23.367 1.620 -2.361 0.243 O1 15L 2
15L C2 C2 C 0 1 N N R N N N 80.236 94.912 -25.090 1.820 -0.064 -0.316 C2 15L 3
15L O2 O2 O 0 1 N N N N N N 79.471 94.337 -26.074 3.176 -0.228 0.105 O2 15L 4
15L C3 C3 C 0 1 N N S N N N 81.486 95.628 -25.459 1.163 1.066 0.487 C3 15L 5
15L O3 O3 O 0 1 N N N N N N 81.466 96.426 -26.591 1.761 2.315 0.132 O3 15L 6
15L C4 C4 C 0 1 N N R N N N 82.349 95.983 -24.324 -0.333 1.103 0.162 C4 15L 7
15L O4 O4 O 0 1 N N N N N N 82.152 97.171 -23.642 -0.512 1.338 -1.236 O4 15L 8
15L C5 C5 C 0 1 N N S N N N 82.775 94.812 -23.540 -0.967 -0.239 0.539 C5 15L 9
15L O5 O5 O 0 1 N N N N N N 81.642 94.048 -23.038 -0.294 -1.308 -0.191 O5 15L 10
15L C6 C6 C 0 1 N N N N N N 83.919 94.897 -22.587 -2.429 -0.226 0.173 C6 15L 11
15L O6A O6A O 0 1 N N N N N N 85.070 95.107 -22.949 -2.845 -0.974 -0.679 O6A 15L 12
15L O6B O6B O 0 1 N N N N N N 83.641 94.571 -21.281 -3.269 0.618 0.794 O6B 15L 13
15L H2 H2 H 0 1 N N N N N N 79.560 95.764 -24.927 1.793 0.176 -1.379 H2 15L 14
15L HO2 HO2 H 0 1 N N N N N N 78.969 93.619 -25.707 3.646 -0.939 -0.351 HO2 15L 15
15L H3 H3 H 0 1 N N N N N N 82.105 94.850 -25.929 1.303 0.885 1.553 H3 15L 16
15L HO3 HO3 H 0 1 N N N N N N 82.320 96.823 -26.714 2.711 2.359 0.303 HO3 15L 17
15L H4 H4 H 0 1 N N N N N N 83.249 96.348 -24.841 -0.809 1.903 0.729 H4 15L 18
15L HO4 HO4 H 0 1 N N N N N N 82.790 97.245 -22.942 -1.438 1.374 -1.513 HO4 15L 19
15L H5 H5 H 0 1 N N N N N N 83.297 94.243 -24.324 -0.861 -0.403 1.612 H5 15L 20
15L H8 H8 H 0 1 N N N N N N 84.449 94.548 -20.781 -4.197 0.590 0.525 H8 15L 21
#
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
15L C1 O1 DOUB N N 1
15L C1 C2 SING N N 2
15L C1 O5 SING N N 3
15L C2 O2 SING N N 4
15L C2 C3 SING N N 5
15L C2 H2 SING N N 6
15L O2 HO2 SING N N 7
15L C3 O3 SING N N 8
15L C3 C4 SING N N 9
15L C3 H3 SING N N 10
15L O3 HO3 SING N N 11
15L C4 O4 SING N N 12
15L C4 C5 SING N N 13
15L C4 H4 SING N N 14
15L O4 HO4 SING N N 15
15L C5 O5 SING N N 16
15L C5 C6 SING N N 17
15L C5 H5 SING N N 18
15L C6 O6A DOUB N N 19
15L C6 O6B SING N N 20
15L O6B H8 SING N N 21
#
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
15L SMILES ACDLabs 12.01 O=C(O)C1OC(=O)C(O)C(O)C1O
15L SMILES_CANONICAL CACTVS 3.370 O[C@H]1[C@@H](O)[C@H](OC(=O)[C@@H]1O)C(O)=O
15L SMILES CACTVS 3.370 O[CH]1[CH](O)[CH](OC(=O)[CH]1O)C(O)=O
15L SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "[C@@H]1([C@H]([C@H](OC(=O)[C@@H]1O)C(=O)O)O)O"
15L SMILES "OpenEye OEToolkits" 1.7.0 C1(C(C(OC(=O)C1O)C(=O)O)O)O
15L InChI InChI 1.03 InChI=1S/C6H8O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,7-9H,(H,10,11)/t1-,2+,3+,4-/m0/s1
15L InChIKey InChI 1.03 YLKFQNUGXOLRNI-KXMYSMCESA-N
#
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
15L "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxotetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)"
15L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxo-oxane-2-carboxylic acid"
#
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
15L "CARBOHYDRATE ISOMER" D PDB ?
15L "CARBOHYDRATE RING" pyranose PDB ?
15L "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
15L 'Create component' 2011-04-11 RCSB
15L 'Modify descriptor' 2011-06-04 RCSB
15L 'Other modification' 2020-07-03 RCSB
15L 'Modify name' 2020-07-17 RCSB
15L 'Modify synonyms' 2020-07-17 RCSB
15L '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
15L galactaro-1,5-lactone wwPDB ?
15L (2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-oxidotetrahydro-2H-pyran-2-carboxylate 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
15L C1 C 5.104 -0.750 1
15L O1 O 3.805 -1.500 2
15L C2 C 5.104 0.750 3
15L O2 O 3.805 1.500 4
15L C3 C 6.404 1.500 5
15L O3 O 6.404 3.000 6
15L C4 C 7.702 0.750 7
15L O4 O 9.002 1.500 8
15L C5 C 7.702 -0.750 9
15L O5 O 6.404 -1.500 10
15L C6 C 9.002 -1.500 11
15L O6A O 9.002 -3.000 12
15L O6B O 10.301 -0.750 13
#
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
15L C1 O1 DOUBLE NONE 1
15L C1 C2 SINGLE NONE 2
15L C1 O5 SINGLE NONE 3
15L C2 O2 SINGLE BEGINDASH 4
15L C2 C3 SINGLE NONE 5
15L C3 O3 SINGLE BEGINWEDGE 6
15L C3 C4 SINGLE NONE 7
15L C4 O4 SINGLE BEGINWEDGE 8
15L C4 C5 SINGLE NONE 9
15L C5 O5 SINGLE NONE 10
15L C5 C6 SINGLE BEGINWEDGE 11
15L C6 O6A DOUBLE NONE 12
15L C6 O6B SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id 15L
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles O=C1CCCCO1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H8O2/c6-5-3-1-2-4-7-5/h1-4H2
_pdbe_chem_comp_substructure.substructure_inchikeys OZJPLYNZGCXSJM-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
15L C1 S1 1
15L O1 S1 1
15L C2 S1 1
15L C3 S1 1
15L C4 S1 1
15L C5 S1 1
15L O5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 15L
_pdbe_chem_comp_rdkit_properties.exactmw 192.027
_pdbe_chem_comp_rdkit_properties.amw 192.123
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 83.758
_pdbe_chem_comp_rdkit_properties.tpsa 124.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.921
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.536
_pdbe_chem_comp_rdkit_properties.chi0v 5.858
_pdbe_chem_comp_rdkit_properties.chi1v 2.883
_pdbe_chem_comp_rdkit_properties.chi2v 1.184
_pdbe_chem_comp_rdkit_properties.chi3v 1.184
_pdbe_chem_comp_rdkit_properties.chi4v 0.619
_pdbe_chem_comp_rdkit_properties.chi0n 13.858
_pdbe_chem_comp_rdkit_properties.chi1n 6.516
_pdbe_chem_comp_rdkit_properties.chi2n 1.184
_pdbe_chem_comp_rdkit_properties.chi3n 1.184
_pdbe_chem_comp_rdkit_properties.chi4n 0.619
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.180
_pdbe_chem_comp_rdkit_properties.kappa1 3.523
_pdbe_chem_comp_rdkit_properties.kappa2 3.286
_pdbe_chem_comp_rdkit_properties.kappa3 1.616
_pdbe_chem_comp_rdkit_properties.Phi 0.890
#
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
15L UniChem PDBe 15L
15L UniChem ChEBI 84190
15L UniChem PubChem 53321658
15L UniChem MetaboLights MTBLC84190
15L UniChem BRENDA 200980
15L UniChem BRENDA 207692
#
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
15L C1 -0.888 1.736 -0.109 ETKDGv3 1
15L O1 -1.389 2.881 -0.266 ETKDGv3 2
15L C2 -1.687 0.512 -0.491 ETKDGv3 3
15L O2 -3.032 0.655 -0.107 ETKDGv3 4
15L C3 -1.087 -0.786 0.098 ETKDGv3 5
15L O3 -1.618 -1.906 -0.562 ETKDGv3 6
15L C4 0.448 -0.796 -0.031 ETKDGv3 7
15L O4 0.830 -0.715 -1.382 ETKDGv3 8
15L C5 1.020 0.400 0.751 ETKDGv3 9
15L O5 0.445 1.628 0.303 ETKDGv3 10
15L C6 2.514 0.461 0.636 ETKDGv3 11
15L O6A 3.053 1.069 -0.327 ETKDGv3 12
15L O6B 3.306 -0.198 1.571 ETKDGv3 13
15L H2 -1.656 0.439 -1.600 ETKDGv3 14
15L HO2 -3.051 0.770 0.880 ETKDGv3 15
15L H3 -1.335 -0.850 1.185 ETKDGv3 16
15L HO3 -2.543 -2.027 -0.224 ETKDGv3 17
15L H4 0.845 -1.736 0.423 ETKDGv3 18
15L HO4 0.745 -1.628 -1.761 ETKDGv3 19
15L H5 0.764 0.274 1.827 ETKDGv3 20
15L H8 4.316 -0.183 1.499 ETKDGv3 21
#