data_GMH
#
_chem_comp.id GMH
_chem_comp.name L-glycero-alpha-D-manno-heptopyranose
_chem_comp.type "D-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C7 H14 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"L-glycero-alpha-D-manno-heptose; L-glycero-D-manno-heptose; L-glycero-manno-heptose; L-GLYCERO-D-MANNO-HEPTOPYRANOSE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 210.182
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GMH
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1FCP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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 GMH L-glycero-alpha-D-manno-heptose PDB ?
2 GMH L-glycero-D-manno-heptose PDB ?
3 GMH L-glycero-manno-heptose PDB ?
4 GMH L-GLYCERO-D-MANNO-HEPTOPYRANOSE 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
GMH C1 C1 C 0 1 N N S N N N 58.655 63.418 56.490 1.729 0.015 -0.981 C1 GMH 1
GMH C2 C2 C 0 1 N N S N N N 58.563 61.916 56.144 0.783 -0.269 -2.149 C2 GMH 2
GMH C3 C3 C 0 1 N N S N N N 57.506 61.262 57.057 -0.529 0.488 -1.925 C3 GMH 3
GMH C4 C4 C 0 1 N N S N N N 57.865 61.475 58.536 -1.075 0.123 -0.540 C4 GMH 4
GMH C5 C5 C 0 1 N N R N N N 57.963 62.990 58.762 0.010 0.379 0.506 C5 GMH 5
GMH C6 C6 C 0 1 N N S N N N 58.260 63.363 60.213 -0.535 0.051 1.897 C6 GMH 6
GMH C7 C7 C 0 1 N N N N N N 57.972 64.840 60.433 0.548 0.311 2.945 C7 GMH 7
GMH O1 O1 O 0 1 N Y N N N N 57.460 64.078 56.108 1.965 1.422 -0.895 O1 GMH 8
GMH O2 O2 O 0 1 N N N N N N 59.830 61.323 56.367 0.521 -1.672 -2.221 O2 GMH 9
GMH O3 O3 O 0 1 N N N N N N 57.238 59.854 56.792 -1.475 0.116 -2.930 O3 GMH 10
GMH O4 O4 O 0 1 N N N N N N 56.828 60.923 59.379 -2.219 0.928 -0.249 O4 GMH 11
GMH O5 O5 O 0 1 N N N N N N 58.957 63.559 57.880 1.144 -0.442 0.236 O5 GMH 12
GMH O6 O6 O 0 1 N N N N N N 59.614 63.083 60.526 -0.924 -1.322 1.944 O6 GMH 13
GMH O7 O7 O 0 1 N N N N N N 58.389 65.218 61.734 0.037 0.004 4.244 O7 GMH 14
GMH H1 H1 H 0 1 N N N N N N 59.479 63.905 55.918 2.675 -0.501 -1.145 H1 GMH 15
GMH H2 H2 H 0 1 N N N N N N 58.268 61.773 55.078 1.243 0.063 -3.080 H2 GMH 16
GMH H3 H3 H 0 1 N N N N N N 56.552 61.785 56.812 -0.345 1.561 -1.976 H3 GMH 17
GMH H4 H4 H 0 1 N N N N N N 58.826 60.969 58.787 -1.356 -0.929 -0.525 H4 GMH 18
GMH H5 H5 H 0 1 N N N N N N 56.960 63.417 58.526 0.307 1.428 0.471 H5 GMH 19
GMH H6 H6 H 0 1 N N N N N N 57.605 62.756 60.882 -1.400 0.681 2.105 H6 GMH 20
GMH H71 H71 H 0 1 N N N N N N 58.429 65.479 59.642 0.844 1.359 2.909 H71 GMH 21
GMH H72 H72 H 0 1 N N N N N N 56.902 65.092 60.244 1.413 -0.318 2.737 H72 GMH 22
GMH HO1 HO1 H 0 1 N Y N N N N 57.516 65.002 56.320 2.568 1.559 -0.151 HO1 GMH 23
GMH HO2 HO2 H 0 1 N Y N N N N 59.773 60.398 56.154 1.373 -2.109 -2.355 HO2 GMH 24
GMH HO3 HO3 H 0 1 N Y N N N N 56.586 59.451 57.354 -1.085 0.352 -3.782 HO3 GMH 25
GMH HO4 HO4 H 0 1 N Y N N N N 57.049 61.054 60.293 -2.874 0.741 -0.936 HO4 GMH 26
GMH HO6 HO6 H 0 1 N Y N N N N 59.798 63.315 61.428 -0.132 -1.843 1.755 HO6 GMH 27
GMH HO7 HO7 H 0 1 N Y N N N N 58.209 66.140 61.871 0.750 0.181 4.874 HO7 GMH 28
#
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
GMH C1 C2 SING N N 1
GMH C1 O1 SING N N 2
GMH C1 O5 SING N N 3
GMH C1 H1 SING N N 4
GMH C2 C3 SING N N 5
GMH C2 O2 SING N N 6
GMH C2 H2 SING N N 7
GMH C3 C4 SING N N 8
GMH C3 O3 SING N N 9
GMH C3 H3 SING N N 10
GMH C4 C5 SING N N 11
GMH C4 O4 SING N N 12
GMH C4 H4 SING N N 13
GMH C5 C6 SING N N 14
GMH C5 O5 SING N N 15
GMH C5 H5 SING N N 16
GMH C6 C7 SING N N 17
GMH C6 O6 SING N N 18
GMH C6 H6 SING N N 19
GMH C7 O7 SING N N 20
GMH C7 H71 SING N N 21
GMH C7 H72 SING N N 22
GMH O1 HO1 SING N N 23
GMH O2 HO2 SING N N 24
GMH O3 HO3 SING N N 25
GMH O4 HO4 SING N N 26
GMH O6 HO6 SING N N 27
GMH O7 HO7 SING N N 28
#
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
GMH SMILES ACDLabs 10.04 OC1C(O)C(OC(O)C1O)C(O)CO
GMH SMILES_CANONICAL CACTVS 3.341 OC[C@H](O)[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
GMH SMILES CACTVS 3.341 OC[CH](O)[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
GMH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O)O
GMH SMILES "OpenEye OEToolkits" 1.5.0 C(C(C1C(C(C(C(O1)O)O)O)O)O)O
GMH InChI InChI 1.03 InChI=1S/C7H14O7/c8-1-2(9)6-4(11)3(10)5(12)7(13)14-6/h2-13H,1H2/t2-,3-,4-,5-,6+,7-/m0/s1
GMH InChIKey InChI 1.03 BGWQRWREUZVRGI-QQABCQGCSA-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
GMH "SYSTEMATIC NAME" ACDLabs 10.04 L-glycero-alpha-D-manno-heptopyranose
GMH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2S,3S,4S,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]oxane-2,3,4,5-tetrol
GMH "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 LDmanHep
GMH "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 L-gro-a-D-manHepp
#
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
GMH "CARBOHYDRATE ISOMER" D PDB ?
GMH "CARBOHYDRATE RING" pyranose PDB ?
GMH "CARBOHYDRATE ANOMER" alpha PDB ?
GMH "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
GMH 'Create component' 1999-07-08 EBI
GMH 'Modify descriptor' 2011-06-04 RCSB
GMH 'Other modification' 2019-08-12 RCSB
GMH 'Other modification' 2019-12-19 RCSB
GMH 'Other modification' 2020-07-03 RCSB
GMH 'Modify name' 2020-07-17 RCSB
GMH 'Modify synonyms' 2020-07-17 RCSB
GMH 'Modify linking type' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id GMH
_pdbe_chem_comp_drugbank_details.drugbank_id DB04526
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name L-Glycero-D-Manno-Heptopyranose
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
GMH L-glycero-alpha-D-manno-heptose wwPDB ?
GMH L-glycero-D-manno-heptose wwPDB ?
GMH L-glycero-manno-heptose wwPDB ?
GMH L-GLYCERO-D-MANNO-HEPTOPYRANOSE wwPDB ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GMH
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04526
_pdbe_chem_comp_drugbank_classification.parent Monosaccharides
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as monosaccharides. These are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.'
#
_pdbe_chem_comp_drugbank_targets.comp_id GMH
_pdbe_chem_comp_drugbank_targets.drugbank_id DB04526
_pdbe_chem_comp_drugbank_targets.name 'Ferrichrome-iron receptor'
_pdbe_chem_comp_drugbank_targets.organism 'Escherichia coli (strain K12)'
_pdbe_chem_comp_drugbank_targets.uniprot_id P06971
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
GMH C1 C 9.002 0.142 1
GMH C2 C 9.002 -1.357 2
GMH C3 C 7.702 -2.107 3
GMH C4 C 6.404 -1.357 4
GMH C5 C 6.404 0.142 5
GMH C6 C 5.104 0.892 6
GMH C7 C 5.104 2.393 7
GMH O1 O 10.301 0.892 8
GMH O2 O 10.301 -2.107 9
GMH O3 O 7.702 -3.607 10
GMH O4 O 5.104 -2.107 11
GMH O5 O 7.702 0.892 12
GMH O6 O 3.805 0.142 13
GMH O7 O 3.805 3.143 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
GMH C1 C2 SINGLE NONE 1
GMH C1 O1 SINGLE BEGINDASH 2
GMH C1 O5 SINGLE NONE 3
GMH C2 C3 SINGLE NONE 4
GMH C2 O2 SINGLE BEGINWEDGE 5
GMH C3 C4 SINGLE NONE 6
GMH C3 O3 SINGLE BEGINWEDGE 7
GMH C4 C5 SINGLE NONE 8
GMH C4 O4 SINGLE BEGINDASH 9
GMH C5 C6 SINGLE NONE 10
GMH C5 O5 SINGLE BEGINWEDGE 11
GMH C6 C7 SINGLE NONE 12
GMH C6 O6 SINGLE BEGINWEDGE 13
GMH C7 O7 SINGLE NONE 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
GMH MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
GMH 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
GMH C1 S1 1
GMH C2 S1 1
GMH C3 S1 1
GMH C4 S1 1
GMH C5 S1 1
GMH O5 S1 1
GMH C4 F1 1
GMH C5 F1 1
GMH O5 F1 1
GMH C1 F1 1
GMH C2 F1 1
GMH C3 F1 1
GMH O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GMH
_pdbe_chem_comp_rdkit_properties.exactmw 210.074
_pdbe_chem_comp_rdkit_properties.amw 210.182
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_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 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 99.992
_pdbe_chem_comp_rdkit_properties.tpsa 130.610
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.860
_pdbe_chem_comp_rdkit_properties.CrippenMR 41.993
_pdbe_chem_comp_rdkit_properties.chi0v 6.358
_pdbe_chem_comp_rdkit_properties.chi1v 3.133
_pdbe_chem_comp_rdkit_properties.chi2v 1.298
_pdbe_chem_comp_rdkit_properties.chi3v 1.298
_pdbe_chem_comp_rdkit_properties.chi4v 0.680
_pdbe_chem_comp_rdkit_properties.chi0n 20.358
_pdbe_chem_comp_rdkit_properties.chi1n 9.582
_pdbe_chem_comp_rdkit_properties.chi2n 1.298
_pdbe_chem_comp_rdkit_properties.chi3n 1.298
_pdbe_chem_comp_rdkit_properties.chi4n 0.680
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.280
_pdbe_chem_comp_rdkit_properties.kappa1 2.889
_pdbe_chem_comp_rdkit_properties.kappa2 4.493
_pdbe_chem_comp_rdkit_properties.kappa3 2.036
_pdbe_chem_comp_rdkit_properties.Phi 0.927
#
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
GMH UniChem DrugBank DB04526
GMH UniChem PDBe GMH
GMH UniChem ChEBI 42976
GMH UniChem 'EPA CompTox Dashboard' DTXSID00156435
GMH UniChem 'Probes And Drugs' PD059226
GMH UniChem Nikkaji J3.516.224K
GMH UniChem SureChEMBL SCHEMBL7706601
GMH UniChem PubChem 125414
GMH UniChem ACTor 130272-67-2
#
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
GMH C1 -0.996 1.383 0.864 ETKDGv3 1
GMH C2 -2.136 0.342 0.692 ETKDGv3 2
GMH C3 -1.969 -0.418 -0.635 ETKDGv3 3
GMH C4 -0.574 -1.095 -0.695 ETKDGv3 4
GMH C5 0.471 -0.297 0.132 ETKDGv3 5
GMH C6 1.908 -0.534 -0.389 ETKDGv3 6
GMH C7 2.957 0.112 0.535 ETKDGv3 7
GMH O1 -0.661 1.504 2.222 ETKDGv3 8
GMH O2 -3.383 0.989 0.736 ETKDGv3 9
GMH O3 -2.116 0.482 -1.705 ETKDGv3 10
GMH O4 -0.653 -2.402 -0.186 ETKDGv3 11
GMH O5 0.167 1.087 0.097 ETKDGv3 12
GMH O6 2.056 -0.073 -1.710 ETKDGv3 13
GMH O7 4.252 -0.206 0.102 ETKDGv3 14
GMH H1 -1.376 2.367 0.505 ETKDGv3 15
GMH H2 -2.076 -0.398 1.526 ETKDGv3 16
GMH H3 -2.769 -1.194 -0.697 ETKDGv3 17
GMH H4 -0.250 -1.139 -1.761 ETKDGv3 18
GMH H5 0.446 -0.664 1.188 ETKDGv3 19
GMH H6 2.096 -1.631 -0.388 ETKDGv3 20
GMH H71 2.832 -0.281 1.567 ETKDGv3 21
GMH H72 2.820 1.217 0.578 ETKDGv3 22
GMH HO1 -0.015 2.254 2.286 ETKDGv3 23
GMH HO2 -4.067 0.284 0.879 ETKDGv3 24
GMH HO3 -2.307 -0.061 -2.514 ETKDGv3 25
GMH HO4 -1.075 -2.962 -0.890 ETKDGv3 26
GMH HO6 1.952 0.914 -1.702 ETKDGv3 27
GMH HO7 4.468 0.420 -0.638 ETKDGv3 28
#