data_6GP
#
_chem_comp.id 6GP
_chem_comp.name N-[methoxy(oxo)acetyl]-beta-D-glucopyranosylamine
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C9 H15 N O8"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;METHYL-N-(BETA-D-GLUCOPYRANOSYL)OXAMATE; N-[methoxy(oxo)acetyl]-beta-D-glucosylamine;
N-[methoxy(oxo)acetyl]-D-glucosylamine; N-[methoxy(oxo)acetyl]-glucosylamine
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-01-25
_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 265.217
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6GP
_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 2F3Q
_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 6GP METHYL-N-(BETA-D-GLUCOPYRANOSYL)OXAMATE PDB ?
2 6GP N-[methoxy(oxo)acetyl]-beta-D-glucosylamine PDB ?
3 6GP N-[methoxy(oxo)acetyl]-D-glucosylamine PDB ?
4 6GP N-[methoxy(oxo)acetyl]-glucosylamine 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
6GP C1 C1 C 0 1 N N R N N N 33.665 22.829 27.763 -0.259 0.271 0.092 C1 6GP 1
6GP C2 C2 C 0 1 N N R N N N 33.940 23.038 26.253 -1.064 1.532 -0.233 C2 6GP 2
6GP O2 O2 O 0 1 N N N N N N 34.080 24.441 25.938 -0.446 2.665 0.380 O2 6GP 3
6GP C3 C3 C 0 1 N N S N N N 32.751 22.460 25.447 -2.489 1.368 0.308 C3 6GP 4
6GP O3 O3 O 0 1 N N N N N N 32.971 22.611 24.035 -3.295 2.470 -0.114 O3 6GP 5
6GP C4 C4 C 0 1 N N S N N N 32.591 20.964 25.806 -3.074 0.062 -0.240 C4 6GP 6
6GP O4 O4 O 0 1 N N N N N N 31.481 20.400 25.093 -4.344 -0.187 0.366 O4 6GP 7
6GP C5 C5 C 0 1 N N R N N N 32.375 20.821 27.353 -2.118 -1.088 0.084 C5 6GP 8
6GP O5 O5 O 0 1 N N N N N N 33.500 21.413 28.067 -0.857 -0.859 -0.541 O5 6GP 9
6GP C6 C6 C 0 1 N N N N N N 32.261 19.333 27.757 -2.710 -2.401 -0.431 C6 6GP 10
6GP O6 O6 O 0 1 N N N N N N 33.334 18.556 27.179 -1.881 -3.491 -0.022 O6 6GP 11
6GP N1 N1 N 0 1 N N N N N N 34.802 23.348 28.524 1.114 0.431 -0.392 N1 6GP 12
6GP C7 C7 C 0 1 N N N N N N 34.649 24.012 29.689 2.140 -0.099 0.302 C7 6GP 13
6GP O7 O7 O 0 1 N N N N N N 33.545 24.205 30.166 1.926 -0.710 1.329 O7 6GP 14
6GP C8 C8 C 0 1 N N N N N N 35.891 24.496 30.339 3.541 0.064 -0.192 C8 6GP 15
6GP O8 O8 O 0 1 N N N N N N 35.787 25.451 31.106 3.754 0.675 -1.218 O8 6GP 16
6GP C9 C9 C 0 1 N N N N N N 38.047 23.836 31.228 5.926 -0.307 0.021 C9 6GP 17
6GP O9 O9 O 0 1 N N N N N N 37.122 23.967 30.123 4.565 -0.466 0.501 O9 6GP 18
6GP H1 H1 H 0 1 N N N N N N 32.740 23.359 28.034 -0.247 0.117 1.171 H1 6GP 19
6GP H2 H2 H 0 1 N N N N N N 34.878 22.526 25.992 -1.099 1.675 -1.313 H2 6GP 20
6GP HO2 HO2 H 0 1 N Y N N N N 34.111 24.945 26.743 0.446 2.730 0.011 HO2 6GP 21
6GP H3 H3 H 0 1 N N N N N N 31.833 23.009 25.705 -2.465 1.329 1.397 H3 6GP 22
6GP HO3 HO3 H 0 1 N Y N N N N 32.135 22.644 23.586 -2.891 3.268 0.252 HO3 6GP 23
6GP H4 H4 H 0 1 N N N N N N 33.502 20.420 25.516 -3.195 0.142 -1.320 H4 6GP 24
6GP HO4 HO4 H 0 1 N Y N N N N 30.752 20.275 25.689 -4.914 0.560 0.137 HO4 6GP 25
6GP H5 H5 H 0 1 N N N N N N 31.442 21.341 27.616 -1.980 -1.151 1.164 H5 6GP 26
6GP H61 H61 H 0 1 N N N N N N 31.303 18.940 27.385 -3.712 -2.533 -0.021 H61 6GP 27
6GP H62 H62 H 0 1 N N N N N N 32.313 19.255 28.853 -2.763 -2.373 -1.519 H62 6GP 28
6GP HO6 HO6 H 0 1 N Y N N N N 33.145 18.386 26.264 -2.289 -4.297 -0.366 HO6 6GP 29
6GP HN1 HN1 H 0 1 N N N N N N 35.726 23.206 28.168 1.285 0.920 -1.213 HN1 6GP 30
6GP H91 H91 H 0 1 N N N N N N 37.831 22.908 31.778 6.169 0.754 -0.038 H91 6GP 31
6GP H92 H92 H 0 1 N N N N N N 37.936 24.697 31.903 6.613 -0.799 0.709 H92 6GP 32
6GP H93 H93 H 0 1 N N N N N N 39.077 23.803 30.843 6.017 -0.756 -0.968 H93 6GP 33
#
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
6GP C1 C2 SING N N 1
6GP C1 O5 SING N N 2
6GP C1 N1 SING N N 3
6GP C1 H1 SING N N 4
6GP C2 O2 SING N N 5
6GP C2 C3 SING N N 6
6GP C2 H2 SING N N 7
6GP O2 HO2 SING N N 8
6GP C3 O3 SING N N 9
6GP C3 C4 SING N N 10
6GP C3 H3 SING N N 11
6GP O3 HO3 SING N N 12
6GP C4 O4 SING N N 13
6GP C4 C5 SING N N 14
6GP C4 H4 SING N N 15
6GP O4 HO4 SING N N 16
6GP C5 O5 SING N N 17
6GP C5 C6 SING N N 18
6GP C5 H5 SING N N 19
6GP C6 O6 SING N N 20
6GP C6 H61 SING N N 21
6GP C6 H62 SING N N 22
6GP O6 HO6 SING N N 23
6GP N1 C7 SING N N 24
6GP N1 HN1 SING N N 25
6GP C7 O7 DOUB N N 26
6GP C7 C8 SING N N 27
6GP C8 O8 DOUB N N 28
6GP C8 O9 SING N N 29
6GP C9 O9 SING N N 30
6GP C9 H91 SING N N 31
6GP C9 H92 SING N N 32
6GP C9 H93 SING N N 33
#
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
6GP SMILES ACDLabs 10.04 O=C(NC1OC(C(O)C(O)C1O)CO)C(=O)OC
6GP SMILES_CANONICAL CACTVS 3.341 COC(=O)C(=O)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
6GP SMILES CACTVS 3.341 COC(=O)C(=O)N[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
6GP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 COC(=O)C(=O)N[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
6GP SMILES "OpenEye OEToolkits" 1.5.0 COC(=O)C(=O)NC1C(C(C(C(O1)CO)O)O)O
6GP InChI InChI 1.03 InChI=1S/C9H15NO8/c1-17-9(16)7(15)10-8-6(14)5(13)4(12)3(2-11)18-8/h3-6,8,11-14H,2H2,1H3,(H,10,15)/t3-,4-,5+,6-,8-/m1/s1
6GP InChIKey InChI 1.03 OHCAXSUQOPLGLU-QOHYDMMQSA-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
6GP "SYSTEMATIC NAME" ACDLabs 10.04 N-[methoxy(oxo)acetyl]-beta-D-glucopyranosylamine
6GP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "methyl 2-oxo-2-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]amino]ethanoate"
#
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
6GP "CARBOHYDRATE ISOMER" D PDB ?
6GP "CARBOHYDRATE RING" pyranose PDB ?
6GP "CARBOHYDRATE ANOMER" beta PDB ?
6GP "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
6GP 'Create component' 2006-01-25 RCSB
6GP 'Modify descriptor' 2011-06-04 RCSB
6GP 'Other modification' 2020-07-03 RCSB
6GP 'Modify name' 2020-07-17 RCSB
6GP 'Modify synonyms' 2020-07-17 RCSB
6GP 'Modify internal type' 2020-07-17 RCSB
6GP 'Modify linking type' 2020-07-17 RCSB
6GP '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
6GP METHYL-N-(BETA-D-GLUCOPYRANOSYL)OXAMATE wwPDB ?
6GP 'N-[methoxy(oxo)acetyl]-beta-D-glucosylamine' wwPDB ?
6GP 'N-[methoxy(oxo)acetyl]-D-glucosylamine' wwPDB ?
6GP 'N-[methoxy(oxo)acetyl]-glucosylamine' wwPDB ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
6GP C1 C 7.702 -0.517 1
6GP C2 C 7.702 -2.018 2
6GP O2 O 9.002 -2.768 3
6GP C3 C 6.404 -2.768 4
6GP O3 O 6.404 -4.268 5
6GP C4 C 5.104 -2.018 6
6GP O4 O 3.805 -2.768 7
6GP C5 C 5.104 -0.517 8
6GP O5 O 6.404 0.233 9
6GP C6 C 3.805 0.233 10
6GP O6 O 3.805 1.732 11
6GP N1 N 9.002 0.233 12
6GP C7 C 9.002 1.732 13
6GP O7 O 7.702 2.482 14
6GP C8 C 10.301 2.482 15
6GP O8 O 11.600 1.732 16
6GP C9 C 11.600 4.732 17
6GP O9 O 10.301 3.982 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
6GP C1 C2 SINGLE NONE 1
6GP C1 O5 SINGLE NONE 2
6GP C1 N1 SINGLE BEGINWEDGE 3
6GP C2 O2 SINGLE BEGINDASH 4
6GP C2 C3 SINGLE NONE 5
6GP C3 O3 SINGLE BEGINWEDGE 6
6GP C3 C4 SINGLE NONE 7
6GP C4 O4 SINGLE BEGINDASH 8
6GP C4 C5 SINGLE NONE 9
6GP C5 O5 SINGLE NONE 10
6GP C5 C6 SINGLE BEGINWEDGE 11
6GP C6 O6 SINGLE NONE 12
6GP N1 C7 SINGLE NONE 13
6GP C7 O7 DOUBLE NONE 14
6GP C7 C8 SINGLE NONE 15
6GP C8 O8 DOUBLE NONE 16
6GP C8 O9 SINGLE NONE 17
6GP C9 O9 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
6GP MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
6GP amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
6GP peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
6GP C1 S1 1
6GP C2 S1 1
6GP C3 S1 1
6GP C4 S1 1
6GP C5 S1 1
6GP O5 S1 1
6GP N1 F1 1
6GP C7 F1 1
6GP O7 F1 1
6GP C8 F1 1
6GP O8 F2 1
6GP C8 F2 1
6GP C7 F2 1
6GP N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 6GP
_pdbe_chem_comp_rdkit_properties.exactmw 265.080
_pdbe_chem_comp_rdkit_properties.amw 265.218
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.778
_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 123.409
_pdbe_chem_comp_rdkit_properties.tpsa 145.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.924
_pdbe_chem_comp_rdkit_properties.CrippenMR 53.926
_pdbe_chem_comp_rdkit_properties.chi0v 8.213
_pdbe_chem_comp_rdkit_properties.chi1v 3.988
_pdbe_chem_comp_rdkit_properties.chi2v 1.575
_pdbe_chem_comp_rdkit_properties.chi3v 1.575
_pdbe_chem_comp_rdkit_properties.chi4v 0.815
_pdbe_chem_comp_rdkit_properties.chi0n 23.213
_pdbe_chem_comp_rdkit_properties.chi1n 11.069
_pdbe_chem_comp_rdkit_properties.chi2n 1.575
_pdbe_chem_comp_rdkit_properties.chi3n 1.575
_pdbe_chem_comp_rdkit_properties.chi4n 0.815
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.260
_pdbe_chem_comp_rdkit_properties.kappa1 4.117
_pdbe_chem_comp_rdkit_properties.kappa2 6.068
_pdbe_chem_comp_rdkit_properties.kappa3 2.945
_pdbe_chem_comp_rdkit_properties.Phi 1.388
#
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
6GP UniChem ZINC ZINC000016052003
6GP UniChem 'PubChem TPHARMA' 22421161
6GP UniChem PubChem 6852179
6GP UniChem BindingDb 50056274
6GP UniChem BRENDA 87903
#
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
6GP C1 -0.235 -1.301 -1.009 ETKDGv3 1
6GP C2 -1.092 -2.131 -0.006 ETKDGv3 2
6GP O2 -1.621 -3.275 -0.631 ETKDGv3 3
6GP C3 -2.231 -1.305 0.630 ETKDGv3 4
6GP O3 -2.487 -1.786 1.926 ETKDGv3 5
6GP C4 -1.839 0.178 0.681 ETKDGv3 6
6GP O4 -2.844 0.949 1.295 ETKDGv3 7
6GP C5 -1.545 0.691 -0.759 ETKDGv3 8
6GP O5 -0.992 -0.282 -1.646 ETKDGv3 9
6GP C6 -0.680 1.965 -0.753 ETKDGv3 10
6GP O6 -1.368 3.031 -0.155 ETKDGv3 11
6GP N1 0.974 -0.745 -0.385 ETKDGv3 12
6GP C7 2.026 -0.163 -1.171 ETKDGv3 13
6GP O7 1.935 -0.137 -2.429 ETKDGv3 14
6GP C8 3.210 0.417 -0.521 ETKDGv3 15
6GP O8 4.130 0.915 -1.227 ETKDGv3 16
6GP C9 4.425 0.970 1.562 ETKDGv3 17
6GP O9 3.310 0.417 0.873 ETKDGv3 18
6GP H1 0.106 -2.002 -1.802 ETKDGv3 19
6GP H2 -0.423 -2.495 0.805 ETKDGv3 20
6GP HO2 -2.149 -2.972 -1.416 ETKDGv3 21
6GP H3 -3.149 -1.406 0.002 ETKDGv3 22
6GP HO3 -3.412 -1.512 2.160 ETKDGv3 23
6GP H4 -0.924 0.272 1.307 ETKDGv3 24
6GP HO4 -3.685 0.816 0.784 ETKDGv3 25
6GP H5 -2.521 0.974 -1.212 ETKDGv3 26
6GP H61 0.257 1.794 -0.185 ETKDGv3 27
6GP H62 -0.394 2.232 -1.796 ETKDGv3 28
6GP HO6 -2.028 3.354 -0.823 ETKDGv3 29
6GP HN1 1.098 -0.804 0.650 ETKDGv3 30
6GP H91 5.355 0.439 1.269 ETKDGv3 31
6GP H92 4.519 2.051 1.327 ETKDGv3 32
6GP H93 4.273 0.852 2.655 ETKDGv3 33
#