data_CGF
#
_chem_comp.id CGF
_chem_comp.name "C-(1-AZIDO-ALPHA-D-GLUCOPYRANOSYL) FORMAMIDE"
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C7 H14 N4 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-04-25
_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 250.209
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CGF
_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 1P4G
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
CGF O5 O5 O 0 1 N N N N N N 33.623 21.306 27.844 0.108 -0.874 -0.771 O5 CGF 1
CGF C1 C1 C 0 1 N N S N N N 33.919 22.737 27.506 0.686 0.351 -0.325 C1 CGF 2
CGF C7 C7 C 0 1 N N R N N N 32.868 23.712 28.190 0.898 0.293 1.189 C7 CGF 3
CGF N7 N7 N 0 1 N N N N N N 32.630 23.574 29.466 1.620 1.494 1.629 N7 CGF 4
CGF O7 O7 O 0 1 N N N N N N 32.298 24.555 27.574 1.660 -0.870 1.519 O7 CGF 5
CGF N1 N1 N 0 1 N N N N N N 35.198 23.137 28.086 1.976 0.551 -0.990 N1 CGF 6
CGF N2 N2 N 1 1 N N N N N N 35.425 23.041 29.257 2.799 -0.203 -0.859 N2 CGF 7
CGF N3 N3 N -1 1 N N N N N N 35.623 22.908 30.417 3.621 -0.958 -0.728 N3 CGF 8
CGF C2 C2 C 0 1 N N R N N N 34.095 22.962 25.957 -0.246 1.517 -0.664 C2 CGF 9
CGF O2 O2 O 0 1 N N N N N N 34.374 24.322 25.641 0.349 2.745 -0.241 O2 CGF 10
CGF C3 C3 C 0 1 N N S N N N 32.777 22.469 25.225 -1.581 1.316 0.062 C3 CGF 11
CGF O3 O3 O 0 1 N N N N N N 32.915 22.652 23.788 -2.514 2.313 -0.360 O3 CGF 12
CGF C4 C4 C 0 1 N N S N N N 32.525 20.957 25.624 -2.124 -0.075 -0.285 C4 CGF 13
CGF O4 O4 O 0 1 N N N N N N 31.336 20.543 24.948 -3.291 -0.343 0.495 O4 CGF 14
CGF C5 C5 C 0 1 N N R N N N 32.378 20.839 27.243 -1.050 -1.120 0.025 C5 CGF 15
CGF C6 C6 C 0 1 N N N N N N 32.151 19.373 27.690 -1.595 -2.515 -0.287 C6 CGF 16
CGF O6 O6 O 0 1 N N N N N N 33.206 18.586 27.133 -0.642 -3.500 0.117 O6 CGF 17
CGF H7 H7 H 0 1 N N N N N N 32.862 24.102 27.145 -0.070 0.247 1.690 H7 CGF 18
CGF HN71 HN71 H 0 0 N N N N N N 31.955 24.200 29.905 1.737 1.413 2.628 HN71 CGF 19
CGF HN72 HN72 H 0 0 N N N N N N 33.512 23.627 29.975 2.543 1.442 1.224 HN72 CGF 20
CGF HO7 HO7 H 0 1 N N N N N N 31.669 25.138 27.983 2.548 -0.733 1.159 HO7 CGF 21
CGF H2 H2 H 0 1 N N N N N N 34.973 22.372 25.604 -0.417 1.546 -1.740 H2 CGF 22
CGF HO2 HO2 H 0 1 N N N N N N 34.480 24.457 24.706 -0.274 3.450 -0.467 HO2 CGF 23
CGF H3 H3 H 0 1 N N N N N N 31.891 23.067 25.541 -1.427 1.391 1.138 H3 CGF 24
CGF HO3 HO3 H 0 1 N N N N N N 32.125 22.356 23.349 -3.340 2.141 0.113 HO3 CGF 25
CGF H4 H4 H 0 1 N N N N N N 33.373 20.298 25.325 -2.376 -0.114 -1.345 H4 CGF 26
CGF HO4 HO4 H 0 1 N N N N N N 31.421 20.611 24.004 -3.593 -1.228 0.250 HO4 CGF 27
CGF H5 H5 H 0 1 N N N N N N 31.501 21.448 27.565 -0.783 -1.063 1.081 H5 CGF 28
CGF H61 H61 H 0 1 N N N N N N 31.137 18.990 27.426 -2.528 -2.670 0.254 H61 CGF 29
CGF H62 H62 H 0 1 N N N N N N 32.064 19.264 28.796 -1.777 -2.603 -1.358 H62 CGF 30
CGF HO6 HO6 H 0 1 N N N N N N 33.066 17.687 27.407 -1.023 -4.363 -0.097 HO6 CGF 31
#
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
CGF O5 C1 SING N N 1
CGF O5 C5 SING N N 2
CGF C1 C7 SING N N 3
CGF C1 N1 SING N N 4
CGF C1 C2 SING N N 5
CGF C7 N7 SING N N 6
CGF C7 O7 SING N N 7
CGF C7 H7 SING N N 8
CGF N7 HN71 SING N N 9
CGF N7 HN72 SING N N 10
CGF O7 HO7 SING N N 11
CGF N1 N2 DOUB N N 12
CGF N2 N3 DOUB N N 13
CGF C2 O2 SING N N 14
CGF C2 C3 SING N N 15
CGF C2 H2 SING N N 16
CGF O2 HO2 SING N N 17
CGF C3 O3 SING N N 18
CGF C3 C4 SING N N 19
CGF C3 H3 SING N N 20
CGF O3 HO3 SING N N 21
CGF C4 O4 SING N N 22
CGF C4 C5 SING N N 23
CGF C4 H4 SING N N 24
CGF O4 HO4 SING N N 25
CGF C5 C6 SING N N 26
CGF C5 H5 SING N N 27
CGF C6 O6 SING N N 28
CGF C6 H61 SING N N 29
CGF C6 H62 SING N N 30
CGF O6 HO6 SING N N 31
#
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
CGF SMILES ACDLabs 10.04 "[N-]=[N+]=N/C1(OC(C(O)C(O)C1O)CO)C(O)N"
CGF SMILES_CANONICAL CACTVS 3.341 N[C@H](O)[C@]1(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)N=[N+]=[N-]
CGF SMILES CACTVS 3.341 N[CH](O)[C]1(O[CH](CO)[CH](O)[CH](O)[CH]1O)N=[N+]=[N-]
CGF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]1[C@H]([C@@H]([C@H]([C@](O1)(C(N)O)N=[N+]=[N-])O)O)O)O
CGF SMILES "OpenEye OEToolkits" 1.5.0 C(C1C(C(C(C(O1)(C(N)O)N=[N+]=[N-])O)O)O)O
CGF InChI InChI 1.03 InChI=1S/C7H14N4O6/c8-6(16)7(10-11-9)5(15)4(14)3(13)2(1-12)17-7/h2-6,12-16H,1,8H2/t2-,3-,4+,5-,6?,7+/m1/s1
CGF InChIKey InChI 1.03 LAKOUYZWWLMCSL-JBFGQTLDSA-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
CGF "SYSTEMATIC NAME" ACDLabs 10.04
;(2S,3R,4S,5S,6R)-2-[(R)-amino(hydroxy)methyl]-2-azido-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol (non-preferred
name)
;
CGF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2S,3R,4S,5S,6R)-2-(amino-hydroxy-methyl)-2-azido-6-(hydroxymethyl)oxane-3,4,5-triol
#
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
CGF "CARBOHYDRATE ISOMER" D PDB ?
CGF "CARBOHYDRATE RING" pyranose PDB ?
CGF "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
CGF 'Create component' 2003-04-25 RCSB
CGF 'Modify descriptor' 2011-06-04 RCSB
CGF 'Other modification' 2020-07-03 RCSB
CGF 'Modify linking type' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id CGF
_pdbe_chem_comp_drugbank_details.drugbank_id DB03286
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'C-(1-Azido-Alpha-D-Glucopyranosyl) Formamide'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id CGF
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03286
_pdbe_chem_comp_drugbank_classification.parent 'C-glycosyl compounds'
_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 c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond.'
#
_pdbe_chem_comp_drugbank_targets.comp_id CGF
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03286
_pdbe_chem_comp_drugbank_targets.name 'Glycogen phosphorylase, muscle form'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P11217
_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
CGF O5 O 7.702 -0.031 1
CGF C1 C 6.404 -0.781 2
CGF C7 C 5.654 -2.080 3
CGF N7 N 4.154 -2.080 4
CGF O7 O 6.404 -3.379 5
CGF N1 N 7.154 -2.080 6
CGF N2 N 8.653 -2.080 7
CGF N3 N 10.153 -2.080 8
CGF C2 C 5.104 -0.031 9
CGF O2 O 3.805 -0.781 10
CGF C3 C 5.104 1.469 11
CGF O3 O 3.805 2.219 12
CGF C4 C 6.404 2.219 13
CGF O4 O 6.404 3.719 14
CGF C5 C 7.702 1.469 15
CGF C6 C 9.002 2.219 16
CGF O6 O 10.301 1.469 17
#
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
CGF O5 C1 SINGLE NONE 1
CGF O5 C5 SINGLE NONE 2
CGF C1 C7 SINGLE BEGINDASH 3
CGF C1 N1 SINGLE NONE 4
CGF C1 C2 SINGLE NONE 5
CGF C7 N7 SINGLE NONE 6
CGF C7 O7 SINGLE NONE 7
CGF N1 N2 DOUBLE NONE 8
CGF N2 N3 DOUBLE NONE 9
CGF C2 O2 SINGLE BEGINDASH 10
CGF C2 C3 SINGLE NONE 11
CGF C3 O3 SINGLE BEGINWEDGE 12
CGF C3 C4 SINGLE NONE 13
CGF C4 O4 SINGLE BEGINDASH 14
CGF C4 C5 SINGLE NONE 15
CGF C5 C6 SINGLE BEGINWEDGE 16
CGF C6 O6 SINGLE NONE 17
#
_pdbe_chem_comp_substructure.comp_id CGF
_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 C1CCOCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2
_pdbe_chem_comp_substructure.substructure_inchikeys DHXVGJBLRPWPCS-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
CGF O5 S1 1
CGF C1 S1 1
CGF C2 S1 1
CGF C3 S1 1
CGF C4 S1 1
CGF C5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CGF
_pdbe_chem_comp_rdkit_properties.exactmw 250.091
_pdbe_chem_comp_rdkit_properties.amw 250.211
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_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 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.labuteASA 115.700
_pdbe_chem_comp_rdkit_properties.tpsa 185.160
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.256
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.050
_pdbe_chem_comp_rdkit_properties.chi0v 7.738
_pdbe_chem_comp_rdkit_properties.chi1v 3.776
_pdbe_chem_comp_rdkit_properties.chi2v 1.744
_pdbe_chem_comp_rdkit_properties.chi3v 1.744
_pdbe_chem_comp_rdkit_properties.chi4v 0.980
_pdbe_chem_comp_rdkit_properties.chi0n 21.738
_pdbe_chem_comp_rdkit_properties.chi1n 10.212
_pdbe_chem_comp_rdkit_properties.chi2n 1.744
_pdbe_chem_comp_rdkit_properties.chi3n 1.744
_pdbe_chem_comp_rdkit_properties.chi4n 0.980
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.970
_pdbe_chem_comp_rdkit_properties.kappa1 4.016
_pdbe_chem_comp_rdkit_properties.kappa2 5.124
_pdbe_chem_comp_rdkit_properties.kappa3 2.204
_pdbe_chem_comp_rdkit_properties.Phi 1.210
#
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
CGF UniChem DrugBank DB03286
CGF UniChem PDBe CGF
CGF UniChem PubChem 131704237
CGF UniChem 'Probes And Drugs' PD059816
#
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
CGF O5 0.255 0.023 1.134 ETKDGv3 1
CGF C1 1.054 -0.324 -0.001 ETKDGv3 2
CGF C7 2.036 0.847 -0.315 ETKDGv3 3
CGF N7 2.981 1.028 0.790 ETKDGv3 4
CGF O7 1.339 2.046 -0.539 ETKDGv3 5
CGF N1 1.849 -1.489 0.408 ETKDGv3 6
CGF N2 2.712 -1.989 -0.318 ETKDGv3 7
CGF N3 3.572 -2.489 -1.041 ETKDGv3 8
CGF C2 0.201 -0.738 -1.260 ETKDGv3 9
CGF O2 -0.140 0.382 -2.040 ETKDGv3 10
CGF C3 -1.082 -1.460 -0.804 ETKDGv3 11
CGF O3 -0.753 -2.662 -0.153 ETKDGv3 12
CGF C4 -1.908 -0.568 0.156 ETKDGv3 13
CGF O4 -2.953 0.052 -0.550 ETKDGv3 14
CGF C5 -1.030 0.528 0.815 ETKDGv3 15
CGF C6 -1.672 1.057 2.107 ETKDGv3 16
CGF O6 -2.924 1.634 1.851 ETKDGv3 17
CGF H7 2.612 0.578 -1.233 ETKDGv3 18
CGF HN71 2.473 1.449 1.602 ETKDGv3 19
CGF HN72 3.706 1.721 0.493 ETKDGv3 20
CGF HO7 1.975 2.670 -0.976 ETKDGv3 21
CGF H2 0.794 -1.433 -1.900 ETKDGv3 22
CGF HO2 -0.446 0.042 -2.921 ETKDGv3 23
CGF H3 -1.700 -1.702 -1.701 ETKDGv3 24
CGF HO3 -0.460 -3.301 -0.855 ETKDGv3 25
CGF H4 -2.340 -1.213 0.959 ETKDGv3 26
CGF HO4 -3.661 -0.633 -0.678 ETKDGv3 27
CGF H5 -0.940 1.398 0.129 ETKDGv3 28
CGF H61 -0.998 1.806 2.581 ETKDGv3 29
CGF H62 -1.802 0.224 2.832 ETKDGv3 30
CGF HO6 -2.750 2.514 1.427 ETKDGv3 31
#