data_AGP
#
_chem_comp.id AGP
_chem_comp.name "2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H16 N O8 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 261.167
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AGP
_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 1MOS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
AGP C1 C1 C 0 1 N N N N N N 27.320 16.336 0.004 -0.552 0.086 -4.935 C1 AGP 1
AGP O1 O1 O 0 1 N N N N N N 26.933 15.368 0.979 0.160 0.618 -6.054 O1 AGP 2
AGP C2 C2 C 0 1 N N S N N N 27.270 15.766 -1.401 0.156 0.489 -3.641 C2 AGP 3
AGP N2 N2 N 0 1 N N N N N N 28.399 14.931 -1.604 1.525 -0.041 -3.646 N2 AGP 4
AGP C3 C3 C 0 1 N N R N N N 27.262 16.867 -2.445 -0.606 -0.080 -2.443 C3 AGP 5
AGP O3 O3 O 0 1 N N N N N N 26.112 17.702 -2.269 -0.648 -1.505 -2.539 O3 AGP 6
AGP C4 C4 C 0 1 N N S N N N 28.460 17.809 -2.368 0.101 0.323 -1.148 C4 AGP 7
AGP O4 O4 O 0 1 N N N N N N 28.285 18.655 -1.227 1.434 -0.192 -1.153 O4 AGP 8
AGP C5 C5 C 0 1 N N R N N N 28.440 18.792 -3.573 -0.661 -0.246 0.049 C5 AGP 9
AGP O5 O5 O 0 1 N N N N N N 28.734 18.080 -4.745 -1.994 0.270 0.054 O5 AGP 10
AGP C6 C6 C 0 1 N N N N N N 29.508 19.841 -3.394 0.046 0.157 1.343 C6 AGP 11
AGP O6 O6 O 0 1 N N N N N N 30.783 19.141 -3.494 -0.665 -0.374 2.462 O6 AGP 12
AGP P P P 0 1 N N N N N N 32.131 19.881 -3.074 0.130 0.086 3.783 P AGP 13
AGP O1P O1P O 0 1 N N N N N N 33.229 18.956 -3.276 0.173 1.564 3.842 O1P AGP 14
AGP O2P O2P O 0 1 N N N N N N 32.299 21.176 -3.812 -0.621 -0.481 5.088 O2P AGP 15
AGP O3P O3P O 0 1 N N N N N N 32.048 20.314 -1.638 1.632 -0.493 3.734 O3P AGP 16
AGP H11 1H1 H 0 1 N N N N N N 26.709 17.265 0.088 -0.583 -1.001 -5.008 H11 AGP 17
AGP H12 2H1 H 0 1 N N N N N N 28.322 16.766 0.233 -1.568 0.479 -4.931 H12 AGP 18
AGP HO1 HO1 H 0 1 N N N N N N 26.964 15.724 1.858 -0.317 0.341 -6.847 HO1 AGP 19
AGP H2 H2 H 0 1 N N N N N N 26.328 15.179 -1.509 0.187 1.576 -3.567 H2 AGP 20
AGP HN21 1HN2 H 0 0 N N N N N N 28.365 14.547 -2.548 1.447 -1.044 -3.714 HN21 AGP 21
AGP HN22 2HN2 H 0 0 N N N N N N 28.476 14.203 -0.893 1.956 0.275 -4.502 HN22 AGP 22
AGP H3 H3 H 0 1 N N N N N N 27.276 16.328 -3.421 -1.623 0.313 -2.439 H3 AGP 23
AGP HO3 HO3 H 0 1 N N N N N N 26.107 18.391 -2.922 0.268 -1.812 -2.539 HO3 AGP 24
AGP H4 H4 H 0 1 N N N N N N 29.391 17.196 -2.339 0.133 1.410 -1.075 H4 AGP 25
AGP HO4 HO4 H 0 1 N N N N N N 29.030 19.241 -1.179 1.360 -1.154 -1.219 HO4 AGP 26
AGP H5 H5 H 0 1 N N N N N N 27.435 19.271 -3.635 -0.693 -1.333 -0.024 H5 AGP 27
AGP HO5 HO5 H 0 1 N N N N N N 28.721 18.680 -5.481 -1.920 1.232 0.119 HO5 AGP 28
AGP H61 1H6 H 0 1 N N N N N N 29.414 20.696 -4.103 1.063 -0.236 1.339 H61 AGP 29
AGP H62 2H6 H 0 1 N N N N N N 29.397 20.431 -2.454 0.078 1.244 1.416 H62 AGP 30
AGP HOP2 2HOP H 0 0 N N N N N N 33.102 21.617 -3.561 -0.113 -0.183 5.855 HOP2 AGP 31
AGP HOP3 3HOP H 0 0 N N N N N N 32.851 20.755 -1.387 1.558 -1.456 3.696 HOP3 AGP 32
#
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
AGP C1 O1 SING N N 1
AGP C1 C2 SING N N 2
AGP C1 H11 SING N N 3
AGP C1 H12 SING N N 4
AGP O1 HO1 SING N N 5
AGP C2 N2 SING N N 6
AGP C2 C3 SING N N 7
AGP C2 H2 SING N N 8
AGP N2 HN21 SING N N 9
AGP N2 HN22 SING N N 10
AGP C3 O3 SING N N 11
AGP C3 C4 SING N N 12
AGP C3 H3 SING N N 13
AGP O3 HO3 SING N N 14
AGP C4 O4 SING N N 15
AGP C4 C5 SING N N 16
AGP C4 H4 SING N N 17
AGP O4 HO4 SING N N 18
AGP C5 O5 SING N N 19
AGP C5 C6 SING N N 20
AGP C5 H5 SING N N 21
AGP O5 HO5 SING N N 22
AGP C6 O6 SING N N 23
AGP C6 H61 SING N N 24
AGP C6 H62 SING N N 25
AGP O6 P SING N N 26
AGP P O1P DOUB N N 27
AGP P O2P SING N N 28
AGP P O3P SING N N 29
AGP O2P HOP2 SING N N 30
AGP O3P HOP3 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
AGP SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(O)C(O)C(N)CO
AGP SMILES_CANONICAL CACTVS 3.341 N[C@@H](CO)[C@@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O
AGP SMILES CACTVS 3.341 N[CH](CO)[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O
AGP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)N)O
AGP SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(C(C(COP(=O)(O)O)O)O)O)N)O
AGP InChI InChI 1.03 InChI=1S/C6H16NO8P/c7-3(1-8)5(10)6(11)4(9)2-15-16(12,13)14/h3-6,8-11H,1-2,7H2,(H2,12,13,14)/t3-,4+,5+,6+/m0/s1
AGP InChIKey InChI 1.03 LBNVXZROMBUNNQ-SLPGGIOYSA-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
AGP "SYSTEMATIC NAME" ACDLabs 10.04 2-amino-2-deoxy-6-O-phosphono-D-glucitol
AGP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5S)-5-amino-2,3,4,6-tetrahydroxy-hexyl] dihydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
AGP 'Create component' 1999-07-08 PDBJ
AGP 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id AGP
_pdbe_chem_comp_drugbank_details.drugbank_id DB02445
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '2-Deoxy-2-Amino Glucitol-6-Phosphate'
_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 AGP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02445
_pdbe_chem_comp_drugbank_classification.parent 'Monosaccharide phosphates'
_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 monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
AGP DB02445 'Glutamine--fructose-6-phosphate aminotransferase [isomerizing]' 'Escherichia coli (strain K12)' P17169 unknown 1
AGP DB02445 'Glucosamine-6-phosphate isomerase 1' Humans P46926 unknown 2
AGP DB02445 'Glucosamine-6-phosphate deaminase' 'Escherichia coli (strain K12)' P0A759 unknown 3
#
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
AGP C1 C 12.899 -1.268 1
AGP O1 O 14.198 -2.018 2
AGP C2 C 12.899 0.233 3
AGP N2 N 14.198 0.983 4
AGP C3 C 11.600 0.983 5
AGP O3 O 11.600 2.482 6
AGP C4 C 10.301 0.233 7
AGP O4 O 10.301 -1.268 8
AGP C5 C 9.002 0.983 9
AGP O5 O 9.002 2.482 10
AGP C6 C 7.702 0.233 11
AGP O6 O 6.404 0.983 12
AGP P P 5.104 0.233 13
AGP O1P O 3.805 -0.517 14
AGP O2P O 4.354 1.532 15
AGP O3P O 5.854 -1.067 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
AGP C1 O1 SINGLE NONE 1
AGP C1 C2 SINGLE NONE 2
AGP C2 N2 SINGLE BEGINWEDGE 3
AGP C2 C3 SINGLE NONE 4
AGP C3 O3 SINGLE BEGINDASH 5
AGP C3 C4 SINGLE NONE 6
AGP C4 O4 SINGLE BEGINDASH 7
AGP C4 C5 SINGLE NONE 8
AGP C5 O5 SINGLE BEGINWEDGE 9
AGP C5 C6 SINGLE NONE 10
AGP C6 O6 SINGLE NONE 11
AGP O6 P SINGLE NONE 12
AGP P O1P DOUBLE NONE 13
AGP P O2P SINGLE NONE 14
AGP P O3P SINGLE NONE 15
#
_pdbe_chem_comp_substructure.comp_id AGP
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-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
AGP O6 F1 1
AGP P F1 1
AGP O1P F1 1
AGP O2P F1 1
AGP O3P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id AGP
_pdbe_chem_comp_rdkit_properties.exactmw 261.061
_pdbe_chem_comp_rdkit_properties.amw 261.167
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 14
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_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 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_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 114.448
_pdbe_chem_comp_rdkit_properties.tpsa 173.700
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.502
_pdbe_chem_comp_rdkit_properties.CrippenMR 51.078
_pdbe_chem_comp_rdkit_properties.chi0v 8.055
_pdbe_chem_comp_rdkit_properties.chi1v 4.685
_pdbe_chem_comp_rdkit_properties.chi2v 1.289
_pdbe_chem_comp_rdkit_properties.chi3v 1.289
_pdbe_chem_comp_rdkit_properties.chi4v 0.595
_pdbe_chem_comp_rdkit_properties.chi0n 23.160
_pdbe_chem_comp_rdkit_properties.chi1n 10.568
_pdbe_chem_comp_rdkit_properties.chi2n 0.974
_pdbe_chem_comp_rdkit_properties.chi3n 0.974
_pdbe_chem_comp_rdkit_properties.chi4n 0.401
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.090
_pdbe_chem_comp_rdkit_properties.kappa1 3.702
_pdbe_chem_comp_rdkit_properties.kappa2 6.598
_pdbe_chem_comp_rdkit_properties.kappa3 5.848
_pdbe_chem_comp_rdkit_properties.Phi 1.527
#
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
AGP UniChem ChEMBL CHEMBL396380
AGP UniChem DrugBank DB02445
AGP UniChem PDBe AGP
AGP UniChem ZINC ZINC000003870803
AGP UniChem SureChEMBL SCHEMBL2847976
AGP UniChem 'PubChem TPHARMA' 15490684
AGP UniChem Nikkaji J711.082K
AGP UniChem BRENDA 114843
AGP UniChem BRENDA 11746
AGP UniChem BRENDA 18225
AGP UniChem BRENDA 19909
AGP UniChem BRENDA 4356
AGP UniChem 'Probes And Drugs' PD060047
AGP UniChem PubChem 446113
#
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
AGP C1 -4.039 -0.054 -0.011 ETKDGv3 1
AGP O1 -5.002 0.633 0.742 ETKDGv3 2
AGP C2 -2.618 0.421 0.359 ETKDGv3 3
AGP N2 -2.437 1.843 0.044 ETKDGv3 4
AGP C3 -1.544 -0.439 -0.354 ETKDGv3 5
AGP O3 -1.596 -0.211 -1.742 ETKDGv3 6
AGP C4 -0.116 -0.161 0.195 ETKDGv3 7
AGP O4 0.269 1.170 -0.053 ETKDGv3 8
AGP C5 0.941 -1.156 -0.368 ETKDGv3 9
AGP O5 0.540 -2.487 -0.148 ETKDGv3 10
AGP C6 2.337 -0.930 0.241 ETKDGv3 11
AGP O6 2.873 0.284 -0.232 ETKDGv3 12
AGP P 4.351 0.576 0.570 ETKDGv3 13
AGP O1P 4.099 0.840 2.038 ETKDGv3 14
AGP O2P 5.082 1.939 -0.116 ETKDGv3 15
AGP O3P 5.396 -0.747 0.393 ETKDGv3 16
AGP H11 -4.225 0.071 -1.103 ETKDGv3 17
AGP H12 -4.136 -1.137 0.218 ETKDGv3 18
AGP HO1 -5.246 1.446 0.227 ETKDGv3 19
AGP H2 -2.495 0.283 1.458 ETKDGv3 20
AGP HN21 -3.026 2.413 0.693 ETKDGv3 21
AGP HN22 -2.765 2.033 -0.931 ETKDGv3 22
AGP H3 -1.792 -1.505 -0.136 ETKDGv3 23
AGP HO3 -1.331 -1.057 -2.188 ETKDGv3 24
AGP H4 -0.148 -0.297 1.298 ETKDGv3 25
AGP HO4 0.348 1.284 -1.036 ETKDGv3 26
AGP H5 1.023 -1.011 -1.467 ETKDGv3 27
AGP HO5 0.467 -2.619 0.834 ETKDGv3 28
AGP H61 2.248 -0.934 1.352 ETKDGv3 29
AGP H62 2.988 -1.776 -0.076 ETKDGv3 30
AGP HOP2 4.393 2.649 -0.061 ETKDGv3 31
AGP HOP3 5.161 -1.363 1.132 ETKDGv3 32
#