data_04N
#
_chem_comp.id 04N
_chem_comp.name 2-amino-2-deoxy-4,6-O-(phenylmethylidene)-alpha-D-glucopyranose
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H17 N O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-07-26
_chem_comp.pdbx_modified_date 2014-09-05
_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 267.278
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 04N
_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 4B3M
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
04N C1 C1 C 0 1 N N S N N N 190.377 87.889 -10.827 -3.595 -0.708 -0.222 C1 04N 1
04N O1 O1 O 0 1 N N N N N N 191.388 88.875 -10.570 -3.541 -0.567 -1.643 O1 04N 2
04N C2 C2 C 0 1 N N R N N N 189.043 88.300 -10.140 -3.362 0.655 0.433 C2 04N 3
04N N2 N2 N 0 1 N N N N N N 188.602 89.636 -10.583 -4.348 1.617 -0.078 N2 04N 4
04N C3 C3 C 0 1 N N R N N N 189.207 88.266 -8.635 -1.948 1.151 0.106 C3 04N 5
04N O3 O3 O 0 1 N N N N N N 187.968 88.614 -8.003 -1.699 2.379 0.792 O3 04N 6
04N C4 C4 C 0 1 N N S N N N 189.665 86.882 -8.203 -0.946 0.092 0.566 C4 04N 7
04N O4 O4 O 0 1 N N N N N N 189.830 86.828 -6.775 0.391 0.472 0.240 O4 04N 8
04N C5 C5 C 0 1 N N R N N N 190.985 86.548 -8.902 -1.266 -1.228 -0.147 C5 04N 9
04N O5 O5 O 0 1 N N N N N N 190.823 86.586 -10.362 -2.588 -1.633 0.202 O5 04N 10
04N C6 C6 C 0 1 N N N N N N 191.437 85.165 -8.447 -0.235 -2.273 0.284 C6 04N 11
04N O6 O6 O 0 1 N N N N N N 191.558 85.144 -6.999 1.072 -1.759 0.001 O6 04N 12
04N CAL CAL C 0 1 Y N N N N N 190.589 85.371 -2.131 5.248 0.803 -0.571 CAL 04N 13
04N CAM CAM C 0 1 Y N N N N N 191.303 86.361 -2.864 5.097 -0.405 0.083 CAM 04N 14
04N CAN CAN C 0 1 Y N N N N N 189.785 84.428 -2.807 4.141 1.589 -0.836 CAN 04N 15
04N CAO CAO C 0 1 Y N N N N N 191.208 86.406 -4.270 3.839 -0.830 0.470 CAO 04N 16
04N CAP CAP C 0 1 Y N N N N N 189.686 84.470 -4.219 2.884 1.164 -0.449 CAP 04N 17
04N CBC CBC C 0 1 Y N N N N N 190.396 85.457 -4.958 2.733 -0.045 0.204 CBC 04N 18
04N CBP CBP C 0 1 N N R N N N 190.272 85.487 -6.361 1.362 -0.508 0.625 CBP 04N 19
04N H1 H1 H 0 1 N N N N N N 190.191 87.836 -11.910 -4.576 -1.085 0.067 H1 04N 20
04N H2 H2 H 0 1 N N N N N N 188.278 87.562 -10.422 -3.472 0.562 1.513 H2 04N 21
04N HN2 HN2 H 0 1 N N N N N N 187.745 89.873 -10.126 -5.288 1.315 0.128 HN2 04N 22
04N HN2A HN2A H 0 0 N N N N N N 189.301 90.312 -10.350 -4.176 2.541 0.290 HN2A 04N 23
04N H3 H3 H 0 1 N N N N N N 189.982 88.993 -8.352 -1.854 1.306 -0.969 H3 04N 24
04N HO3 HO3 H 0 1 N N N N N N 188.076 88.591 -7.059 -2.310 3.091 0.559 HO3 04N 25
04N H4 H4 H 0 1 N N N N N N 188.908 86.148 -8.517 -1.032 -0.046 1.643 H4 04N 26
04N H5 H5 H 0 1 N N N N N N 191.742 87.286 -8.597 -1.204 -1.083 -1.225 H5 04N 27
04N H6 H6 H 0 1 N N N N N N 190.697 84.415 -8.763 -0.331 -2.464 1.353 H6 04N 28
04N H6A H6A H 0 1 N N N N N N 192.412 84.931 -8.899 -0.395 -3.197 -0.271 H6A 04N 29
04N HAL HAL H 0 1 N N N N N N 190.663 85.341 -1.054 6.231 1.137 -0.870 HAL 04N 30
04N HAM HAM H 0 1 N N N N N N 191.918 87.079 -2.342 5.961 -1.019 0.289 HAM 04N 31
04N HAN HAN H 0 1 N N N N N N 189.247 83.676 -2.249 4.259 2.533 -1.347 HAN 04N 32
04N HAO HAO H 0 1 N N N N N N 191.749 87.158 -4.825 3.722 -1.774 0.980 HAO 04N 33
04N HAP HAP H 0 1 N N N N N N 189.069 83.750 -4.737 2.020 1.777 -0.657 HAP 04N 34
04N HBP HBP H 0 1 N N N N N N 189.516 84.754 -6.679 1.341 -0.630 1.708 HBP 04N 35
04N H7 H7 H 0 1 N Y N N N N 192.198 88.616 -10.993 -3.680 -1.393 -2.126 H7 04N 36
#
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
04N C1 O1 SING N N 1
04N C1 C2 SING N N 2
04N C1 O5 SING N N 3
04N C2 N2 SING N N 4
04N C2 C3 SING N N 5
04N C3 O3 SING N N 6
04N C3 C4 SING N N 7
04N C4 O4 SING N N 8
04N C4 C5 SING N N 9
04N O4 CBP SING N N 10
04N C5 O5 SING N N 11
04N C5 C6 SING N N 12
04N C6 O6 SING N N 13
04N O6 CBP SING N N 14
04N CAL CAM DOUB Y N 15
04N CAL CAN SING Y N 16
04N CAM CAO SING Y N 17
04N CAN CAP DOUB Y N 18
04N CAO CBC DOUB Y N 19
04N CAP CBC SING Y N 20
04N CBC CBP SING N N 21
04N C1 H1 SING N N 22
04N C2 H2 SING N N 23
04N N2 HN2 SING N N 24
04N N2 HN2A SING N N 25
04N C3 H3 SING N N 26
04N O3 HO3 SING N N 27
04N C4 H4 SING N N 28
04N C5 H5 SING N N 29
04N C6 H6 SING N N 30
04N C6 H6A SING N N 31
04N CAL HAL SING N N 32
04N CAM HAM SING N N 33
04N CAN HAN SING N N 34
04N CAO HAO SING N N 35
04N CAP HAP SING N N 36
04N CBP HBP SING N N 37
04N O1 H7 SING N N 38
#
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
04N SMILES ACDLabs 12.01 O1C(O)C(N)C(O)C2OC(OCC12)c3ccccc3
04N InChI InChI 1.03 InChI=1S/C13H17NO5/c14-9-10(15)11-8(18-12(9)16)6-17-13(19-11)7-4-2-1-3-5-7/h1-5,8-13,15-16H,6,14H2/t8-,9-,10-,11-,12+,13-/m1/s1
04N InChIKey InChI 1.03 BIHZUORUPXZYTO-WXCVZDNMSA-N
04N SMILES_CANONICAL CACTVS 3.385 N[C@H]1[C@@H](O)O[C@@H]2CO[C@H](O[C@H]2[C@@H]1O)c3ccccc3
04N SMILES CACTVS 3.385 N[CH]1[CH](O)O[CH]2CO[CH](O[CH]2[CH]1O)c3ccccc3
04N SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1ccc(cc1)[C@@H]2OC[C@@H]3[C@@H](O2)[C@@H]([C@H]([C@H](O3)O)N)O
04N SMILES "OpenEye OEToolkits" 1.9.2 c1ccc(cc1)C2OCC3C(O2)C(C(C(O3)O)N)O
#
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
04N "SYSTEMATIC NAME" ACDLabs 12.01 2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranose
04N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (2R,4aR,6S,7R,8R,8aS)-7-azanyl-2-phenyl-4,4a,6,7,8,8a-hexahydropyrano[3,2-d][1,3]dioxine-6,8-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
04N 'Create component' 2012-07-26 EBI
04N 'Initial release' 2013-08-07 RCSB
04N 'Modify descriptor' 2014-09-05 RCSB
#
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
04N C1 C 3.759 -1.622 1
04N O1 O 5.057 -2.372 2
04N C2 C 3.760 -0.122 3
04N N2 N 5.060 0.628 4
04N C3 C 2.462 0.630 5
04N O3 O 2.463 2.130 6
04N C4 C 1.162 -0.119 7
04N O4 O -0.136 0.632 8
04N C5 C 1.161 -1.619 9
04N O5 O 2.459 -2.370 10
04N C6 C -0.139 -2.368 11
04N O6 O -1.437 -1.617 12
04N CAL C -5.331 2.136 13
04N CAM C -5.332 0.636 14
04N CAN C -4.031 2.885 15
04N CAO C -4.034 -0.115 16
04N CAP C -2.733 2.134 17
04N CBC C -2.734 0.634 18
04N CBP C -1.436 -0.117 19
#
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
04N C1 O1 SINGLE BEGINWEDGE 1
04N C1 C2 SINGLE NONE 2
04N C1 O5 SINGLE NONE 3
04N C2 N2 SINGLE BEGINWEDGE 4
04N C2 C3 SINGLE NONE 5
04N C3 O3 SINGLE BEGINDASH 6
04N C3 C4 SINGLE NONE 7
04N C4 O4 SINGLE NONE 8
04N C4 C5 SINGLE NONE 9
04N O4 CBP SINGLE NONE 10
04N C5 O5 SINGLE NONE 11
04N C5 C6 SINGLE NONE 12
04N C6 O6 SINGLE NONE 13
04N O6 CBP SINGLE NONE 14
04N CAL CAM DOUBLE NONE 15
04N CAL CAN SINGLE NONE 16
04N CAM CAO SINGLE NONE 17
04N CAN CAP DOUBLE NONE 18
04N CAO CBC DOUBLE NONE 19
04N CAP CBC SINGLE NONE 20
04N CBP CBC SINGLE BEGINWEDGE 21
#
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
04N MurckoScaffold S1 scaffold 'c1ccc([C@@H]2OC[C@H]3OCCC[C@@H]3O2)cc1' InChI=1S/C13H16O3/c1-2-5-10(6-3-1)13-15-9-12-11(16-13)7-4-8-14-12/h1-3,5-6,11-13H,4,7-9H2/t11-,12+,13+/m0/s1 RWAOABYFTHPWDP-YNEHKIRRSA-N
04N phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
04N pyranose F2 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
04N C1 S1 1
04N C2 S1 1
04N C3 S1 1
04N C4 S1 1
04N O4 S1 1
04N C5 S1 1
04N O5 S1 1
04N C6 S1 1
04N O6 S1 1
04N CAL S1 1
04N CAM S1 1
04N CAN S1 1
04N CAO S1 1
04N CAP S1 1
04N CBC S1 1
04N CBP S1 1
04N CAL F1 1
04N CAM F1 1
04N CAO F1 1
04N CBC F1 1
04N CAP F1 1
04N CAN F1 1
04N C4 F2 1
04N C5 F2 1
04N O5 F2 1
04N C1 F2 1
04N C2 F2 1
04N C3 F2 1
04N O1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 04N
_pdbe_chem_comp_rdkit_properties.exactmw 267.111
_pdbe_chem_comp_rdkit_properties.amw 267.281
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.538
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_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 134.417
_pdbe_chem_comp_rdkit_properties.tpsa 94.170
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.549
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.604
_pdbe_chem_comp_rdkit_properties.chi0v 8.988
_pdbe_chem_comp_rdkit_properties.chi1v 4.857
_pdbe_chem_comp_rdkit_properties.chi2v 2.151
_pdbe_chem_comp_rdkit_properties.chi3v 2.151
_pdbe_chem_comp_rdkit_properties.chi4v 1.311
_pdbe_chem_comp_rdkit_properties.chi0n 25.988
_pdbe_chem_comp_rdkit_properties.chi1n 13.068
_pdbe_chem_comp_rdkit_properties.chi2n 2.151
_pdbe_chem_comp_rdkit_properties.chi3n 2.151
_pdbe_chem_comp_rdkit_properties.chi4n 1.311
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.020
_pdbe_chem_comp_rdkit_properties.kappa1 3.791
_pdbe_chem_comp_rdkit_properties.kappa2 5.163
_pdbe_chem_comp_rdkit_properties.kappa3 2.384
_pdbe_chem_comp_rdkit_properties.Phi 1.030
#
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
04N UniChem PDBe 04N
04N UniChem ZINC ZINC000098207762
#
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
04N C1 -3.573 0.266 0.358 ETKDGv3 1
04N O1 -4.963 0.154 0.198 ETKDGv3 2
04N C2 -3.055 1.553 -0.344 ETKDGv3 3
04N N2 -3.477 1.575 -1.748 ETKDGv3 4
04N C3 -1.506 1.697 -0.214 ETKDGv3 5
04N O3 -1.185 2.766 0.639 ETKDGv3 6
04N C4 -0.874 0.412 0.342 ETKDGv3 7
04N O4 0.517 0.404 0.085 ETKDGv3 8
04N C5 -1.543 -0.802 -0.332 ETKDGv3 9
04N O5 -2.940 -0.932 -0.086 ETKDGv3 10
04N C6 -0.809 -2.051 0.151 ETKDGv3 11
04N O6 0.580 -1.927 -0.084 ETKDGv3 12
04N CAL 5.364 -0.625 -0.104 ETKDGv3 13
04N CAM 4.901 -0.747 1.145 ETKDGv3 14
04N CAN 4.419 -0.547 -1.237 ETKDGv3 15
04N CAO 3.445 -0.804 1.395 ETKDGv3 16
04N CAP 3.100 -0.599 -1.015 ETKDGv3 17
04N CBC 2.576 -0.733 0.369 ETKDGv3 18
04N CBP 1.089 -0.790 0.596 ETKDGv3 19
04N H1 -3.390 0.370 1.450 ETKDGv3 20
04N H2 -3.543 2.415 0.164 ETKDGv3 21
04N HN2 -2.969 0.833 -2.282 ETKDGv3 22
04N HN2A -3.212 2.498 -2.162 ETKDGv3 23
04N H3 -1.056 1.889 -1.217 ETKDGv3 24
04N HO3 -1.356 3.600 0.128 ETKDGv3 25
04N H4 -1.052 0.381 1.444 ETKDGv3 26
04N H5 -1.387 -0.733 -1.431 ETKDGv3 27
04N H6 -1.185 -2.931 -0.412 ETKDGv3 28
04N H6A -1.011 -2.238 1.231 ETKDGv3 29
04N HAL 6.429 -0.583 -0.288 ETKDGv3 30
04N HAM 5.592 -0.805 1.977 ETKDGv3 31
04N HAN 4.797 -0.449 -2.246 ETKDGv3 32
04N HAO 3.096 -0.904 2.416 ETKDGv3 33
04N HAP 2.414 -0.541 -1.851 ETKDGv3 34
04N HBP 0.896 -0.877 1.695 ETKDGv3 35
04N H7 -5.128 -0.193 -0.718 ETKDGv3 36
#