data_YKR
#

_chem_comp.id                                   YKR
_chem_comp.name                                 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranose
_chem_comp.type                                 "D-saccharide, alpha linking"
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C13 H19 N O5"
_chem_comp.mon_nstd_parent_comp_id              PA1
_chem_comp.pdbx_synonyms                        
;4-benzyl-alpha-D-glucosamine; 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucose; 2-amino-4-O-benzyl-2-deoxy-D-glucose;
2-amino-4-O-benzyl-2-deoxy-glucose
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2012-07-31
_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                       269.294
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YKR
_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       4B3S
_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  YKR  4-benzyl-alpha-D-glucosamine                PDB  ?  
2  YKR  2-amino-4-O-benzyl-2-deoxy-alpha-D-glucose  PDB  ?  
3  YKR  2-amino-4-O-benzyl-2-deoxy-D-glucose        PDB  ?  
4  YKR  2-amino-4-O-benzyl-2-deoxy-glucose          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.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
YKR  C1    C1    C  0  1  N  N  S  190.255  87.059  -11.126  -3.615  -0.031  -0.120  C1    YKR   1  
YKR  O1    O1    O  0  1  N  Y  N  190.932  88.324  -11.034  -3.604   0.024  -1.547  O1    YKR   2  
YKR  C2    C2    C  0  1  N  N  R  188.865  87.213  -10.475  -2.953   1.228   0.445  C2    YKR   3  
YKR  N2    N2    N  0  1  N  N  N  188.082  88.225  -11.188  -3.656   2.418  -0.051  N2    YKR   4  
YKR  C3    C3    C  0  1  N  N  R  189.037  87.614   -9.001  -1.490   1.273  -0.006  C3    YKR   5  
YKR  O3    O3    O  0  1  N  N  N  187.753  87.768   -8.372  -0.844   2.406   0.576  O3    YKR   6  
YKR  C4    C4    C  0  1  N  N  S  189.875  86.543   -8.274  -0.787  -0.009   0.451  C4    YKR   7  
YKR  O4    O4    O  0  1  N  N  N  190.075  86.925   -6.894   0.560  -0.012  -0.028  O4    YKR   8  
YKR  C5    C5    C  0  1  N  N  R  191.258  86.409   -9.007  -1.533  -1.221  -0.115  C5    YKR   9  
YKR  O5    O5    O  0  1  N  N  N  191.041  86.054  -10.423  -2.894  -1.184   0.318  O5    YKR  10  
YKR  C6    C6    C  0  1  N  N  N  192.133  85.326   -8.322  -0.872  -2.506   0.387  C6    YKR  11  
YKR  O6    O6    O  0  1  N  N  N  192.709  84.442   -9.290  -1.498  -3.635  -0.227  O6    YKR  12  
YKR  CAL   CAL   C  0  1  Y  N  N  189.193  86.691   -2.354   4.745   1.179  -0.906  CAL   YKR  13  
YKR  CAM   CAM   C  0  1  Y  N  N  188.958  86.378   -3.725   3.470   1.329  -0.395  CAM   YKR  14  
YKR  CAN   CAN   C  0  1  Y  N  N  190.536  86.777   -1.865   5.454   0.017  -0.665  CAN   YKR  15  
YKR  CAO   CAO   C  0  1  Y  N  N  190.059  86.147   -4.604   2.903   0.318   0.358  CAO   YKR  16  
YKR  CAP   CAP   C  0  1  Y  N  N  191.639  86.546   -2.746   4.887  -0.995   0.087  CAP   YKR  17  
YKR  CAU   CAU   C  0  1  N  N  N  189.847  85.852   -5.947   1.513   0.482   0.916  CAU   YKR  18  
YKR  CBC   CBC   C  0  1  Y  N  N  191.399  86.233   -4.112   3.612  -0.844   0.599  CBC   YKR  19  
YKR  H1    H1    H  0  1  N  N  N  190.126  86.769  -12.179  -4.645  -0.090   0.234  H1    YKR  20  
YKR  H2    H2    H  0  1  N  N  N  188.346  86.244  -10.519  -2.998   1.206   1.534  H2    YKR  21  
YKR  HN21  HN2   H  0  0  N  N  N  187.184  88.316  -10.758  -4.625   2.409   0.230  HN21  YKR  22  
YKR  HN22  HN2A  H  0  0  N  Y  N  188.560  89.103  -11.151  -3.199   3.263   0.256  HN22  YKR  23  
YKR  H3    H3    H  0  1  N  N  N  189.585  88.567   -8.963  -1.446   1.347  -1.093  H3    YKR  24  
YKR  HO3   HO3   H  0  1  N  Y  N  187.873  88.016   -7.463  -1.242   3.253   0.335  HO3   YKR  25  
YKR  H4    H4    H  0  1  N  N  N  189.351  85.578   -8.332  -0.786  -0.056   1.540  H4    YKR  26  
YKR  H5    H5    H  0  1  N  N  N  191.780  87.375   -8.944  -1.497  -1.194  -1.204  H5    YKR  27  
YKR  H61   H6    H  0  1  N  N  N  192.940  85.819   -7.760   0.187  -2.494   0.130  H61   YKR  28  
YKR  H62   H6A   H  0  1  N  N  N  191.507  84.743   -7.630  -0.982  -2.573   1.469  H62   YKR  29  
YKR  HO6   HO6   H  0  1  N  Y  N  193.239  83.789   -8.848  -1.129  -4.486   0.045  HO6   YKR  30  
YKR  HAL   HAL   H  0  1  N  N  N  188.361  86.863   -1.687   5.186   1.968  -1.498  HAL   YKR  31  
YKR  HAM   HAM   H  0  1  N  N  N  187.947  86.316   -4.099   2.916   2.237  -0.583  HAM   YKR  32  
YKR  HAN   HAN   H  0  1  N  N  N  190.717  87.017   -0.828   6.450  -0.101  -1.065  HAN   YKR  33  
YKR  HAP   HAP   H  0  1  N  N  N  192.651  86.609   -2.375   5.440  -1.903   0.274  HAP   YKR  34  
YKR  HAU   HAU   H  0  1  N  N  N  188.801  85.528   -6.056   1.321   1.537   1.108  HAU   YKR  35  
YKR  HAUA  HAUA  H  0  0  N  N  N  190.518  85.022   -6.216   1.426  -0.079   1.847  HAUA  YKR  36  
YKR  HBC   HBC   H  0  1  N  N  N  192.230  86.060   -4.779   3.169  -1.635   1.187  HBC   YKR  37  
YKR  HO1   H7    H  0  1  N  Y  N  191.793  88.253  -11.430  -4.009  -0.743  -1.974  HO1   YKR  38  
#   #
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
YKR  C1   O1    SING  N  N   1  
YKR  C1   C2    SING  N  N   2  
YKR  C1   O5    SING  N  N   3  
YKR  C2   N2    SING  N  N   4  
YKR  C2   C3    SING  N  N   5  
YKR  C3   O3    SING  N  N   6  
YKR  C3   C4    SING  N  N   7  
YKR  C4   O4    SING  N  N   8  
YKR  C4   C5    SING  N  N   9  
YKR  O4   CAU   SING  N  N  10  
YKR  C5   O5    SING  N  N  11  
YKR  C5   C6    SING  N  N  12  
YKR  C6   O6    SING  N  N  13  
YKR  CAL  CAM   DOUB  Y  N  14  
YKR  CAL  CAN   SING  Y  N  15  
YKR  CAM  CAO   SING  Y  N  16  
YKR  CAN  CAP   DOUB  Y  N  17  
YKR  CAO  CAU   SING  N  N  18  
YKR  CAO  CBC   DOUB  Y  N  19  
YKR  CAP  CBC   SING  Y  N  20  
YKR  C1   H1    SING  N  N  21  
YKR  C2   H2    SING  N  N  22  
YKR  N2   HN21  SING  N  N  23  
YKR  N2   HN22  SING  N  N  24  
YKR  C3   H3    SING  N  N  25  
YKR  O3   HO3   SING  N  N  26  
YKR  C4   H4    SING  N  N  27  
YKR  C5   H5    SING  N  N  28  
YKR  C6   H61   SING  N  N  29  
YKR  C6   H62   SING  N  N  30  
YKR  O6   HO6   SING  N  N  31  
YKR  CAL  HAL   SING  N  N  32  
YKR  CAM  HAM   SING  N  N  33  
YKR  CAN  HAN   SING  N  N  34  
YKR  CAP  HAP   SING  N  N  35  
YKR  CAU  HAU   SING  N  N  36  
YKR  CAU  HAUA  SING  N  N  37  
YKR  CBC  HBC   SING  N  N  38  
YKR  O1   HO1   SING  N  N  39  
#   #
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
YKR  SMILES            ACDLabs               12.01  "OC2C(OCc1ccccc1)C(OC(O)C2N)CO"  
YKR  InChI             InChI                 1.03   "InChI=1S/C13H19NO5/c14-10-11(16)12(9(6-15)19-13(10)17)18-7-8-4-2-1-3-5-8/h1-5,9-13,15-17H,6-7,14H2/t9-,10-,11-,12-,13+/m1/s1"  
YKR  InChIKey          InChI                 1.03   IFOCVXNXLGGVEE-VEGXAWMVSA-N  
YKR  SMILES_CANONICAL  CACTVS                3.385  "N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](OCc2ccccc2)[C@@H]1O"  
YKR  SMILES            CACTVS                3.385  "N[CH]1[CH](O)O[CH](CO)[CH](OCc2ccccc2)[CH]1O"  
YKR  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "c1ccc(cc1)CO[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)N)O)CO"  
YKR  SMILES            "OpenEye OEToolkits"  1.9.2  "c1ccc(cc1)COC2C(OC(C(C2O)N)O)CO"  
#   #
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
YKR  "SYSTEMATIC NAME"  ACDLabs               12.01  2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranose  
YKR  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "(2S,3R,4R,5S,6R)-3-azanyl-6-(hydroxymethyl)-5-phenylmethoxy-oxane-2,4-diol"  
#
_pdbx_chem_comp_related.comp_id            YKR
_pdbx_chem_comp_related.related_comp_id    PA1
_pdbx_chem_comp_related.relationship_type  "Carbohydrate core"
_pdbx_chem_comp_related.details            ?
#   #
loop_
_pdbx_chem_comp_atom_related.ordinal
_pdbx_chem_comp_atom_related.comp_id
_pdbx_chem_comp_atom_related.atom_id
_pdbx_chem_comp_atom_related.related_comp_id
_pdbx_chem_comp_atom_related.related_atom_id
_pdbx_chem_comp_atom_related.related_type
 1  YKR  C1    PA1  C1    "Carbohydrate core"  
 2  YKR  C2    PA1  C2    "Carbohydrate core"  
 3  YKR  C3    PA1  C3    "Carbohydrate core"  
 4  YKR  C4    PA1  C4    "Carbohydrate core"  
 5  YKR  C5    PA1  C5    "Carbohydrate core"  
 6  YKR  C6    PA1  C6    "Carbohydrate core"  
 7  YKR  N2    PA1  N2    "Carbohydrate core"  
 8  YKR  O1    PA1  O1    "Carbohydrate core"  
 9  YKR  O3    PA1  O3    "Carbohydrate core"  
10  YKR  O4    PA1  O4    "Carbohydrate core"  
11  YKR  O5    PA1  O5    "Carbohydrate core"  
12  YKR  O6    PA1  O6    "Carbohydrate core"  
13  YKR  H1    PA1  H1    "Carbohydrate core"  
14  YKR  H2    PA1  H2    "Carbohydrate core"  
15  YKR  H3    PA1  H3    "Carbohydrate core"  
16  YKR  H4    PA1  H4    "Carbohydrate core"  
17  YKR  H5    PA1  H5    "Carbohydrate core"  
18  YKR  H61   PA1  H61   "Carbohydrate core"  
19  YKR  H62   PA1  H62   "Carbohydrate core"  
20  YKR  HO1   PA1  HO1   "Carbohydrate core"  
21  YKR  HN21  PA1  HN21  "Carbohydrate core"  
22  YKR  HN22  PA1  HN22  "Carbohydrate core"  
23  YKR  HO3   PA1  HO3   "Carbohydrate core"  
24  YKR  HO6   PA1  HO6   "Carbohydrate core"  
#   #
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
YKR  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
YKR  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
YKR  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
YKR  "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
YKR  "Create component"          2012-07-31  EBI   
YKR  "Initial release"           2013-08-07  RCSB  
YKR  "Modify descriptor"         2014-09-05  RCSB  
YKR  "Other modification"        2020-07-03  RCSB  
YKR  "Modify parent residue"     2020-07-17  RCSB  
YKR  "Modify synonyms"           2020-07-17  RCSB  
YKR  "Modify internal type"      2020-07-17  RCSB  
YKR  "Modify linking type"       2020-07-17  RCSB  
YKR  "Modify atom id"            2020-07-17  RCSB  
YKR  "Modify component atom id"  2020-07-17  RCSB  
YKR  "Modify leaving atom flag"  2020-07-17  RCSB  
##
