data_D8M
#

_chem_comp.id                                   D8M
_chem_comp.name                                 "2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H19 N3 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-10-23
_chem_comp.pdbx_modified_date                   2020-04-17
_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                       281.308
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D8M
_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       5QBH
_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.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
D8M  O3   O1   O  0  1  N  N  N   3.202   6.490   8.994   3.348  -2.683   0.079  O3   D8M   1  
D8M  C4   C1   C  0  1  Y  N  N  -2.995   2.830  10.254  -4.915  -0.720   0.831  C4   D8M   2  
D8M  C5   C2   C  0  1  N  N  N  -2.185   4.123   8.239  -2.744   0.516   0.868  C5   D8M   3  
D8M  C6   C3   C  0  1  N  N  N  -0.902   6.124   8.790  -0.447  -0.154   0.409  C6   D8M   4  
D8M  N1   N1   N  0  1  N  N  N  -1.151   5.110   7.965  -1.753  -0.221   0.081  N1   D8M   5  
D8M  C7   C4   C  0  1  N  N  N   0.112   7.133   8.296   0.573  -0.912  -0.400  C7   D8M   6  
D8M  C8   C5   C  0  1  N  N  S   1.077   7.585   9.391   1.968  -0.668   0.179  C8   D8M   7  
D8M  N2   N2   N  0  1  N  N  N   0.714  11.708   9.904   4.011   3.161   0.264  N2   D8M   8  
D8M  C9   C6   C  0  1  N  N  R   2.532   7.743   8.986   3.026  -1.472  -0.608  C9   D8M   9  
D8M  C10  C7   C  0  1  N  N  S   3.066   8.659  10.083   4.252  -0.534  -0.656  C10  D8M  10  
D8M  C11  C8   C  0  1  N  N  R   1.885   9.591  10.344   3.790   0.727   0.109  C11  D8M  11  
D8M  C12  C9   C  0  1  N  N  N   1.971  10.961   9.640   4.363   1.986  -0.545  C12  D8M  12  
D8M  O    O2   O  0  1  N  N  N  -1.455   6.249   9.880  -0.094   0.515   1.357  O    D8M  13  
D8M  C3   C10  C  0  1  Y  N  N  -1.942   3.308   9.488  -4.118   0.275   0.297  C3   D8M  14  
D8M  N    N3   N  0  1  Y  N  N  -0.660   3.042   9.781  -4.546   1.016  -0.706  N    D8M  15  
D8M  C2   C11  C  0  1  Y  N  N  -0.418   2.265  10.848  -5.740   0.841  -1.237  C2   D8M  16  
D8M  C1   C12  C  0  1  Y  N  N  -1.407   1.739  11.652  -6.592  -0.134  -0.756  C1   D8M  17  
D8M  C    C13  C  0  1  Y  N  N  -2.712   2.032  11.347  -6.177  -0.934   0.298  C    D8M  18  
D8M  O1   O3   O  0  1  N  N  N   0.706   8.889   9.885   2.350   0.714   0.004  O1   D8M  19  
D8M  O2   O4   O  0  1  N  N  N   3.412   7.924  11.252   5.370  -1.136   0.001  O2   D8M  20  
D8M  H1   H1   H  0  1  N  N  N   4.108   6.613   8.738   4.008  -3.227  -0.371  H1   D8M  21  
D8M  H2   H2   H  0  1  N  N  N  -4.016   3.076  10.002  -4.557  -1.327   1.650  H2   D8M  22  
D8M  H3   H3   H  0  1  N  N  N  -3.144   4.649   8.351  -2.715   0.172   1.902  H3   D8M  23  
D8M  H4   H4   H  0  1  N  N  N  -2.242   3.435   7.383  -2.518   1.581   0.833  H4   D8M  24  
D8M  H5   H5   H  0  1  N  N  N  -0.610   5.023   7.129  -2.035  -0.756  -0.677  H5   D8M  25  
D8M  H6   H6   H  0  1  N  N  N   0.693   6.677   7.481   0.347  -1.978  -0.365  H6   D8M  26  
D8M  H7   H7   H  0  1  N  N  N  -0.425   8.014   7.915   0.544  -0.569  -1.434  H7   D8M  27  
D8M  H8   H8   H  0  1  N  N  N   1.026   6.857  10.214   1.992  -0.938   1.235  H8   D8M  28  
D8M  H9   H9   H  0  1  N  N  N   0.755  12.600   9.453   4.331   3.053   1.215  H9   D8M  29  
D8M  H10  H10  H  0  1  N  N  N  -0.063  11.189   9.547   4.379   4.006  -0.147  H10  D8M  30  
D8M  H12  H12  H  0  1  N  N  N   2.605   8.239   8.007   2.669  -1.689  -1.615  H12  D8M  31  
D8M  H13  H13  H  0  1  N  N  N   3.922   9.237   9.704   4.503  -0.285  -1.687  H13  D8M  32  
D8M  H14  H14  H  0  1  N  N  N   1.811   9.764  11.428   4.096   0.670   1.153  H14  D8M  33  
D8M  H15  H15  H  0  1  N  N  N   2.095  10.814   8.557   3.947   2.096  -1.546  H15  D8M  34  
D8M  H16  H16  H  0  1  N  N  N   2.828  11.527  10.033   5.448   1.901  -0.610  H16  D8M  35  
D8M  H17  H17  H  0  1  N  N  N   0.610   2.039  11.091  -6.056   1.468  -2.058  H17  D8M  36  
D8M  H18  H18  H  0  1  N  N  N  -1.161   1.114  12.498  -7.569  -0.273  -1.196  H18  D8M  37  
D8M  H19  H19  H  0  1  N  N  N  -3.513   1.642  11.957  -6.820  -1.707   0.692  H19  D8M  38  
D8M  H20  H20  H  0  1  N  N  N   3.740   8.519  11.915   5.663  -1.964  -0.402  H20  D8M  39  
#   #
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
D8M  N1   C5   SING  N  N   1  
D8M  N1   C6   SING  N  N   2  
D8M  C5   C3   SING  N  N   3  
D8M  C7   C6   SING  N  N   4  
D8M  C7   C8   SING  N  N   5  
D8M  C6   O    DOUB  N  N   6  
D8M  C9   O3   SING  N  N   7  
D8M  C9   C8   SING  N  N   8  
D8M  C9   C10  SING  N  N   9  
D8M  C8   O1   SING  N  N  10  
D8M  C3   N    DOUB  Y  N  11  
D8M  C3   C4   SING  Y  N  12  
D8M  C12  N2   SING  N  N  13  
D8M  C12  C11  SING  N  N  14  
D8M  N    C2   SING  Y  N  15  
D8M  O1   C11  SING  N  N  16  
D8M  C10  C11  SING  N  N  17  
D8M  C10  O2   SING  N  N  18  
D8M  C4   C    DOUB  Y  N  19  
D8M  C2   C1   DOUB  Y  N  20  
D8M  C    C1   SING  Y  N  21  
D8M  O3   H1   SING  N  N  22  
D8M  C4   H2   SING  N  N  23  
D8M  C5   H3   SING  N  N  24  
D8M  C5   H4   SING  N  N  25  
D8M  N1   H5   SING  N  N  26  
D8M  C7   H6   SING  N  N  27  
D8M  C7   H7   SING  N  N  28  
D8M  C8   H8   SING  N  N  29  
D8M  N2   H9   SING  N  N  30  
D8M  N2   H10  SING  N  N  31  
D8M  C9   H12  SING  N  N  32  
D8M  C10  H13  SING  N  N  33  
D8M  C11  H14  SING  N  N  34  
D8M  C12  H15  SING  N  N  35  
D8M  C12  H16  SING  N  N  36  
D8M  C2   H17  SING  N  N  37  
D8M  C1   H18  SING  N  N  38  
D8M  C    H19  SING  N  N  39  
D8M  O2   H20  SING  N  N  40  
#   #
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
D8M  SMILES            ACDLabs               12.01  "OC2C(CC(=O)NCc1ccccn1)OC(C2O)CN"  
D8M  InChI             InChI                 1.03   "InChI=1S/C13H19N3O4/c14-6-10-13(19)12(18)9(20-10)5-11(17)16-7-8-3-1-2-4-15-8/h1-4,9-10,12-13,18-19H,5-7,14H2,(H,16,17)/t9-,10+,12-,13+/m0/s1"  
D8M  InChIKey          InChI                 1.03   BIGFPMOCLWRIMB-JULQROHOSA-N  
D8M  SMILES_CANONICAL  CACTVS                3.385  "NC[C@H]1O[C@@H](CC(=O)NCc2ccccn2)[C@H](O)[C@@H]1O"  
D8M  SMILES            CACTVS                3.385  "NC[CH]1O[CH](CC(=O)NCc2ccccn2)[CH](O)[CH]1O"  
D8M  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1ccnc(c1)CNC(=O)C[C@H]2[C@@H]([C@@H]([C@H](O2)CN)O)O"  
D8M  SMILES            "OpenEye OEToolkits"  2.0.6  "c1ccnc(c1)CNC(=O)CC2C(C(C(O2)CN)O)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
D8M  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide (non-preferred name)"  
D8M  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "2-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-~{N}-(pyridin-2-ylmethyl)ethanamide"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D8M  "Create component"  2017-10-23  RCSB  
D8M  "Initial release"   2020-04-22  RCSB  
##
