data_D5V
#

_chem_comp.id                                   D5V
_chem_comp.name                                 "(1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C12 H15 N O3 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-10-20
_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                       253.317
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D5V
_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       5QB5
_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
D5V  C4   C1   C  0  1  Y  N  N  -4.718   1.116  11.171   3.202   1.154   0.075  C4   D5V   1  
D5V  C5   C2   C  0  1  Y  N  N  -5.550   0.138  10.655   4.409   0.554  -0.222  C5   D5V   2  
D5V  C6   C3   C  0  1  N  N  R  -1.586   3.013  10.219  -0.606  -0.272   0.770  C6   D5V   3  
D5V  C7   C4   C  0  1  N  N  S  -0.054   2.997  10.258  -0.808  -0.820  -0.647  C7   D5V   4  
D5V  C8   C5   C  0  1  N  N  S   0.525   3.854   9.132  -1.576   0.210  -1.484  C8   D5V   5  
D5V  C9   C6   C  0  1  N  N  S  -0.318   5.117   8.965  -2.845   0.615  -0.717  C9   D5V   6  
D5V  C10  C7   C  0  1  N  N  N  -1.470   4.950   7.979  -3.499  -0.678  -0.174  C10  D5V   7  
D5V  C11  C8   C  0  1  N  N  R  -2.118   4.472  10.095  -1.963   0.192   1.321  C11  D5V   8  
D5V  O2   O1   O  0  1  N  N  N   0.428   1.662  10.140  -1.555  -2.037  -0.585  O2   D5V   9  
D5V  N    N1   N  0  1  N  N  N   1.939   4.226   9.454  -0.733   1.393  -1.703  N    D5V  10  
D5V  O1   O2   O  0  1  N  N  N  -1.023   5.356  10.204  -2.418   1.286   0.495  O1   D5V  11  
D5V  O    O3   O  0  1  N  N  N  -2.610   4.641   8.790  -2.914  -0.871   1.127  O    D5V  12  
D5V  S    S1   S  0  1  N  N  N  -2.251   2.218  11.715   0.542   1.132   0.720  S    D5V  13  
D5V  C3   C9   C  0  1  Y  N  N  -3.342   0.990  11.044   2.083   0.371   0.334  C3   D5V  14  
D5V  C2   C10  C  0  1  Y  N  N  -2.811  -0.113  10.392   2.184  -1.015   0.287  C2   D5V  15  
D5V  C1   C11  C  0  1  Y  N  N  -3.654  -1.084   9.880   3.393  -1.608  -0.016  C1   D5V  16  
D5V  C    C12  C  0  1  Y  N  N  -5.020  -0.961  10.013   4.505  -0.825  -0.268  C    D5V  17  
D5V  H1   H1   H  0  1  N  N  N  -5.139   1.976  11.672   3.128   2.231   0.111  H1   D5V  18  
D5V  H2   H2   H  0  1  N  N  N  -6.621   0.236  10.756   5.280   1.162  -0.419  H2   D5V  19  
D5V  H3   H3   H  0  1  N  N  N  -1.943   2.420   9.364  -0.198  -1.055   1.409  H3   D5V  20  
D5V  H4   H4   H  0  1  N  N  N   0.270   3.424  11.218   0.162  -1.012  -1.105  H4   D5V  21  
D5V  H5   H5   H  0  1  N  N  N   0.501   3.279   8.194  -1.848  -0.228  -2.444  H5   D5V  22  
D5V  H6   H6   H  0  1  N  N  N   0.315   5.971   8.682  -3.522   1.221  -1.319  H6   D5V  23  
D5V  H7   H7   H  0  1  N  N  N  -1.262   4.130   7.276  -4.578  -0.549  -0.089  H7   D5V  24  
D5V  H8   H8   H  0  1  N  N  N  -1.636   5.881   7.417  -3.267  -1.522  -0.823  H8   D5V  25  
D5V  H9   H9   H  0  1  N  N  N  -2.885   4.661  10.860  -1.886   0.488   2.367  H9   D5V  26  
D5V  H10  H10  H  0  1  N  N  N   0.067   1.131  10.841  -1.129  -2.734  -0.068  H10  D5V  27  
D5V  H11  H11  H  0  1  N  N  N   2.486   3.396   9.562   0.115   1.148  -2.191  H11  D5V  28  
D5V  H12  H12  H  0  1  N  N  N   2.316   4.779   8.711  -1.241   2.112  -2.197  H12  D5V  29  
D5V  H14  H14  H  0  1  N  N  N  -1.741  -0.214  10.284   1.316  -1.627   0.488  H14  D5V  30  
D5V  H15  H15  H  0  1  N  N  N  -3.239  -1.943   9.373   3.472  -2.684  -0.053  H15  D5V  31  
D5V  H16  H16  H  0  1  N  N  N  -5.674  -1.723   9.615   5.450  -1.292  -0.505  H16  D5V  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
D5V  C10  O    SING  N  N   1  
D5V  C10  C9   SING  N  N   2  
D5V  O    C11  SING  N  N   3  
D5V  C9   C8   SING  N  N   4  
D5V  C9   O1   SING  N  N   5  
D5V  C8   N    SING  N  N   6  
D5V  C8   C7   SING  N  N   7  
D5V  C1   C    DOUB  Y  N   8  
D5V  C1   C2   SING  Y  N   9  
D5V  C    C5   SING  Y  N  10  
D5V  C11  O1   SING  N  N  11  
D5V  C11  C6   SING  N  N  12  
D5V  O2   C7   SING  N  N  13  
D5V  C6   C7   SING  N  N  14  
D5V  C6   S    SING  N  N  15  
D5V  C2   C3   DOUB  Y  N  16  
D5V  C5   C4   DOUB  Y  N  17  
D5V  C3   C4   SING  Y  N  18  
D5V  C3   S    SING  N  N  19  
D5V  C4   H1   SING  N  N  20  
D5V  C5   H2   SING  N  N  21  
D5V  C6   H3   SING  N  N  22  
D5V  C7   H4   SING  N  N  23  
D5V  C8   H5   SING  N  N  24  
D5V  C9   H6   SING  N  N  25  
D5V  C10  H7   SING  N  N  26  
D5V  C10  H8   SING  N  N  27  
D5V  C11  H9   SING  N  N  28  
D5V  O2   H10  SING  N  N  29  
D5V  N    H11  SING  N  N  30  
D5V  N    H12  SING  N  N  31  
D5V  C2   H14  SING  N  N  32  
D5V  C1   H15  SING  N  N  33  
D5V  C    H16  SING  N  N  34  
#   #
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
D5V  SMILES            ACDLabs               12.01  "c1ccccc1SC2C(C(N)C3OC2OC3)O"  
D5V  InChI             InChI                 1.03   "InChI=1S/C12H15NO3S/c13-9-8-6-15-12(16-8)11(10(9)14)17-7-4-2-1-3-5-7/h1-5,8-12,14H,6,13H2/t8-,9-,10+,11-,12-/m1/s1"  
D5V  InChIKey          InChI                 1.03   OFCUYBHPAYPQJR-RMPHRYRLSA-N  
D5V  SMILES_CANONICAL  CACTVS                3.385  "N[C@@H]1[C@H]2CO[C@H](O2)[C@H](Sc3ccccc3)[C@H]1O"  
D5V  SMILES            CACTVS                3.385  "N[CH]1[CH]2CO[CH](O2)[CH](Sc3ccccc3)[CH]1O"  
D5V  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1ccc(cc1)S[C@@H]2[C@H]([C@@H]([C@H]3CO[C@@H]2O3)N)O"  
D5V  SMILES            "OpenEye OEToolkits"  2.0.6  "c1ccc(cc1)SC2C(C(C3COC2O3)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
D5V  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)"  
D5V  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "(1~{S},2~{S},3~{S},4~{R},5~{R})-2-azanyl-4-phenylsulfanyl-6,8-dioxabicyclo[3.2.1]octan-3-ol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D5V  "Create component"  2017-10-20  RCSB  
D5V  "Initial release"   2020-04-22  RCSB  
##
