data_GMD
#

_chem_comp.id                                   GMD
_chem_comp.name                                 "(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H25 N5 O2 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        hydroxybutylthio-DADMe-Immucillin-A
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-05-29
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       351.467
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GMD
_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       4WKO
_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
GMD  C      C1   C  0  1  N  N  N  -39.766  -43.633  17.433   -8.665   1.400   0.111  C      GMD   1  
GMD  OXT    O1   O  0  1  N  N  N  -39.967  -42.230  17.275   -9.909   1.053   0.723  OXT    GMD   2  
GMD  CA     C2   C  0  1  N  N  N  -38.579  -44.043  16.582   -7.619   0.333   0.443  CA     GMD   3  
GMD  CB     C3   C  0  1  N  N  N  -38.841  -43.930  15.077   -6.287   0.704  -0.211  CB     GMD   4  
GMD  CG     C4   C  0  1  N  N  N  -37.719  -44.675  14.360   -5.241  -0.363   0.121  CG     GMD   5  
GMD  "S5'"  S1   S  0  1  N  N  N  -37.944  -44.853  12.616   -3.662   0.077  -0.655  "S5'"  GMD   6  
GMD  "C5'"  C5   C  0  1  N  N  N  -36.625  -45.932  12.177   -2.569  -1.283  -0.155  "C5'"  GMD   7  
GMD  "C4'"  C6   C  0  1  N  N  S  -35.270  -45.219  12.126   -1.174  -1.057  -0.740  "C4'"  GMD   8  
GMD  "C1'"  C7   C  0  1  N  N  N  -34.162  -46.256  12.098   -0.508   0.169  -0.079  "C1'"  GMD   9  
GMD  "C3'"  C8   C  0  1  N  N  R  -35.077  -44.436  10.845   -0.252  -2.247  -0.402  "C3'"  GMD  10  
GMD  "O3'"  O2   O  0  1  N  N  N  -34.040  -43.456  10.955    0.264  -2.830  -1.600  "O3'"  GMD  11  
GMD  "C2'"  C9   C  0  1  N  N  N  -34.600  -45.491   9.871    0.894  -1.641   0.437  "C2'"  GMD  12  
GMD  "N1'"  N1   N  0  1  N  N  N  -33.615  -46.205  10.718    0.924  -0.205   0.047  "N1'"  GMD  13  
GMD  C10    C10  C  0  1  N  N  N  -33.243  -47.505  10.152    1.593   0.605   1.074  C10    GMD  14  
GMD  C9     C11  C  0  1  Y  N  N  -34.188  -48.671  10.295    3.066   0.290   1.082  C9     GMD  15  
GMD  C8     C12  C  0  1  Y  N  N  -34.058  -49.745  11.186    3.706  -0.524   1.942  C8     GMD  16  
GMD  N7     N2   N  0  1  Y  N  N  -35.072  -50.646  11.007    5.036  -0.565   1.641  N7     GMD  17  
GMD  C5     C13  C  0  1  Y  N  N  -35.896  -50.244  10.025    5.292   0.239   0.554  C5     GMD  18  
GMD  C4     C14  C  0  1  Y  N  N  -35.392  -48.983   9.507    4.069   0.805   0.155  C4     GMD  19  
GMD  N3     N3   N  0  1  Y  N  N  -36.013  -48.316   8.504    4.047   1.634  -0.892  N3     GMD  20  
GMD  C2     C15  C  0  1  Y  N  N  -37.139  -48.845   7.966    5.155   1.918  -1.540  C2     GMD  21  
GMD  N1     N4   N  0  1  Y  N  N  -37.693  -50.016   8.394    6.325   1.408  -1.198  N1     GMD  22  
GMD  C6     C16  C  0  1  Y  N  N  -37.131  -50.750   9.391    6.441   0.571  -0.172  C6     GMD  23  
GMD  N6     N5   N  0  1  N  N  N  -37.680  -51.924   9.813    7.674   0.044   0.176  N6     GMD  24  
GMD  H1     H1   H  0  1  N  N  N  -40.664  -44.177  17.105   -8.794   1.457  -0.969  H1     GMD  25  
GMD  H2     H2   H  0  1  N  N  N  -39.563  -43.863  18.489   -8.331   2.366   0.490  H2     GMD  26  
GMD  H3     H3   H  0  1  N  N  N  -40.708  -41.954  17.802  -10.620   1.687   0.554  H3     GMD  27  
GMD  H4     H4   H  0  1  N  N  N  -38.328  -45.088  16.815   -7.490   0.275   1.524  H4     GMD  28  
GMD  H5     H5   H  0  1  N  N  N  -37.727  -43.396  16.837   -7.953  -0.633   0.065  H5     GMD  29  
GMD  H6     H6   H  0  1  N  N  N  -38.843  -42.872  14.774   -6.416   0.762  -1.292  H6     GMD  30  
GMD  H7     H7   H  0  1  N  N  N  -39.812  -44.384  14.829   -5.953   1.670   0.167  H7     GMD  31  
GMD  H8     H8   H  0  1  N  N  N  -37.640  -45.680  14.799   -5.112  -0.421   1.202  H8     GMD  32  
GMD  H9     H9   H  0  1  N  N  N  -36.781  -44.126  14.530   -5.575  -1.329  -0.257  H9     GMD  33  
GMD  H10    H10  H  0  1  N  N  N  -36.835  -46.360  11.186   -2.507  -1.318   0.932  H10    GMD  34  
GMD  H11    H11  H  0  1  N  N  N  -36.569  -46.741  12.921   -2.970  -2.226  -0.527  H11    GMD  35  
GMD  H12    H12  H  0  1  N  N  N  -35.155  -44.560  12.999   -1.234  -0.919  -1.819  H12    GMD  36  
GMD  H13    H13  H  0  1  N  N  N  -34.564  -47.256  12.317   -0.617   1.049  -0.714  H13    GMD  37  
GMD  H14    H14  H  0  1  N  N  N  -33.381  -46.006  12.832   -0.942   0.354   0.904  H14    GMD  38  
GMD  H15    H15  H  0  1  N  N  N  -36.028  -43.996  10.509   -0.795  -2.993   0.179  H15    GMD  39  
GMD  H16    H16  H  0  1  N  N  N  -34.309  -42.776  11.562    0.851  -3.584  -1.449  H16    GMD  40  
GMD  H17    H17  H  0  1  N  N  N  -34.126  -45.043   8.985    0.680  -1.742   1.501  H17    GMD  41  
GMD  H18    H18  H  0  1  N  N  N  -35.420  -46.153   9.554    1.841  -2.122   0.191  H18    GMD  42  
GMD  H20    H20  H  0  1  N  N  N  -32.295  -47.801  10.625    1.449   1.663   0.853  H20    GMD  43  
GMD  H21    H21  H  0  1  N  N  N  -33.084  -47.352   9.074    1.167   0.377   2.051  H21    GMD  44  
GMD  H22    H22  H  0  1  N  N  N  -33.266  -49.847  11.914    3.236  -1.064   2.751  H22    GMD  45  
GMD  H23    H23  H  0  1  N  N  N  -35.184  -51.488  11.535    5.701  -1.084   2.120  H23    GMD  46  
GMD  H24    H24  H  0  1  N  N  N  -37.621  -48.313   7.159    5.108   2.594  -2.381  H24    GMD  47  
GMD  H25    H25  H  0  1  N  N  N  -38.507  -52.115   9.284    8.465   0.285  -0.332  H25    GMD  48  
GMD  H26    H26  H  0  1  N  N  N  -37.022  -52.666   9.682    7.747  -0.566   0.926  H26    GMD  49  
#   #
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
GMD  C2     N1     DOUB  Y  N   1  
GMD  C2     N3     SING  Y  N   2  
GMD  N1     C6     SING  Y  N   3  
GMD  N3     C4     DOUB  Y  N   4  
GMD  C6     N6     SING  N  N   5  
GMD  C6     C5     DOUB  Y  N   6  
GMD  C4     C5     SING  Y  N   7  
GMD  C4     C9     SING  Y  N   8  
GMD  "C2'"  "N1'"  SING  N  N   9  
GMD  "C2'"  "C3'"  SING  N  N  10  
GMD  C5     N7     SING  Y  N  11  
GMD  C10    C9     SING  N  N  12  
GMD  C10    "N1'"  SING  N  N  13  
GMD  C9     C8     DOUB  Y  N  14  
GMD  "N1'"  "C1'"  SING  N  N  15  
GMD  "C3'"  "O3'"  SING  N  N  16  
GMD  "C3'"  "C4'"  SING  N  N  17  
GMD  N7     C8     SING  Y  N  18  
GMD  "C1'"  "C4'"  SING  N  N  19  
GMD  "C4'"  "C5'"  SING  N  N  20  
GMD  "C5'"  "S5'"  SING  N  N  21  
GMD  "S5'"  CG     SING  N  N  22  
GMD  CG     CB     SING  N  N  23  
GMD  CB     CA     SING  N  N  24  
GMD  CA     C      SING  N  N  25  
GMD  OXT    C      SING  N  N  26  
GMD  C      H1     SING  N  N  27  
GMD  C      H2     SING  N  N  28  
GMD  OXT    H3     SING  N  N  29  
GMD  CA     H4     SING  N  N  30  
GMD  CA     H5     SING  N  N  31  
GMD  CB     H6     SING  N  N  32  
GMD  CB     H7     SING  N  N  33  
GMD  CG     H8     SING  N  N  34  
GMD  CG     H9     SING  N  N  35  
GMD  "C5'"  H10    SING  N  N  36  
GMD  "C5'"  H11    SING  N  N  37  
GMD  "C4'"  H12    SING  N  N  38  
GMD  "C1'"  H13    SING  N  N  39  
GMD  "C1'"  H14    SING  N  N  40  
GMD  "C3'"  H15    SING  N  N  41  
GMD  "O3'"  H16    SING  N  N  42  
GMD  "C2'"  H17    SING  N  N  43  
GMD  "C2'"  H18    SING  N  N  44  
GMD  C10    H20    SING  N  N  45  
GMD  C10    H21    SING  N  N  46  
GMD  C8     H22    SING  N  N  47  
GMD  N7     H23    SING  N  N  48  
GMD  C2     H24    SING  N  N  49  
GMD  N6     H25    SING  N  N  50  
GMD  N6     H26    SING  N  N  51  
#   #
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
GMD  SMILES            ACDLabs               12.01  "C(O)CCCSCC1CN(CC1O)Cc2cnc3c2ncnc3N"  
GMD  InChI             InChI                 1.03   "InChI=1S/C16H25N5O2S/c17-16-15-14(19-10-20-16)11(5-18-15)6-21-7-12(13(23)8-21)9-24-4-2-1-3-22/h5,10,12-13,18,22-23H,1-4,6-9H2,(H2,17,19,20)/t12-,13+/m1/s1"  
GMD  InChIKey          InChI                 1.03   LDGNPMXZDVLXIT-OLZOCXBDSA-N  
GMD  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCCCO)C3)c[nH]c12"  
GMD  SMILES            CACTVS                3.385  "Nc1ncnc2c(CN3C[CH](O)[CH](CSCCCCO)C3)c[nH]c12"  
GMD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1c(c2c([nH]1)c(ncn2)N)CN3C[C@@H]([C@H](C3)O)CSCCCCO"  
GMD  SMILES            "OpenEye OEToolkits"  2.0.6  "c1c(c2c([nH]1)c(ncn2)N)CN3CC(C(C3)O)CSCCCCO"  
#   #
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
GMD  "SYSTEMATIC NAME"  ACDLabs               12.01  "(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol"  
GMD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "(3~{R},4~{S})-1-[(4-azanyl-5~{H}-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(4-oxidanylbutylsulfanylmethyl)pyrrolidin-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
GMD  "Create component"  2018-05-29  RCSB  
GMD  "Initial release"   2018-06-06  RCSB  
GMD  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     GMD
_pdbx_chem_comp_synonyms.name        hydroxybutylthio-DADMe-Immucillin-A
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
