data_HD3
#

_chem_comp.id                                   HD3
_chem_comp.name                                 "2-azanyl-7-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-3H-pyrrolo[2,3-d]pyrimidin-4-one"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H14 N4 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-18
_chem_comp.pdbx_modified_date                   2022-01-28
_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                       282.253
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    HD3
_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       7DOW
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
HD3  C05  C1   C  0  1  Y  N  N  -49.749  -16.897  -3.432   2.290   1.192   0.185  C05  HD3   1  
HD3  C06  C2   C  0  1  N  N  N  -50.712  -16.499  -2.308   3.682   0.951   0.187  C06  HD3   2  
HD3  C01  C3   C  0  1  Y  N  N  -49.687  -16.518  -4.747   1.450   2.354   0.468  C01  HD3   3  
HD3  C02  C4   C  0  1  Y  N  N  -48.595  -17.183  -5.328   0.177   1.962   0.290  C02  HD3   4  
HD3  C04  C5   C  0  1  Y  N  N  -48.709  -17.791  -3.198   1.418   0.149  -0.156  C04  HD3   5  
HD3  C12  C6   C  0  1  N  N  R  -46.898  -18.760  -4.622  -1.067  -0.124  -0.366  C12  HD3   6  
HD3  C09  C7   C  0  1  N  N  N  -49.456  -18.022  -0.754   3.223  -1.263  -0.469  C09  HD3   7  
HD3  C13  C8   C  0  1  N  N  R  -45.472  -17.939  -4.321  -1.524  -0.904   0.894  C13  HD3   8  
HD3  C14  C9   C  0  1  N  N  S  -44.591  -18.865  -4.421  -3.039  -1.087   0.630  C14  HD3   9  
HD3  C15  C10  C  0  1  N  N  R  -45.329  -20.165  -3.881  -3.379   0.011  -0.396  C15  HD3  10  
HD3  C17  C11  C  0  1  N  N  N  -44.851  -20.523  -2.651  -4.463   0.932   0.168  C17  HD3  11  
HD3  N03  N1   N  0  1  Y  N  N  -48.032  -17.937  -4.382   0.149   0.643  -0.085  N03  HD3  12  
HD3  N08  N2   N  0  1  N  N  N  -50.543  -17.072  -1.000   4.117  -0.286  -0.144  N08  HD3  13  
HD3  N10  N3   N  0  1  N  N  N  -48.531  -18.387  -1.827   1.927  -1.051  -0.472  N10  HD3  14  
HD3  N11  N4   N  0  1  N  N  N  -49.278  -18.588   0.560   3.693  -2.509  -0.801  N11  HD3  15  
HD3  O07  O1   O  0  1  N  N  N  -51.588  -15.743  -2.523   4.470   1.834   0.478  O07  HD3  16  
HD3  O16  O2   O  0  1  N  N  N  -46.838  -19.770  -3.812  -2.176   0.761  -0.634  O16  HD3  17  
HD3  O18  O3   O  0  1  N  N  N  -45.696  -19.986  -1.647  -4.855   1.875  -0.831  O18  HD3  18  
HD3  O19  O4   O  0  1  N  N  N  -44.228  -19.089  -5.841  -3.298  -2.381   0.082  O19  HD3  19  
HD3  O20  O5   O  0  1  N  N  N  -45.264  -16.874  -5.302  -0.864  -2.169   0.978  O20  HD3  20  
HD3  H1   H1   H  0  1  N  N  N  -50.356  -15.833  -5.246   1.786   3.336   0.765  H1   HD3  21  
HD3  H2   H2   H  0  1  N  N  N  -48.270  -17.099  -6.354  -0.691   2.591   0.421  H2   HD3  22  
HD3  H3   H3   H  0  1  N  N  N  -46.873  -19.072  -5.677  -0.906  -0.805  -1.201  H3   HD3  23  
HD3  H4   H4   H  0  1  N  N  N  -45.541  -17.514  -3.309  -1.355  -0.318   1.797  H4   HD3  24  
HD3  H5   H5   H  0  1  N  N  N  -43.689  -18.688  -3.817  -3.606  -0.940   1.549  H5   HD3  25  
HD3  H6   H6   H  0  1  N  N  N  -45.204  -20.972  -4.618  -3.723  -0.443  -1.325  H6   HD3  26  
HD3  H7   H7   H  0  1  N  N  N  -44.833  -21.620  -2.568  -5.327   0.337   0.465  H7   HD3  27  
HD3  H8   H8   H  0  1  N  N  N  -43.832  -20.129  -2.524  -4.073   1.464   1.036  H8   HD3  28  
HD3  H9   H9   H  0  1  N  N  N  -51.167  -16.822  -0.259   5.068  -0.478  -0.152  H9   HD3  29  
HD3  H10  H10  H  0  1  N  N  N  -48.527  -19.225   0.732   4.647  -2.683  -0.803  H10  HD3  30  
HD3  H11  H11  H  0  1  N  N  N  -49.906  -18.344   1.299   3.071  -3.216  -1.035  H11  HD3  31  
HD3  H12  H12  H  0  1  N  N  N  -45.367  -20.233  -0.791  -5.541   2.492  -0.543  H12  HD3  32  
HD3  H13  H13  H  0  1  N  N  N  -43.575  -19.777  -5.897  -4.232  -2.550  -0.102  H13  HD3  33  
HD3  H14  H14  H  0  1  N  N  N  -44.450  -16.422  -5.112  -1.117  -2.694   1.749  H14  HD3  34  
#   #
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
HD3  O19  C14  SING  N  N   1  
HD3  C02  C01  DOUB  Y  N   2  
HD3  C02  N03  SING  Y  N   3  
HD3  O20  C13  SING  N  N   4  
HD3  C01  C05  SING  Y  N   5  
HD3  C12  N03  SING  N  N   6  
HD3  C12  C13  SING  N  N   7  
HD3  C12  O16  SING  N  N   8  
HD3  C14  C13  SING  N  N   9  
HD3  C14  C15  SING  N  N  10  
HD3  N03  C04  SING  Y  N  11  
HD3  C15  O16  SING  N  N  12  
HD3  C15  C17  SING  N  N  13  
HD3  C05  C04  DOUB  Y  N  14  
HD3  C05  C06  SING  N  N  15  
HD3  C04  N10  SING  N  N  16  
HD3  C17  O18  SING  N  N  17  
HD3  O07  C06  DOUB  N  N  18  
HD3  C06  N08  SING  N  N  19  
HD3  N10  C09  DOUB  N  N  20  
HD3  N08  C09  SING  N  N  21  
HD3  C09  N11  SING  N  N  22  
HD3  C01  H1   SING  N  N  23  
HD3  C02  H2   SING  N  N  24  
HD3  C12  H3   SING  N  N  25  
HD3  C13  H4   SING  N  N  26  
HD3  C14  H5   SING  N  N  27  
HD3  C15  H6   SING  N  N  28  
HD3  C17  H7   SING  N  N  29  
HD3  C17  H8   SING  N  N  30  
HD3  N08  H9   SING  N  N  31  
HD3  N11  H10  SING  N  N  32  
HD3  N11  H11  SING  N  N  33  
HD3  O18  H12  SING  N  N  34  
HD3  O19  H13  SING  N  N  35  
HD3  O20  H14  SING  N  N  36  
#   #
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
HD3  InChI             InChI                 1.03   "InChI=1S/C11H14N4O5/c12-11-13-8-4(9(19)14-11)1-2-15(8)10-7(18)6(17)5(3-16)20-10/h1-2,5-7,10,16-18H,3H2,(H3,12,13,14,19)/t5-,6-,7-,10-/m1/s1"  
HD3  InChIKey          InChI                 1.03   JRYMOPZHXMVHTA-DAGMQNCNSA-N  
HD3  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(ccc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O"  
HD3  SMILES            CACTVS                3.385  "NC1=Nc2n(ccc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O"  
HD3  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O"  
HD3  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)CO)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          HD3
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "2-azanyl-7-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-3~{H}-pyrrolo[2,3-d]pyrimidin-4-one"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HD3  "Create component"  2020-12-18  PDBJ  
HD3  "Initial release"   2022-02-02  RCSB  
##
