data_XNY
#

_chem_comp.id                                   XNY
_chem_comp.name                                 "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-3~{H}-imidazo[4,5-c]pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H15 N4 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-22
_chem_comp.pdbx_modified_date                   2021-04-30
_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                       346.233
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XNY
_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       7L3R
_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
XNY  C2      C1   C  0  1  Y  N  N  -14.473  -0.316  -4.432   5.234  -0.559  -1.259  C2      XNY   1  
XNY  C5      C2   C  0  1  Y  N  N  -15.442  -0.178  -1.897   3.792   1.180   0.277  C5      XNY   2  
XNY  C3      C3   C  0  1  Y  N  N  -15.615   0.464  -4.269   3.896  -0.788  -1.105  C3      XNY   3  
XNY  C8      C4   C  0  1  Y  N  N  -17.225   0.902  -1.098   1.696   1.279   0.835  C8      XNY   4  
XNY  N7      N1   N  0  1  Y  N  N  -16.193   0.094  -0.743   2.850   1.866   0.970  N7      XNY   5  
XNY  "C1'"   C5   C  0  1  N  N  R  -18.110   1.989  -3.190   0.751  -0.744  -0.341  "C1'"   XNY   6  
XNY  "C2'"   C6   C  0  1  N  N  R  -19.082   1.104  -3.963   0.661  -1.915   0.663  "C2'"   XNY   7  
XNY  "C3'"   C7   C  0  1  N  N  S  -20.197   0.976  -2.947  -0.855  -2.189   0.785  "C3'"   XNY   8  
XNY  C4      C8   C  0  1  Y  N  N  -16.076   0.501  -2.968   3.144   0.088  -0.326  C4      XNY   9  
XNY  "C4'"   C9   C  0  1  N  N  R  -20.264   2.388  -2.404  -1.501  -1.152  -0.159  "C4'"   XNY  10  
XNY  "C5'"   C10  C  0  1  N  N  N  -20.968   2.568  -1.092  -2.809  -0.629   0.438  "C5'"   XNY  11  
XNY  C6      C11  C  0  1  Y  N  N  -14.286  -0.918  -2.145   5.170   1.341   0.066  C6      XNY  12  
XNY  N1      N2   N  0  1  Y  N  N  -13.850  -0.967  -3.431   5.829   0.475  -0.685  N1      XNY  13  
XNY  N6      N3   N  0  1  N  N  N  -13.638  -1.603  -1.148   5.842   2.409   0.647  N6      XNY  14  
XNY  N9      N4   N  0  1  Y  N  N  -17.158   1.169  -2.441   1.823   0.177   0.044  N9      XNY  15  
XNY  "O2'"   O1   O  0  1  N  N  N  -19.533   1.804  -5.110   1.338  -3.065   0.154  "O2'"   XNY  16  
XNY  "O3'"   O2   O  0  1  N  N  N  -21.419   0.546  -3.507  -1.160  -3.517   0.355  "O3'"   XNY  17  
XNY  "O4'"   O3   O  0  1  N  N  N  -18.869   2.760  -2.287  -0.532  -0.086  -0.255  "O4'"   XNY  18  
XNY  "O5'"   O4   O  0  1  N  N  N  -20.377   1.768  -0.088  -3.449   0.238  -0.500  "O5'"   XNY  19  
XNY  OP1     O5   O  0  1  N  N  N  -22.143   2.339   1.571  -5.867  -0.042   0.166  OP1     XNY  20  
XNY  OP2     O6   O  0  1  N  N  N  -20.051   0.998   2.251  -4.668   2.012   1.010  OP2     XNY  21  
XNY  P       P1   P  0  1  N  N  N  -20.688   2.062   1.433  -4.852   0.970  -0.203  P       XNY  22  
XNY  H2      H1   H  0  1  N  N  N  -14.060  -0.405  -5.426   5.820  -1.239  -1.859  H2      XNY  23  
XNY  H3      H2   H  0  1  N  N  N  -16.094   0.989  -5.082   3.428  -1.636  -1.582  H3      XNY  24  
XNY  H8      H3   H  0  1  N  N  N  -17.982   1.277  -0.425   0.774   1.617   1.283  H8      XNY  25  
XNY  "H1'"   H5   H  0  1  N  N  N  -17.572   2.636  -3.898   0.918  -1.120  -1.350  "H1'"   XNY  26  
XNY  "H2'"   H6   H  0  1  N  N  N  -18.635   0.127  -4.200   1.075  -1.623   1.628  "H2'"   XNY  27  
XNY  "H3'"   H7   H  0  1  N  N  N  -19.878   0.295  -2.144  -1.190  -2.033   1.811  "H3'"   XNY  28  
XNY  "H4'"   H8   H  0  1  N  N  N  -20.750   3.028  -3.155  -1.680  -1.592  -1.140  "H4'"   XNY  29  
XNY  "H5'"   H9   H  0  1  N  N  N  -20.907   3.625  -0.793  -3.467  -1.469   0.663  "H5'"   XNY  30  
XNY  "H5''"  H10  H  0  0  N  N  N  -22.023   2.280  -1.207  -2.596  -0.080   1.355  "H5''"  XNY  31  
XNY  H61     H11  H  0  1  N  N  N  -12.857  -2.094  -1.534   5.358   3.044   1.198  H61     XNY  32  
XNY  H62     H12  H  0  1  N  N  N  -13.316  -0.958  -0.455   6.794   2.520   0.501  H62     XNY  33  
XNY  "HO2'"  H13  H  0  0  N  N  N  -20.139   1.258  -5.597   1.313  -3.830   0.744  "HO2'"  XNY  34  
XNY  "HO3'"  H14  H  0  0  N  Y  N  -22.077   0.485  -2.824  -0.730  -4.208   0.877  "HO3'"  XNY  35  
XNY  HOP2    H16  H  0  0  N  N  N  -20.705   0.592   2.808  -4.016   2.705   0.837  HOP2    XNY  36  
XNY  OP3     OP3  O  0  1  N  Y  N  -19.979   3.471   1.710  -5.335   1.759  -1.520  OP3     XNY  37  
XNY  HOP3    H15  H  0  0  N  Y  N  -20.640   4.129   1.891  -6.176   2.224  -1.414  HOP3    XNY  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
XNY  "O2'"  "C2'"   SING  N  N   1  
XNY  C2     C3      DOUB  Y  N   2  
XNY  C2     N1      SING  Y  N   3  
XNY  C3     C4      SING  Y  N   4  
XNY  "C2'"  "C1'"   SING  N  N   5  
XNY  "C2'"  "C3'"   SING  N  N   6  
XNY  "O3'"  "C3'"   SING  N  N   7  
XNY  N1     C6      DOUB  Y  N   8  
XNY  "C1'"  N9      SING  N  N   9  
XNY  "C1'"  "O4'"   SING  N  N  10  
XNY  C4     N9      SING  Y  N  11  
XNY  C4     C5      DOUB  Y  N  12  
XNY  "C3'"  "C4'"   SING  N  N  13  
XNY  N9     C8      SING  Y  N  14  
XNY  "C4'"  "O4'"   SING  N  N  15  
XNY  "C4'"  "C5'"   SING  N  N  16  
XNY  C6     C5      SING  Y  N  17  
XNY  C6     N6      SING  N  N  18  
XNY  C5     N7      SING  Y  N  19  
XNY  C8     N7      DOUB  Y  N  20  
XNY  "C5'"  "O5'"   SING  N  N  21  
XNY  "O5'"  P       SING  N  N  22  
XNY  P      OP1     DOUB  N  N  23  
XNY  P      OP2     SING  N  N  24  
XNY  C2     H2      SING  N  N  25  
XNY  C3     H3      SING  N  N  26  
XNY  C8     H8      SING  N  N  27  
XNY  "C1'"  "H1'"   SING  N  N  28  
XNY  "C2'"  "H2'"   SING  N  N  29  
XNY  "C3'"  "H3'"   SING  N  N  30  
XNY  "C4'"  "H4'"   SING  N  N  31  
XNY  "C5'"  "H5'"   SING  N  N  32  
XNY  "C5'"  "H5''"  SING  N  N  33  
XNY  N6     H61     SING  N  N  34  
XNY  N6     H62     SING  N  N  35  
XNY  "O2'"  "HO2'"  SING  N  N  36  
XNY  "O3'"  "HO3'"  SING  N  N  37  
XNY  OP2    HOP2    SING  N  N  38  
XNY  P      OP3     SING  N  N  39  
XNY  OP3    HOP3    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
XNY  SMILES            ACDLabs               12.01  "c3cc2c(ncn2C1OC(C(C1O)O)COP(=O)(O)O)c(N)n3"  
XNY  InChI             InChI                 1.03   "InChI=1S/C11H15N4O7P/c12-10-7-5(1-2-13-10)15(4-14-7)11-9(17)8(16)6(22-11)3-21-23(18,19)20/h1-2,4,6,8-9,11,16-17H,3H2,(H2,12,13)(H2,18,19,20)/t6-,8-,9-,11-/m1/s1"  
XNY  InChIKey          InChI                 1.03   YZVSCCUSJPOQJU-PNHWDRBUSA-N  
XNY  SMILES_CANONICAL  CACTVS                3.385  "Nc1nccc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O"  
XNY  SMILES            CACTVS                3.385  "Nc1nccc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O"  
XNY  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cnc(c2c1n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N"  
XNY  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cnc(c2c1n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N"  
#   #
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
XNY  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazo[4,5-c]pyridin-4-amine"  
XNY  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylimidazo[4,5-c]pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XNY  "Create component"  2020-12-22  RCSB  
XNY  "Initial release"   2021-05-05  RCSB  
##
