data_XYA
#

_chem_comp.id                                   XYA
_chem_comp.name                                 "2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H13 N5 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        9-BETA-D-XYLOFURANOSYL-ADENINE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2003-06-23
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       267.241
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XYA
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1PR6
_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
XYA  "O5'"   "O5'"   O  0  1  N  N  N  94.357  65.880  17.586  -4.519   1.826  -1.189  "O5'"   XYA   1  
XYA  "C5'"   "C5'"   C  0  1  N  N  N  94.019  65.045  18.688  -4.276   0.880  -0.146  "C5'"   XYA   2  
XYA  "C4'"   "C4'"   C  0  1  N  N  R  94.431  65.705  20.014  -3.129  -0.047  -0.556  "C4'"   XYA   3  
XYA  "O4'"   "O4'"   O  0  1  N  N  N  93.719  66.925  20.239  -1.892   0.693  -0.643  "O4'"   XYA   4  
XYA  "C1'"   "C1'"   C  0  1  N  N  R  92.551  66.686  21.079  -0.848  -0.299  -0.539  "C1'"   XYA   5  
XYA  N9      N9      N  0  1  Y  N  N  91.438  67.218  20.222   0.411   0.327  -0.126  N9      XYA   6  
XYA  C8      C8      C  0  1  Y  N  N  91.299  68.535  19.904   0.545   1.517   0.525  C8      XYA   7  
XYA  N7      N7      N  0  1  Y  N  N  90.361  68.841  19.070   1.804   1.769   0.736  N7      XYA   8  
XYA  C5      C5      C  0  1  Y  N  N  89.790  67.602  18.786   2.556   0.757   0.240  C5      XYA   9  
XYA  C6      C6      C  0  1  Y  N  N  88.724  67.221  17.944   3.934   0.492   0.172  C6      XYA  10  
XYA  N1      N1      N  0  1  Y  N  N  88.377  65.898  17.866   4.334  -0.632  -0.413  N1      XYA  11  
XYA  C2      C2      C  0  1  Y  N  N  89.058  65.000  18.589   3.465  -1.484  -0.924  C2      XYA  12  
XYA  N3      N3      N  0  1  Y  N  N  90.097  65.249  19.425   2.166  -1.275  -0.888  N3      XYA  13  
XYA  C4      C4      C  0  1  Y  N  N  90.423  66.585  19.483   1.672  -0.178  -0.324  C4      XYA  14  
XYA  N6      N6      N  0  1  N  N  N  88.061  68.121  17.232   4.853   1.379   0.705  N6      XYA  15  
XYA  "C2'"   "C2'"   C  0  1  N  N  R  92.617  65.175  21.405  -1.340  -1.282   0.546  "C2'"   XYA  16  
XYA  "O2'"   "O2'"   O  0  1  N  N  N  92.250  64.890  22.747  -0.985  -2.626   0.212  "O2'"   XYA  17  
XYA  "C3'"   "C3'"   C  0  1  N  N  R  94.100  64.899  21.231  -2.878  -1.110   0.535  "C3'"   XYA  18  
XYA  "O3'"   "O3'"   O  0  1  N  N  N  94.463  63.557  21.055  -3.342  -0.645   1.804  "O3'"   XYA  19  
XYA  "H5'"   "H5'"   H  0  1  N  N  N  94.102  65.472  16.767  -5.247   2.389  -0.891  "H5'"   XYA  20  
XYA  "H5'1"  "1H5'"  H  0  0  N  N  N  94.453  64.024  18.582  -5.176   0.290   0.026  "H5'1"  XYA  21  
XYA  "H5'2"  "2H5'"  H  0  0  N  N  N  92.939  64.769  18.682  -4.007   1.408   0.768  "H5'2"  XYA  22  
XYA  "H4'"   "H4'"   H  0  1  N  N  N  95.532  65.833  19.894  -3.352  -0.526  -1.509  "H4'"   XYA  23  
XYA  "H1'"   "H1'"   H  0  1  N  N  N  92.442  67.174  22.075  -0.719  -0.816  -1.490  "H1'"   XYA  24  
XYA  H8      H8      H  0  1  N  N  N  91.934  69.338  20.314  -0.274   2.156   0.821  H8      XYA  25  
XYA  H2      H2      H  0  1  N  N  N  88.731  63.952  18.486   3.833  -2.386  -1.390  H2      XYA  26  
XYA  HN61    1HN6    H  0  0  N  N  N  88.736  68.642  16.672   5.802   1.183   0.655  HN61    XYA  27  
XYA  HN62    2HN6    H  0  0  N  N  N  87.290  67.846  16.623   4.549   2.199   1.125  HN62    XYA  28  
XYA  "H2'"   "H2'"   H  0  1  N  N  N  91.928  64.569  20.773  -0.932  -1.011   1.519  "H2'"   XYA  29  
XYA  H1      H1      H  0  1  N  N  N  92.291  63.962  22.947  -1.372  -3.194   0.892  H1      XYA  30  
XYA  "H3'"   "H3'"   H  0  1  N  N  N  94.659  65.166  22.158  -3.364  -2.050   0.273  "H3'"   XYA  31  
XYA  H3      H3      H  0  1  N  N  N  94.253  63.045  21.827  -4.294  -0.500   1.717  H3      XYA  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
XYA  "O5'"  "C5'"   SING  N  N   1  
XYA  "O5'"  "H5'"   SING  N  N   2  
XYA  "C5'"  "C4'"   SING  N  N   3  
XYA  "C5'"  "H5'1"  SING  N  N   4  
XYA  "C5'"  "H5'2"  SING  N  N   5  
XYA  "C4'"  "O4'"   SING  N  N   6  
XYA  "C4'"  "C3'"   SING  N  N   7  
XYA  "C4'"  "H4'"   SING  N  N   8  
XYA  "O4'"  "C1'"   SING  N  N   9  
XYA  "C1'"  N9      SING  N  N  10  
XYA  "C1'"  "C2'"   SING  N  N  11  
XYA  "C1'"  "H1'"   SING  N  N  12  
XYA  N9     C8      SING  Y  N  13  
XYA  N9     C4      SING  Y  N  14  
XYA  C8     N7      DOUB  Y  N  15  
XYA  C8     H8      SING  N  N  16  
XYA  N7     C5      SING  Y  N  17  
XYA  C5     C6      DOUB  Y  N  18  
XYA  C5     C4      SING  Y  N  19  
XYA  C6     N1      SING  Y  N  20  
XYA  C6     N6      SING  N  N  21  
XYA  N1     C2      DOUB  Y  N  22  
XYA  C2     N3      SING  Y  N  23  
XYA  C2     H2      SING  N  N  24  
XYA  N3     C4      DOUB  Y  N  25  
XYA  N6     HN61    SING  N  N  26  
XYA  N6     HN62    SING  N  N  27  
XYA  "C2'"  "O2'"   SING  N  N  28  
XYA  "C2'"  "C3'"   SING  N  N  29  
XYA  "C2'"  "H2'"   SING  N  N  30  
XYA  "O2'"  H1      SING  N  N  31  
XYA  "C3'"  "O3'"   SING  N  N  32  
XYA  "C3'"  "H3'"   SING  N  N  33  
XYA  "O3'"  H3      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
XYA  SMILES            ACDLabs               10.04  "n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N"  
XYA  SMILES_CANONICAL  CACTVS                3.341  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H](O)[C@H]3O"  
XYA  SMILES            CACTVS                3.341  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O"  
XYA  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@H](O3)CO)O)O)N"  
XYA  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N"  
XYA  InChI             InChI                 1.03   "InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6+,7-,10-/m1/s1"  
XYA  InChIKey          InChI                 1.03   OIRDTQYFTABQOQ-GAWUUDPSSA-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
XYA  "SYSTEMATIC NAME"  ACDLabs               10.04  9-beta-D-xylofuranosyl-9H-purin-6-amine  
XYA  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2R,3R,4R,5R)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XYA  "Create component"   2003-06-23  RCSB  
XYA  "Modify descriptor"  2011-06-04  RCSB  
XYA  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     XYA
_pdbx_chem_comp_synonyms.name        9-BETA-D-XYLOFURANOSYL-ADENINE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
