data_56B
#

_chem_comp.id                                   56B
_chem_comp.name                                 "2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C17 H24 N5 O10 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-08-03
_chem_comp.pdbx_modified_date                   2020-06-27
_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                       489.374
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    56B
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       5D0B
_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
56B  N9      N1   N  0  1  Y  N  N  -24.162  -16.737  -35.563   0.257   1.569   0.022  N9     56B   1  
56B  "C2'"   C1   C  0  1  N  N  R  -26.225  -17.695  -34.440   2.345   2.464   0.996  "C2'"  56B   2  
56B  "O2'"   O1   O  0  1  N  N  N  -26.070  -19.093  -34.559   2.504   3.854   0.709  "O2'"  56B   3  
56B  P       P1   P  0  1  N  N  N  -28.699  -12.960  -32.525   5.159  -2.961  -0.403  P      56B   4  
56B  "C1'"   C2   C  0  1  N  N  R  -25.610  -16.953  -35.625   1.696   1.735  -0.201  "C1'"  56B   5  
56B  N10     N2   N  0  1  N  N  N  -19.577  -16.001  -34.489  -3.316  -1.045   0.010  N10    56B   6  
56B  O11     O2   O  0  1  N  N  N  -17.623  -14.033  -32.154  -3.763  -4.296  -0.240  O11    56B   7  
56B  C8      C3   C  0  1  Y  N  N  -23.449  -16.247  -34.488  -0.332   0.448   0.552  C8     56B   8  
56B  N3      N3   N  0  1  N  N  N  -23.629  -17.437  -37.818  -0.643   3.743  -0.780  N3     56B   9  
56B  O12     O3   O  0  1  N  N  N  -15.652  -13.561  -34.024  -6.277  -4.477   0.461  O12    56B  10  
56B  C7      C4   C  0  1  Y  N  N  -22.108  -16.143  -34.803  -1.661   0.627   0.620  C7     56B  11  
56B  N2      N4   N  0  1  N  N  N  -22.771  -17.991  -39.888  -1.633   5.707  -1.498  N2     56B  12  
56B  O6      O4   O  0  1  N  N  N  -19.729  -16.489  -36.859  -4.198   2.293   0.197  O6     56B  13  
56B  C9      C5   C  0  1  N  N  N  -20.928  -15.650  -33.976  -2.676  -0.359   1.140  C9     56B  14  
56B  N1      N5   N  0  1  N  N  N  -21.305  -17.223  -38.288  -2.970   3.969  -0.634  N1     56B  15  
56B  "O4'"   O5   O  0  1  N  N  N  -26.252  -15.692  -35.666   2.349   0.448  -0.249  "O4'"  56B  16  
56B  C10     C6   C  0  1  N  N  S  -18.495  -15.842  -33.505  -4.313  -2.016   0.480  C10    56B  17  
56B  "O5'"   O6   O  0  1  N  N  N  -28.522  -14.418  -33.140   4.489  -1.505  -0.556  "O5'"  56B  18  
56B  C11     C7   C  0  1  N  N  R  -17.961  -14.407  -33.489  -4.519  -3.130  -0.573  C11    56B  19  
56B  OP2     O7   O  0  1  N  N  N  -27.953  -11.995  -33.363   5.147  -3.710  -1.828  OP2    56B  20  
56B  C12     C8   C  0  1  N  N  S  -16.706  -14.449  -34.403  -6.036  -3.397  -0.444  C12    56B  21  
56B  C13     C9   C  0  1  N  N  N  -16.240  -15.884  -34.346  -6.607  -2.111   0.108  C13    56B  22  
56B  OP1     O8   O  0  1  N  N  N  -28.442  -13.023  -31.070   6.556  -2.815   0.065  OP1    56B  23  
56B  C14     C10  C  0  1  N  N  N  -17.242  -16.673  -33.851  -5.667  -1.358   0.612  C14    56B  24  
56B  "O3'"   O9   O  0  1  N  N  N  -28.263  -17.870  -35.657   4.778   2.727   0.963  "O3'"  56B  25  
56B  C5      C11  C  0  1  Y  N  N  -22.003  -16.608  -36.170  -1.934   1.962   0.092  C5     56B  26  
56B  C4      C12  C  0  1  Y  N  N  -23.297  -16.964  -36.598  -0.691   2.507  -0.262  C4     56B  27  
56B  C2      C13  C  0  1  N  N  N  -22.584  -17.548  -38.644  -1.736   4.448  -0.961  C2     56B  28  
56B  C6      C14  C  0  1  N  N  N  -20.917  -16.740  -37.054  -3.101   2.732  -0.104  C6     56B  29  
56B  "C4'"   C15  C  0  1  N  N  R  -27.462  -15.742  -34.868   3.741   0.717   0.028  "C4'"  56B  30  
56B  "C5'"   C16  C  0  1  N  N  N  -27.276  -14.841  -33.674   4.444  -0.554   0.509  "C5'"  56B  31  
56B  "C3'"   C17  C  0  1  N  N  S  -27.664  -17.215  -34.535   3.723   1.782   1.152  "C3'"  56B  32  
56B  H1      H1   H  0  1  N  N  N  -25.776  -17.326  -33.506   1.747   2.326   1.897  H1     56B  33  
56B  H2      H2   H  0  1  N  N  N  -26.463  -19.521  -33.807   2.934   4.355   1.416  H2     56B  34  
56B  H3      H3   H  0  1  N  N  N  -25.846  -17.516  -36.540   1.875   2.287  -1.124  H3     56B  35  
56B  H4      H4   H  0  1  N  N  N  -19.593  -16.956  -34.785  -3.730  -0.382  -0.628  H4     56B  36  
56B  H6      H6   H  0  1  N  N  N  -18.409  -14.016  -31.621  -3.860  -5.021  -0.872  H6     56B  37  
56B  H7      H7   H  0  1  N  N  N  -23.879  -15.982  -33.534   0.194  -0.441   0.866  H7     56B  38  
56B  H8      H8   H  0  1  N  N  N  -15.963  -12.664  -34.066  -7.214  -4.656   0.618  H8     56B  39  
56B  H9      H9   H  0  1  N  N  N  -23.689  -18.238  -40.198  -2.431   6.241  -1.638  H9     56B  40  
56B  H10     H10  H  0  1  N  N  N  -21.993  -18.076  -40.511  -0.763   6.063  -1.736  H10    56B  41  
56B  H11     H11  H  0  1  N  N  N  -20.992  -14.553  -33.920  -3.432   0.170   1.720  H11    56B  42  
56B  H12     H12  H  0  1  N  N  N  -21.025  -16.075  -32.966  -2.178  -1.092   1.775  H12    56B  43  
56B  H13     H13  H  0  1  N  N  N  -20.592  -17.345  -38.978  -3.756   4.519  -0.779  H13    56B  44  
56B  H14     H14  H  0  1  N  N  N  -18.848  -16.115  -32.500  -4.004  -2.446   1.433  H14    56B  45  
56B  H15     H15  H  0  1  N  N  N  -18.709  -13.725  -33.920  -4.267  -2.775  -1.572  H15    56B  46  
56B  H16     H16  H  0  1  N  N  N  -27.355  -11.497  -32.818   5.536  -4.595  -1.811  H16    56B  47  
56B  H17     H17  H  0  1  N  N  N  -17.026  -14.225  -35.431  -6.469  -3.616  -1.420  H17    56B  48  
56B  H18     H18  H  0  1  N  N  N  -15.265  -16.234  -34.650  -7.654  -1.849   0.088  H18    56B  49  
56B  H21     H21  H  0  1  N  N  N  -17.166  -17.742  -33.719  -5.835  -0.392   1.064  H21    56B  50  
56B  H23     H23  H  0  1  N  N  N  -28.392  -18.789  -35.456   4.813   3.417   1.639  H23    56B  51  
56B  H24     H24  H  0  1  N  N  N  -28.319  -15.387  -35.460   4.235   1.112  -0.859  H24    56B  52  
56B  H25     H25  H  0  1  N  N  N  -26.722  -15.388  -32.897   3.895  -0.976   1.351  H25    56B  53  
56B  H26     H26  H  0  1  N  N  N  -26.700  -13.956  -33.981   5.459  -0.311   0.823  H26    56B  54  
56B  H27     H27  H  0  1  N  N  N  -28.214  -17.357  -33.593   3.808   1.307   2.129  H27    56B  55  
56B  OP3     O10  O  0  1  N  Y  N        ?        ?        ?   4.324  -3.828   0.666  O1     56B  56  
56B  HOP3    H5   H  0  0  N  Y  N        ?        ?        ?   3.398  -3.964   0.424  H5     56B  57  
#   #
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
56B  N2     C2      SING  N  N   1  
56B  C2     N1      SING  N  N   2  
56B  C2     N3      DOUB  N  N   3  
56B  N1     C6      SING  N  N   4  
56B  N3     C4      SING  N  N   5  
56B  C6     O6      DOUB  N  N   6  
56B  C6     C5      SING  N  N   7  
56B  C4     C5      DOUB  Y  N   8  
56B  C4     N9      SING  Y  N   9  
56B  C5     C7      SING  Y  N  10  
56B  "O4'"  "C1'"   SING  N  N  11  
56B  "O4'"  "C4'"   SING  N  N  12  
56B  "O3'"  "C3'"   SING  N  N  13  
56B  "C1'"  N9      SING  N  N  14  
56B  "C1'"  "C2'"   SING  N  N  15  
56B  N9     C8      SING  Y  N  16  
56B  "C4'"  "C3'"   SING  N  N  17  
56B  "C4'"  "C5'"   SING  N  N  18  
56B  C7     C8      DOUB  Y  N  19  
56B  C7     C9      SING  N  N  20  
56B  "O2'"  "C2'"   SING  N  N  21  
56B  "C3'"  "C2'"   SING  N  N  22  
56B  N10    C9      SING  N  N  23  
56B  N10    C10     SING  N  N  24  
56B  C12    C13     SING  N  N  25  
56B  C12    O12     SING  N  N  26  
56B  C12    C11     SING  N  N  27  
56B  C13    C14     DOUB  N  N  28  
56B  C14    C10     SING  N  N  29  
56B  "C5'"  "O5'"   SING  N  N  30  
56B  C10    C11     SING  N  N  31  
56B  C11    O11     SING  N  N  32  
56B  OP2    P       SING  N  N  33  
56B  "O5'"  P       SING  N  N  34  
56B  P      OP1     DOUB  N  N  35  
56B  "C2'"  H1      SING  N  N  36  
56B  "O2'"  H2      SING  N  N  37  
56B  "C1'"  H3      SING  N  N  38  
56B  N10    H4      SING  N  N  39  
56B  O11    H6      SING  N  N  40  
56B  C8     H7      SING  N  N  41  
56B  O12    H8      SING  N  N  42  
56B  N2     H9      SING  N  N  43  
56B  N2     H10     SING  N  N  44  
56B  C9     H11     SING  N  N  45  
56B  C9     H12     SING  N  N  46  
56B  N1     H13     SING  N  N  47  
56B  C10    H14     SING  N  N  48  
56B  C11    H15     SING  N  N  49  
56B  OP2    H16     SING  N  N  50  
56B  C12    H17     SING  N  N  51  
56B  C13    H18     SING  N  N  52  
56B  C14    H21     SING  N  N  53  
56B  "O3'"  H23     SING  N  N  54  
56B  "C4'"  H24     SING  N  N  55  
56B  "C5'"  H25     SING  N  N  56  
56B  "C5'"  H26     SING  N  N  57  
56B  "C3'"  H27     SING  N  N  58  
56B  P      OP3     SING  N  N  59  
56B  OP3    HOP3    SING  N  N  60  
#   #
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
56B  SMILES            ACDLabs               12.01  "n2(cc(CNC1C(O)C(O)C=C1)c3c2N=C(N)NC3=O)C4C(O)C(O)C(O4)COP(=O)(O)O"  
56B  InChI             InChI                 1.03   "InChI=1S/C17H24N5O10P/c18-17-20-14-10(15(27)21-17)6(3-19-7-1-2-8(23)11(7)24)4-22(14)16-13(26)12(25)9(32-16)5-31-33(28,29)30/h1-2,4,7-9,11-13,16,19,23-26H,3,5H2,(H2,28,29,30)(H3,18,20,21,27)/t7-,8-,9+,11+,12+,13+,16+/m0/s1"  
56B  InChIKey          InChI                 1.03   BSABGNSIPKXNDL-AEZJAUAXSA-N  
56B  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cc(CN[C@H]3C=C[C@H](O)[C@@H]3O)c2C(=O)N1)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O"  
56B  SMILES            CACTVS                3.385  "NC1=Nc2n(cc(CN[CH]3C=C[CH](O)[CH]3O)c2C(=O)N1)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O"  
56B  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "c1c(c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CN[C@H]4C=C[C@@H]([C@@H]4O)O"  
56B  SMILES            "OpenEye OEToolkits"  1.9.2  "c1c(c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CNC4C=CC(C4O)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
56B  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one"  
56B  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "[(2R,3S,4R,5R)-5-[2-azanyl-5-[[[(1S,4S,5R)-4,5-bis(oxidanyl)cyclopent-2-en-1-yl]amino]methyl]-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-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
56B  "Create component"    2015-08-03  RCSB  
56B  "Initial release"     2016-09-28  RCSB  
56B  "Other modification"  2020-06-27  RCSB  
##
