data_5JO
#

_chem_comp.id                                   5JO
_chem_comp.name                                 "2'-O-prop-2-yn-1-yladenosine 5'-(dihydrogen phosphate)"
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C13 H16 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2'-Propargyl-Adenosine"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-10-02
_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                       385.269
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5JO
_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       5E36
_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
5JO  "O5'"  O1   O  0  1  N  N  N  10.293  20.969   -9.088   3.763  -0.285  -0.506  "O5'"  5JO   1  
5JO  "C5'"  C1   C  0  1  N  N  N   9.041  21.641   -9.281   3.010   0.543   0.383  "C5'"  5JO   2  
5JO  "C4'"  C2   C  0  1  N  N  R   8.028  21.154   -8.276   1.651   0.861  -0.245  "C4'"  5JO   3  
5JO  "O4'"  O2   O  0  1  N  N  N   7.731  19.750   -8.505   0.826  -0.324  -0.287  "O4'"  5JO   4  
5JO  "C3'"  C3   C  0  1  N  N  R   8.449  21.191   -6.812   0.869   1.856   0.640  "C3'"  5JO   5  
5JO  "O3'"  O3   O  0  1  N  Y  N   8.391  22.516   -6.283   1.007   3.187   0.139  "O3'"  5JO   6  
5JO  "C2'"  C4   C  0  1  N  N  R   7.442  20.226   -6.202  -0.598   1.384   0.529  "C2'"  5JO   7  
5JO  "O2'"  O4   O  0  1  N  N  N   6.176  20.840   -6.033  -1.412   2.410  -0.044  "O2'"  5JO   8  
5JO  "C1'"  C5   C  0  1  N  N  R   7.407  19.128   -7.269  -0.529   0.160  -0.411  "C1'"  5JO   9  
5JO  N9     N1   N  0  1  Y  N  N   8.371  18.052   -7.024  -1.479  -0.868   0.021  N9     5JO  10  
5JO  C8     C6   C  0  1  Y  N  N   9.653  17.935   -7.502  -1.220  -1.898   0.875  C8     5JO  11  
5JO  N7     N2   N  0  1  Y  N  N  10.272  16.853   -7.096  -2.290  -2.621   1.037  N7     5JO  12  
5JO  C5     C7   C  0  1  Y  N  N   9.335  16.213   -6.297  -3.301  -2.101   0.299  C5     5JO  13  
5JO  C6     C8   C  0  1  Y  N  N   9.375  15.011   -5.570  -4.647  -2.446   0.085  C6     5JO  14  
5JO  N6     N3   N  0  1  N  N  N  10.441  14.207   -5.527  -5.203  -3.549   0.709  N6     5JO  15  
5JO  N1     N4   N  0  1  Y  N  N   8.274  14.665   -4.869  -5.372  -1.689  -0.731  N1     5JO  16  
5JO  C2     C9   C  0  1  Y  N  N   7.206  15.473   -4.912  -4.850  -0.635  -1.331  C2     5JO  17  
5JO  N3     N5   N  0  1  Y  N  N   7.048  16.627   -5.557  -3.595  -0.274  -1.160  N3     5JO  18  
5JO  C4     C10  C  0  1  Y  N  N   8.162  16.944   -6.240  -2.794  -0.967  -0.357  C4     5JO  19  
5JO  P      P1   P  0  1  N  N  N  11.537  21.262  -10.036   5.245  -0.815  -0.166  P      5JO  20  
5JO  OP1    O5   O  0  1  N  N  N  11.661  22.720  -10.306   6.120   0.336   0.151  OP1    5JO  21  
5JO  OP2    O6   O  0  1  N  N  N  12.693  20.534   -9.455   5.183  -1.806   1.101  OP2    5JO  22  
5JO  "C6'"  C11  C  0  1  N  N  N   5.267  19.976   -5.384  -2.011   3.281   0.917  "C6'"  5JO  23  
5JO  "C7'"  C12  C  0  1  N  N  N   4.430  20.869   -4.675  -2.823   4.294   0.222  "C7'"  5JO  24  
5JO  "C8'"  C13  C  0  1  N  N  N   3.649  21.627   -4.054  -3.470   5.101  -0.332  "C8'"  5JO  25  
5JO  H1     H1   H  0  1  N  N  N   9.187  22.724   -9.154   2.859   0.020   1.327  H1     5JO  26  
5JO  H2     H2   H  0  1  N  N  N   8.672  21.437  -10.297   3.553   1.470   0.563  H2     5JO  27  
5JO  H3     H3   H  0  1  N  N  N   7.107  21.745   -8.389   1.784   1.268  -1.248  H3     5JO  28  
5JO  H4     H4   H  0  1  N  N  N   9.462  20.775   -6.712   1.213   1.800   1.673  H4     5JO  29  
5JO  H5     H5   H  0  1  N  N  N   8.658  22.506   -5.371   1.917   3.512   0.130  H5     5JO  30  
5JO  H6     H6   H  0  1  N  N  N   7.829  19.821   -5.255  -0.982   1.096   1.508  H6     5JO  31  
5JO  H7     H7   H  0  1  N  N  N   6.391  18.709   -7.310  -0.733   0.457  -1.439  H7     5JO  32  
5JO  H8     H8   H  0  1  N  N  N  10.109  18.667   -8.152  -0.268  -2.087   1.347  H8     5JO  33  
5JO  H9     H9   H  0  1  N  N  N  10.243  13.421   -4.942  -4.663  -4.094   1.303  H9     5JO  34  
5JO  H10    H10  H  0  1  N  N  N  10.656  13.889   -6.450  -6.133  -3.777   0.553  H10    5JO  35  
5JO  H11    H11  H  0  1  N  N  N   6.351  15.141   -4.342  -5.475  -0.047  -1.986  H11    5JO  36  
5JO  H13    H13  H  0  1  N  N  N  13.414  21.138   -9.322   4.627  -2.585   0.964  H13    5JO  37  
5JO  H14    H14  H  0  1  N  N  N   4.690  19.389   -6.114  -2.648   2.701   1.585  H14    5JO  38  
5JO  H15    H15  H  0  1  N  N  N   5.791  19.295   -4.697  -1.231   3.775   1.496  H15    5JO  39  
5JO  H16    H16  H  0  1  N  N  N   2.988  22.268   -3.529  -4.049   5.824  -0.827  H16    5JO  40  
5JO  OP3    OP3  O  0  1  N  Y  N  11.129  20.546  -11.408   5.837  -1.605  -1.438  OP3    5JO  41  
5JO  H12    H12  H  0  1  N  Y  N  11.054  21.197  -12.095   6.729  -1.953  -1.304  H12    5JO  42  
#   #
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
5JO  OP1    P      DOUB  N  N   1  
5JO  P      OP2    SING  N  N   2  
5JO  P      "O5'"  SING  N  N   3  
5JO  "C5'"  "O5'"  SING  N  N   4  
5JO  "C5'"  "C4'"  SING  N  N   5  
5JO  "O4'"  "C4'"  SING  N  N   6  
5JO  "O4'"  "C1'"  SING  N  N   7  
5JO  "C4'"  "C3'"  SING  N  N   8  
5JO  C8     N7     DOUB  Y  N   9  
5JO  C8     N9     SING  Y  N  10  
5JO  "C1'"  N9     SING  N  N  11  
5JO  "C1'"  "C2'"  SING  N  N  12  
5JO  N7     C5     SING  Y  N  13  
5JO  N9     C4     SING  Y  N  14  
5JO  "C3'"  "O3'"  SING  N  N  15  
5JO  "C3'"  "C2'"  SING  N  N  16  
5JO  C5     C4     DOUB  Y  N  17  
5JO  C5     C6     SING  Y  N  18  
5JO  C4     N3     SING  Y  N  19  
5JO  "C2'"  "O2'"  SING  N  N  20  
5JO  "O2'"  "C6'"  SING  N  N  21  
5JO  C6     N6     SING  N  N  22  
5JO  C6     N1     DOUB  Y  N  23  
5JO  N3     C2     DOUB  Y  N  24  
5JO  "C6'"  "C7'"  SING  N  N  25  
5JO  C2     N1     SING  Y  N  26  
5JO  "C7'"  "C8'"  TRIP  N  N  27  
5JO  "C5'"  H1     SING  N  N  28  
5JO  "C5'"  H2     SING  N  N  29  
5JO  "C4'"  H3     SING  N  N  30  
5JO  "C3'"  H4     SING  N  N  31  
5JO  "O3'"  H5     SING  N  N  32  
5JO  "C2'"  H6     SING  N  N  33  
5JO  "C1'"  H7     SING  N  N  34  
5JO  C8     H8     SING  N  N  35  
5JO  N6     H9     SING  N  N  36  
5JO  N6     H10    SING  N  N  37  
5JO  C2     H11    SING  N  N  38  
5JO  OP2    H13    SING  N  N  39  
5JO  "C6'"  H14    SING  N  N  40  
5JO  "C6'"  H15    SING  N  N  41  
5JO  "C8'"  H16    SING  N  N  42  
5JO  P      OP3    SING  N  N  43  
5JO  OP3    H12    SING  N  N  44  
#   #
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
5JO  SMILES            ACDLabs               12.01  "O(CC1C(O)C(OCC#C)C(O1)n2c3c(nc2)c(N)ncn3)P(O)(O)=O"  
5JO  InChI             InChI                 1.03   "InChI=1S/C13H16N5O7P/c1-2-3-23-10-9(19)7(4-24-26(20,21)22)25-13(10)18-6-17-8-11(14)15-5-16-12(8)18/h1,5-7,9-10,13,19H,3-4H2,(H2,14,15,16)(H2,20,21,22)/t7-,9-,10-,13-/m1/s1"  
5JO  InChIKey          InChI                 1.03   ODQWOSMBGNICLO-QYVSTXNMSA-N  
5JO  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3OCC#C"  
5JO  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3OCC#C"  
5JO  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "C#CCO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP(=O)(O)O)O"  
5JO  SMILES            "OpenEye OEToolkits"  1.9.2  "C#CCOC1C(C(OC1n2cnc3c2ncnc3N)COP(=O)(O)O)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
5JO  "SYSTEMATIC NAME"  ACDLabs               12.01  "2'-O-prop-2-yn-1-yladenosine 5'-(dihydrogen phosphate)"  
5JO  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-prop-2-ynoxy-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
5JO  "Create component"  2015-10-02  RCSB  
5JO  "Modify synonyms"   2015-10-05  RCSB  
5JO  "Initial release"   2015-12-02  RCSB  
5JO  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5JO
_pdbx_chem_comp_synonyms.name        "2'-Propargyl-Adenosine"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
