data_JNT
# 
_chem_comp.id                                    JNT 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H25 N5 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-03-13 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        561.332 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     JNT 
_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        6R0R 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
JNT "O5'" O1  O 0 1 N N N N N N 11.482 7.295 10.123 -0.739 1.996  -0.105 "O5'"  JNT 1  
JNT "C5'" C1  C 0 1 N N N N N N 12.844 7.010 10.389 -2.030 2.596  0.026  "C5'"  JNT 2  
JNT "C4'" C2  C 0 1 N N R N N N 13.597 7.017 9.086  -3.013 1.903  -0.918 "C4'"  JNT 3  
JNT "O4'" O2  O 0 1 N N N N N N 13.102 6.090 8.127  -3.224 0.546  -0.495 "O4'"  JNT 4  
JNT "C3'" C3  C 0 1 N N S N N N 13.403 8.349 8.465  -4.378 2.618  -0.871 "C3'"  JNT 5  
JNT "O3'" O3  O 0 1 N N N N N N 14.646 9.028 8.469  -4.726 3.117  -2.164 "O3'"  JNT 6  
JNT "C2'" C4  C 0 1 N N R N N N 12.827 8.195 7.072  -5.370 1.515  -0.430 "C2'"  JNT 7  
JNT "O2'" O4  O 0 1 N N N N N N 13.543 8.890 6.048  -6.593 1.607  -1.162 "O2'"  JNT 8  
JNT "C1'" C5  C 0 1 N N R N N N 12.921 6.711 6.856  -4.597 0.218  -0.799 "C1'"  JNT 9  
JNT N9    N1  N 0 1 Y N N N N N 11.652 6.123 6.358  -5.054 -0.906 0.022  N9     JNT 10 
JNT C8    C6  C 0 1 Y N N N N N 10.410 6.605 6.541  -4.484 -1.344 1.180  C8     JNT 11 
JNT N7    N2  N 0 1 Y N N N N N 9.487  5.820 5.986  -5.147 -2.363 1.645  N7     JNT 12 
JNT C5    C7  C 0 1 Y N N N N N 10.171 4.781 5.429  -6.182 -2.643 0.817  C5     JNT 13 
JNT C4    C8  C 0 1 Y N N N N N 11.588 4.983 5.665  -6.138 -1.708 -0.232 C4     JNT 14 
JNT N3    N3  N 0 1 Y N N N N N 12.509 4.088 5.200  -7.058 -1.768 -1.189 N3     JNT 15 
JNT C2    C9  C 0 1 Y N N N N N 12.067 3.026 4.509  -7.998 -2.689 -1.160 C2     JNT 16 
JNT N1    N4  N 0 1 Y N N N N N 10.756 2.791 4.302  -8.080 -3.588 -0.196 N1     JNT 17 
JNT C6    C10 C 0 1 Y N N N N N 9.780  3.619 4.681  -7.210 -3.601 0.809  C6     JNT 18 
JNT N6    N5  N 0 1 N N N N N N 8.472  3.377 4.459  -7.303 -4.547 1.814  N6     JNT 19 
JNT O1C   O5  O 0 1 N N N N N N 4.712  5.445 14.372 9.744  -4.227 -0.550 "O1'A" JNT 20 
JNT C1A   C11 C 0 1 N N N N N N 4.439  6.394 13.544 9.393  -2.887 -0.201 "C1'A" JNT 21 
JNT C2A   C12 C 0 1 N N S N N N 5.630  7.245 13.110 7.908  -2.657 -0.491 "C2'A" JNT 22 
JNT O2C   O6  O 0 1 N N N N N N 6.601  6.389 12.474 7.676  -2.754 -1.897 "O2'A" JNT 23 
JNT C3A   C13 C 0 1 N N S N N N 6.262  7.947 14.328 7.503  -1.265 -0.002 "C3'A" JNT 24 
JNT O3C   O7  O 0 1 N N N N N N 5.340  8.834 15.037 7.735  -1.167 1.405  "O3'A" JNT 25 
JNT C4A   C14 C 0 1 N N R N N N 7.480  8.810 13.994 6.018  -1.035 -0.291 "C4'A" JNT 26 
JNT O4C   O8  O 0 1 N N N N N N 7.573  9.150 12.613 5.786  -1.132 -1.698 "O4'A" JNT 27 
JNT C5A   C15 C 0 1 N N N N N N 8.808  8.179 14.393 5.613  0.357  0.197  "C5'A" JNT 28 
JNT O5A   O9  O 0 1 N N N N N N 9.881  9.133 14.238 4.203  0.528  0.033  "O5'A" JNT 29 
JNT PB    P1  P 0 1 N N N N N N 11.367 8.653 13.894 3.430  1.879  0.445  PB     JNT 30 
JNT O2B   O10 O 0 1 N N N N N N 11.794 7.633 14.940 3.934  3.091  -0.487 O2B    JNT 31 
JNT O1B   O11 O 0 1 N N N N N N 12.223 9.863 13.705 3.712  2.197  1.862  O1B    JNT 32 
JNT O3A   O12 O 0 1 N N N N N N 11.296 7.829 12.530 1.846  1.672  0.246  O3A    JNT 33 
JNT PA    P2  P 0 1 N N N N N N 10.576 8.155 11.122 0.542  2.476  0.742  PA     JNT 34 
JNT O1A   O13 O 0 1 N N N N N N 10.649 9.616 10.830 0.751  3.927  0.540  O1A    JNT 35 
JNT O2A   O14 O 0 1 N N N N N N 9.234  7.547 11.107 0.293  2.182  2.305  O2A    JNT 36 
JNT H1    H1  H 0 1 N N N N N N 12.930 6.021 10.862 -2.376 2.490  1.054  H1     JNT 37 
JNT H2    H2  H 0 1 N N N N N N 13.259 7.776 11.061 -1.965 3.654  -0.228 H2     JNT 38 
JNT H3    H3  H 0 1 N N N N N N 14.667 6.846 9.278  -2.623 1.918  -1.936 H3     JNT 39 
JNT H4    H4  H 0 1 N N N N N N 12.679 8.913 9.072  -4.358 3.429  -0.142 H4     JNT 40 
JNT H5    H5  H 0 1 N N N N N N 14.965 9.100 9.361  -5.577 3.577  -2.191 H5     JNT 41 
JNT H6    H6  H 0 1 N N N N N N 11.770 8.499 7.079  -5.556 1.565  0.643  H6     JNT 42 
JNT H7    H7  H 0 1 N N N N N N 13.477 9.826 6.194  -7.067 2.440  -1.033 H7     JNT 43 
JNT H8    H8  H 0 1 N N N N N N 13.750 6.477 6.172  -4.711 -0.008 -1.859 H8     JNT 44 
JNT H9    H9  H 0 1 N N N N N N 10.187 7.518 7.073  -3.611 -0.909 1.643  H9     JNT 45 
JNT H10   H10 H 0 1 N N N N N N 12.789 2.333 4.103  -8.731 -2.710 -1.953 H10    JNT 46 
JNT H11   H11 H 0 1 N N N N N N 8.370  2.505 3.981  -8.010 -5.211 1.791  H11    JNT 47 
JNT H12   H12 H 0 1 N N N N N N 7.988  3.336 5.333  -6.662 -4.547 2.542  H12    JNT 48 
JNT H13   H13 H 0 1 N N N N N N 3.917  4.971 14.585 10.673 -4.444 -0.393 H13    JNT 49 
JNT H14   H14 H 0 1 N N N N N N 3.702  7.058 14.019 9.585  -2.725 0.859  H14    JNT 50 
JNT H15   H15 H 0 1 N N N N N N 3.998  5.942 12.643 9.990  -2.190 -0.789 H15    JNT 51 
JNT H16   H16 H 0 1 N N N N N N 5.281  8.011 12.402 7.316  -3.411 0.029  H16    JNT 52 
JNT H17   H17 H 0 1 N N N N N N 7.348  6.907 12.199 8.172  -2.112 -2.423 H17    JNT 53 
JNT H18   H18 H 0 1 N N N N N N 6.593  7.163 15.025 8.095  -0.511 -0.521 H18    JNT 54 
JNT H19   H19 H 0 1 N N N N N N 5.788  9.234 15.773 7.239  -1.809 1.930  H19    JNT 55 
JNT H20   H20 H 0 1 N N N N N N 7.380  9.741 14.571 5.426  -1.788 0.228  H20    JNT 56 
JNT H21   H21 H 0 1 N N N N N N 8.346  9.684 12.469 6.282  -0.490 -2.224 H21    JNT 57 
JNT H22   H22 H 0 1 N N N N N N 8.756  7.858 15.444 5.872  0.462  1.250  H22    JNT 58 
JNT H23   H23 H 0 1 N N N N N N 9.003  7.306 13.752 6.140  1.114  -0.384 H23    JNT 59 
JNT H24   H24 H 0 1 N N N N N N 12.597 7.923 15.356 3.781  2.951  -1.432 H24    JNT 60 
JNT H25   H25 H 0 1 N N N N N N 8.587  8.212 10.903 0.148  1.248  2.512  H25    JNT 61 
# 
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 
JNT N1    C2    DOUB Y N 1  
JNT N1    C6    SING Y N 2  
JNT N6    C6    SING N N 3  
JNT C2    N3    SING Y N 4  
JNT C6    C5    DOUB Y N 5  
JNT N3    C4    DOUB Y N 6  
JNT C5    C4    SING Y N 7  
JNT C5    N7    SING Y N 8  
JNT C4    N9    SING Y N 9  
JNT N7    C8    DOUB Y N 10 
JNT "O2'" "C2'" SING N N 11 
JNT N9    C8    SING Y N 12 
JNT N9    "C1'" SING N N 13 
JNT "C1'" "C2'" SING N N 14 
JNT "C1'" "O4'" SING N N 15 
JNT "C2'" "C3'" SING N N 16 
JNT "O4'" "C4'" SING N N 17 
JNT "C3'" "O3'" SING N N 18 
JNT "C3'" "C4'" SING N N 19 
JNT "C4'" "C5'" SING N N 20 
JNT "O5'" "C5'" SING N N 21 
JNT "O5'" PA    SING N N 22 
JNT O1A   PA    DOUB N N 23 
JNT O2A   PA    SING N N 24 
JNT PA    O3A   SING N N 25 
JNT O2C   C2A   SING N N 26 
JNT O3A   PB    SING N N 27 
JNT O4C   C4A   SING N N 28 
JNT C2A   C1A   SING N N 29 
JNT C2A   C3A   SING N N 30 
JNT C1A   O1C   SING N N 31 
JNT O1B   PB    DOUB N N 32 
JNT PB    O5A   SING N N 33 
JNT PB    O2B   SING N N 34 
JNT C4A   C3A   SING N N 35 
JNT C4A   C5A   SING N N 36 
JNT O5A   C5A   SING N N 37 
JNT "C5'" H1    SING N N 38 
JNT "C5'" H2    SING N N 39 
JNT "C4'" H3    SING N N 40 
JNT "C3'" H4    SING N N 41 
JNT "O3'" H5    SING N N 42 
JNT "C2'" H6    SING N N 43 
JNT "O2'" H7    SING N N 44 
JNT "C1'" H8    SING N N 45 
JNT C8    H9    SING N N 46 
JNT C2    H10   SING N N 47 
JNT N6    H11   SING N N 48 
JNT N6    H12   SING N N 49 
JNT O1C   H13   SING N N 50 
JNT C1A   H14   SING N N 51 
JNT C1A   H15   SING N N 52 
JNT C2A   H16   SING N N 53 
JNT O2C   H17   SING N N 54 
JNT C3A   H18   SING N N 55 
JNT O3C   H19   SING N N 56 
JNT C4A   H20   SING N N 57 
JNT O4C   H21   SING N N 58 
JNT C5A   H22   SING N N 59 
JNT C5A   H23   SING N N 60 
JNT O2B   H24   SING N N 61 
JNT O2A   H25   SING N N 62 
JNT C3A   O3C   SING N N 63 
# 
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 
JNT InChI            InChI                1.03  "InChI=1S/C15H25N5O14P2/c16-13-9-14(18-4-17-13)20(5-19-9)15-12(26)11(25)8(33-15)3-32-36(29,30)34-35(27,28)31-2-7(23)10(24)6(22)1-21/h4-8,10-12,15,21-26H,1-3H2,(H,27,28)(H,29,30)(H2,16,17,18)/t6-,7+,8+,10-,11+,12+,15+/m0/s1" 
JNT InChIKey         InChI                1.03  QKJRZYRQRSLXSV-AOOZFPJJSA-N                                                                                                                                                                                                     
JNT SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CO)[C@@H](O)[C@H]3O"                                                                                                                         
JNT SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CO)[CH](O)[CH]3O"                                                                                                                                     
JNT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O)N"                                                                                                                          
JNT SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(C(CO)O)O)O)O)O)N"                                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           JNT 
_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~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen 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 
JNT "Create component" 2019-03-13 RCSB 
JNT "Initial release"  2020-04-01 RCSB 
JNT "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            JNT 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C1A 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
