data_LTE
# 
_chem_comp.id                                    LTE 
_chem_comp.name                                  "1-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]-3-[(4~{S})-4-azanyl-5-oxidanylidene-pentyl]guanidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H29 N9 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-09-04 
_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                        451.480 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LTE 
_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        6SQK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
LTE C    C    C 0 1 N N N N Y Y 9.429  39.709 5.306  10.774 1.080  0.256  C    LTE 1  
LTE O    O    O 0 1 N N N N Y Y 9.437  38.854 6.145  11.260 1.944  -0.434 O    LTE 2  
LTE CA   CA   C 0 1 N N S N Y N 10.065 41.088 5.617  9.360  1.222  0.758  CA   LTE 3  
LTE CB   CB   C 0 1 N N N N N N 8.904  42.066 5.787  8.422  0.389  -0.117 CB   LTE 4  
LTE N    N    N 0 1 N N N Y Y N 10.903 41.498 4.542  8.960  2.634  0.700  N    LTE 5  
LTE CG   CG   C 0 1 N N N N N N 9.314  43.407 6.365  7.008  0.433  0.465  CG   LTE 6  
LTE CD   CD   C 0 1 N N N N N N 8.125  44.130 6.971  6.070  -0.399 -0.411 CD   LTE 7  
LTE NE   NE   N 0 1 N N N N N N 7.485  45.077 6.063  4.716  -0.357 0.147  NE   LTE 8  
LTE CZ   CZ   C 0 1 N N N N N N 6.787  46.126 6.488  3.695  -1.037 -0.475 CZ   LTE 9  
LTE NH1  NH1  N 0 1 N N N N N N 6.654  46.333 7.790  3.932  -1.719 -1.560 NH1  LTE 10 
LTE NH2  NH2  N 0 1 N N N N N N 6.239  46.976 5.613  2.424  -0.998 0.049  NH2  LTE 11 
LTE C24  C24  C 0 1 N N N N N N 6.120  46.755 4.176  1.336  -1.722 -0.614 C24  LTE 12 
LTE C28  C28  C 0 1 N N N N N N 4.745  46.228 3.708  0.037  -1.515 0.166  C28  LTE 13 
LTE C31  C31  C 0 1 N N N N N N 4.524  46.556 2.220  -1.099 -2.271 -0.525 C31  LTE 14 
LTE C36  C36  C 0 1 N N R N N N 3.189  46.154 1.624  -2.399 -2.064 0.254  C36  LTE 15 
LTE C38  C38  C 0 1 N N R N N N 2.863  46.098 -0.703 -4.242 -0.711 0.467  C38  LTE 16 
LTE C39  C39  C 0 1 N N R N N N 3.464  44.760 -0.286 -4.784 -1.979 -0.235 C39  LTE 17 
LTE C40  C40  C 0 1 N N S N N N 3.027  44.704 1.182  -3.543 -2.888 -0.377 C40  LTE 18 
LTE C49  C49  C 0 1 Y N N N N N 4.835  46.925 -2.046 -4.435 1.290  -1.059 C49  LTE 19 
LTE C50  C50  C 0 1 Y N N N N N 3.893  47.886 -3.690 -6.323 2.148  -0.427 C50  LTE 20 
LTE C51  C51  C 0 1 Y N N N N N 2.877  47.328 -2.930 -6.102 1.002  0.355  C51  LTE 21 
LTE C53  C53  C 0 1 Y N N N N N 1.320  48.118 -4.284 -8.085 1.389  1.450  C53  LTE 22 
LTE C55  C55  C 0 1 Y N N N N N 3.512  48.605 -4.841 -7.497 2.888  -0.204 C55  LTE 23 
LTE N47  N47  N 0 1 Y N N N N N 3.491  46.722 -1.862 -4.901 0.486  -0.062 N47  LTE 24 
LTE N48  N48  N 0 1 Y N N N N N 5.131  47.615 -3.121 -5.270 2.264  -1.271 N48  LTE 25 
LTE N52  N52  N 0 1 Y N N N N N 1.558  47.400 -3.181 -7.002 0.663  1.273  N52  LTE 26 
LTE N54  N54  N 0 1 Y N N N N N 2.191  48.710 -5.102 -8.338 2.472  0.737  N54  LTE 27 
LTE N57  N57  N 0 1 N N N N N N 4.369  49.179 -5.694 -7.772 4.022  -0.947 N57  LTE 28 
LTE O37  O37  O 0 1 N N N N N N 3.042  46.948 0.416  -2.833 -0.690 0.153  O37  LTE 29 
LTE O41  O41  O 0 1 N N N N N N 2.952  43.685 -1.066 -5.779 -2.612 0.572  O41  LTE 30 
LTE O42  O42  O 0 1 N N N N N N 1.685  44.242 1.342  -3.733 -4.110 0.339  O42  LTE 31 
LTE HA   HA   H 0 1 N N N N Y N 10.632 41.022 6.557  9.304  0.870  1.788  HA   LTE 32 
LTE HB3  HB3  H 0 1 N N N N N N 8.448  42.238 4.801  8.412  0.797  -1.128 HB3  LTE 33 
LTE HB2  HB2  H 0 1 N N N N N N 8.162  41.610 6.460  8.772  -0.643 -0.146 HB2  LTE 34 
LTE H2   H2   H 0 1 N Y N Y Y N 11.307 42.388 4.754  9.004  2.984  -0.245 H2   LTE 35 
LTE H    H3   H 0 1 N N N Y Y N 11.631 40.825 4.411  8.039  2.765  1.092  H    LTE 36 
LTE HG2  HG2  H 0 1 N N N N N N 10.071 43.245 7.146  7.018  0.026  1.476  HG2  LTE 37 
LTE HG3  HG3  H 0 1 N N N N N N 9.741  44.028 5.564  6.658  1.465  0.493  HG3  LTE 38 
LTE HD2  HD2  H 0 1 N N N N N N 8.470  44.680 7.859  6.059  0.008  -1.422 HD2  LTE 39 
LTE HD3  HD3  H 0 1 N N N N N N 7.379  43.379 7.271  6.419  -1.431 -0.439 HD3  LTE 40 
LTE HE   HE   H 0 1 N N N N N N 7.575  44.930 5.078  4.539  0.150  0.954  HE   LTE 41 
LTE HH11 HH11 H 0 0 N N N N N N 7.122  45.634 8.330  4.828  -1.747 -1.929 HH11 LTE 42 
LTE HH21 HH21 H 0 0 N N N N N N 5.880  47.837 5.975  2.248  -0.490 0.856  HH21 LTE 43 
LTE H30  H30  H 0 1 N N N N N N 6.885  46.023 3.879  1.215  -1.345 -1.629 H30  LTE 44 
LTE H29  H29  H 0 1 N N N N N N 6.310  47.711 3.667  1.575  -2.785 -0.647 H29  LTE 45 
LTE H32  H32  H 0 1 N N N N N N 3.952  46.702 4.305  0.158  -1.891 1.182  H32  LTE 46 
LTE H33  H33  H 0 1 N N N N N N 4.708  45.138 3.848  -0.202 -0.451 0.199  H33  LTE 47 
LTE H35  H35  H 0 1 N N N N N N 5.312  46.047 1.646  -1.221 -1.894 -1.541 H35  LTE 48 
LTE H34  H34  H 0 1 N N N N N N 4.628  47.644 2.100  -0.861 -3.334 -0.558 H34  LTE 49 
LTE H61  H61  H 0 1 N N N N N N 2.388  46.402 2.336  -2.263 -2.342 1.299  H61  LTE 50 
LTE H62  H62  H 0 1 N N N N N N 1.790  45.954 -0.900 -4.390 -0.782 1.545  H62  LTE 51 
LTE H44  H44  H 0 1 N N N N N N 4.561  44.809 -0.345 -5.188 -1.730 -1.216 H44  LTE 52 
LTE H43  H43  H 0 1 N N N N N N 3.727  44.070 1.746  -3.334 -3.089 -1.428 H43  LTE 53 
LTE H58  H58  H 0 1 N N N N N N 5.584  46.549 -1.365 -3.506 1.142  -1.590 H58  LTE 54 
LTE H56  H56  H 0 1 N N N N N N 0.279  48.234 -4.549 -8.797 1.086  2.204  H56  LTE 55 
LTE H59  H59  H 0 1 N N N N N N 3.860  49.620 -6.433 -7.150 4.316  -1.631 H59  LTE 56 
LTE H60  H60  H 0 1 N N N N N N 4.913  49.864 -5.209 -8.585 4.524  -0.784 H60  LTE 57 
LTE H46  H46  H 0 1 N N N N N N 3.347  42.870 -0.780 -6.153 -3.413 0.179  H46  LTE 58 
LTE H45  H45  H 0 1 N N N N N N 1.463  44.226 2.266  -4.477 -4.640 0.022  H45  LTE 59 
LTE OXT  OXT  O 0 1 N Y N N Y Y ?      ?      ?      11.492 -0.009 0.572  O1   LTE 60 
LTE HXT  HXT  H 0 1 N Y N N Y Y ?      ?      ?      12.394 -0.056 0.227  H1   LTE 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 
LTE N57 C55  SING N N 1  
LTE N54 C55  DOUB Y N 2  
LTE N54 C53  SING Y N 3  
LTE C55 C50  SING Y N 4  
LTE C53 N52  DOUB Y N 5  
LTE C50 N48  SING Y N 6  
LTE C50 C51  DOUB Y N 7  
LTE N52 C51  SING Y N 8  
LTE N48 C49  DOUB Y N 9  
LTE C51 N47  SING Y N 10 
LTE C49 N47  SING Y N 11 
LTE N47 C38  SING N N 12 
LTE O41 C39  SING N N 13 
LTE C38 C39  SING N N 14 
LTE C38 O37  SING N N 15 
LTE C39 C40  SING N N 16 
LTE O37 C36  SING N N 17 
LTE C40 O42  SING N N 18 
LTE C40 C36  SING N N 19 
LTE C36 C31  SING N N 20 
LTE C31 C28  SING N N 21 
LTE C28 C24  SING N N 22 
LTE C24 NH2  SING N N 23 
LTE N   CA   SING N N 24 
LTE C   CA   SING N N 25 
LTE C   O    DOUB N N 26 
LTE NH2 CZ   SING N N 27 
LTE CA  CB   SING N N 28 
LTE CB  CG   SING N N 29 
LTE NE  CZ   SING N N 30 
LTE NE  CD   SING N N 31 
LTE CG  CD   SING N N 32 
LTE CZ  NH1  DOUB N N 33 
LTE CA  HA   SING N N 34 
LTE CB  HB3  SING N N 35 
LTE CB  HB2  SING N N 36 
LTE N   H2   SING N N 37 
LTE N   H    SING N N 38 
LTE CG  HG2  SING N N 39 
LTE CG  HG3  SING N N 40 
LTE CD  HD2  SING N N 41 
LTE CD  HD3  SING N N 42 
LTE NE  HE   SING N N 43 
LTE NH1 HH11 SING N N 44 
LTE NH2 HH21 SING N N 45 
LTE C24 H30  SING N N 46 
LTE C24 H29  SING N N 47 
LTE C28 H32  SING N N 48 
LTE C28 H33  SING N N 49 
LTE C31 H35  SING N N 50 
LTE C31 H34  SING N N 51 
LTE C36 H61  SING N N 52 
LTE C38 H62  SING N N 53 
LTE C39 H44  SING N N 54 
LTE C40 H43  SING N N 55 
LTE C49 H58  SING N N 56 
LTE C53 H56  SING N N 57 
LTE N57 H59  SING N N 58 
LTE N57 H60  SING N N 59 
LTE O41 H46  SING N N 60 
LTE O42 H45  SING N N 61 
LTE C   OXT  SING N N 62 
LTE OXT HXT  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 
LTE InChI            InChI                1.06  "InChI=1S/C18H29N9O5/c19-9(17(30)31)3-1-5-22-18(21)23-6-2-4-10-12(28)13(29)16(32-10)27-8-26-11-14(20)24-7-25-15(11)27/h7-10,12-13,16,28-29H,1-6,19H2,(H,30,31)(H2,20,24,25)(H3,21,22,23)/t9-,10+,12+,13+,16+/m0/s1" 
LTE InChIKey         InChI                1.06  BMAYSUQGGXYXQD-UOYPZJKHSA-N                                                                                                                                                                                         
LTE SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCCNC(=N)NCCC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                                        
LTE SMILES           CACTVS               3.385 "N[CH](CCCNC(=N)NCCC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                                               
LTE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/NCCC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)\NCCC[C@@H](C(=O)O)N"                                                                                                                                 
LTE SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CCCNC(=N)NCCCC(C(=O)O)N)O)O)N"                                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           LTE 
_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~{S})-5-[[~{N}-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]carbamimidoyl]amino]-2-azanyl-pentanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
LTE "Create component"   2019-09-04 PDBE 
LTE "Initial release"    2020-09-30 RCSB 
LTE "Modify backbone"    2023-11-03 PDBE 
LTE "Other modification" 2024-06-28 PDBE 
LTE "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            LTE 
_pdbx_chem_comp_pcm.modified_residue_id                ? 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_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               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
