data_P2J
# 
_chem_comp.id                                    P2J 
_chem_comp.name                                  "9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H31 N7 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-07-25 
_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                        437.493 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     P2J 
_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        6PVB 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              N 
# 
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 
P2J C4  C1  C 0 1 Y N N N N N -24.176 19.381 -10.973 -6.114 1.156  0.307  C4  P2J 1  
P2J C6  C2  C 0 1 Y N N N N N -25.422 20.605 -9.443  -5.698 -0.733 1.567  C6  P2J 2  
P2J C8  C3  C 0 1 Y N N N N N -23.683 19.520 -6.511  -2.252 -0.978 0.714  C8  P2J 3  
P2J C10 C4  C 0 1 N N S N N N -21.874 17.943 -7.183  -1.780 0.951  -0.842 C10 P2J 4  
P2J C12 C5  C 0 1 N N S N N N -20.847 15.958 -6.581  0.393  1.202  -1.602 C12 P2J 5  
P2J N3  N1  N 0 1 Y N N N N N -23.442 18.894 -9.988  -4.871 1.228  -0.119 N3  P2J 6  
P2J C13 C6  C 0 1 N N R N N N -20.263 16.291 -7.680  -0.462 0.952  -2.859 C13 P2J 7  
P2J C14 C7  C 0 1 N N R N N N -21.243 17.242 -8.390  -1.811 0.435  -2.304 C14 P2J 8  
P2J C15 C8  C 0 1 N N N N N N -21.269 14.475 -6.681  1.672  0.364  -1.664 C15 P2J 9  
P2J C1  C9  C 0 1 Y N N N N N -24.653 20.103 -8.381  -4.360 -0.698 1.140  C1  P2J 10 
P2J C18 C10 C 0 1 N N N N N N -19.681 13.491 -4.923  3.582  -0.357 -0.363 C18 P2J 11 
P2J C19 C11 C 0 1 N N N N N N -19.284 11.989 -5.066  3.047  -1.720 0.080  C19 P2J 12 
P2J C2  C12 C 0 1 Y N N N N N -23.633 19.213 -8.683  -3.969 0.332  0.268  C2  P2J 13 
P2J C20 C13 C 0 1 N N S N N N -19.334 11.528 -6.547  4.200  -2.725 0.144  C20 P2J 14 
P2J C24 C14 C 0 1 N N N N N N -22.065 14.047 -4.288  2.962  1.983  -0.408 C24 P2J 15 
P2J C25 C15 C 0 1 N N N N N N -22.993 12.766 -3.962  3.431  2.310  1.011  C25 P2J 16 
P2J C26 C16 C 0 1 N N N N N N -23.664 12.863 -2.481  3.814  3.789  1.093  C26 P2J 17 
P2J C27 C17 C 0 1 N N N N N N -25.263 12.583 -2.500  4.283  4.117  2.512  C27 P2J 18 
P2J C28 C18 C 0 1 N N N N N N -25.617 11.239 -1.670  4.667  5.596  2.593  C28 P2J 19 
P2J C75 C19 C 0 1 N N N N N N -18.108 10.699 -6.887  3.697  -4.033 0.697  C75 P2J 20 
P2J N16 N2  N 0 1 N N N N N N -21.097 13.662 -5.402  2.471  0.599  -0.454 N16 P2J 21 
P2J N17 N3  N 0 1 N N N N N N -26.515 21.547 -9.164  -6.142 -1.724 2.425  N17 P2J 22 
P2J N21 N4  N 0 1 N N N N N N -20.534 10.756 -6.785  4.738  -2.938 -1.207 N21 P2J 23 
P2J N5  N5  N 0 1 Y N N N N N -25.159 20.230 -10.695 -6.528 0.207  1.126  N5  P2J 24 
P2J N7  N6  N 0 1 Y N N N N N -24.656 20.260 -7.040  -3.266 -1.462 1.372  N7  P2J 25 
P2J N9  N7  N 0 1 Y N N N N N -23.052 18.866 -7.481  -2.635 0.129  0.017  N9  P2J 26 
P2J O11 O1  O 0 1 N N N N N N -22.155 16.935 -6.438  -0.393 0.809  -0.465 O11 P2J 27 
P2J O22 O2  O 0 1 N N N N N N -18.965 17.014 -7.403  -0.653 2.168  -3.584 O22 P2J 28 
P2J O23 O3  O 0 1 N N N N N N -22.184 16.527 -9.067  -1.864 -0.993 -2.339 O23 P2J 29 
P2J O76 O4  O 0 1 N N N N N N -17.834 9.666  -6.218  3.536  -4.185 2.021  O76 P2J 30 
P2J O77 O5  O 0 1 N N N N N N -17.365 11.048 -7.846  3.437  -4.945 -0.052 O77 P2J 31 
P2J H1  H1  H 0 1 N N N N N N -23.978 19.091 -11.995 -6.821 1.903  -0.023 H1  P2J 32 
P2J H2  H2  H 0 1 N N N N N N -23.444 19.461 -5.459  -1.255 -1.393 0.719  H2  P2J 33 
P2J H3  H3  H 0 1 N N N N N N -21.089 18.558 -6.719  -2.085 1.997  -0.798 H3  P2J 34 
P2J H4  H4  H 0 1 N N N N N N -20.215 16.098 -5.691  0.647  2.259  -1.530 H4  P2J 35 
P2J H5  H5  H 0 1 N N N N N N -20.066 15.429 -8.335  0.004  0.199  -3.495 H5  P2J 36 
P2J H6  H6  H 0 1 N N N N N N -20.700 17.961 -9.020  -2.649 0.868  -2.851 H6  P2J 37 
P2J H7  H7  H 0 1 N N N N N N -22.331 14.442 -6.965  1.411  -0.693 -1.728 H7  P2J 38 
P2J H8  H8  H 0 1 N N N N N N -20.664 14.002 -7.469  2.251  0.649  -2.543 H8  P2J 39 
P2J H9  H9  H 0 1 N N N N N N -19.007 14.112 -5.531  4.311  0.001  0.364  H9  P2J 40 
P2J H10 H10 H 0 1 N N N N N N -19.608 13.795 -3.868  4.060  -0.454 -1.338 H10 P2J 41 
P2J H11 H11 H 0 1 N N N N N N -19.983 11.377 -4.477  2.591  -1.629 1.066  H11 P2J 42 
P2J H12 H12 H 0 1 N N N N N N -18.262 11.851 -4.683  2.302  -2.068 -0.634 H12 P2J 43 
P2J H13 H13 H 0 1 N N N N N N -19.340 12.424 -7.185  4.986  -2.335 0.790  H13 P2J 44 
P2J H14 H14 H 0 1 N N N N N N -21.502 14.337 -3.389  2.158  2.663  -0.691 H14 P2J 45 
P2J H15 H15 H 0 1 N N N N N N -22.693 14.889 -4.615  3.795  2.096  -1.101 H15 P2J 46 
P2J H16 H16 H 0 1 N N N N N N -23.795 12.708 -4.713  2.625  2.105  1.717  H16 P2J 47 
P2J H17 H17 H 0 1 N N N N N N -22.375 11.857 -4.014  4.296  1.696  1.259  H17 P2J 48 
P2J H18 H18 H 0 1 N N N N N N -23.184 12.120 -1.827  4.619  3.995  0.387  H18 P2J 49 
P2J H19 H19 H 0 1 N N N N N N -23.488 13.872 -2.080  2.948  4.404  0.845  H19 P2J 50 
P2J H20 H20 H 0 1 N N N N N N -25.785 13.437 -2.044  3.478  3.911  3.217  H20 P2J 51 
P2J H21 H21 H 0 1 N N N N N N -25.596 12.463 -3.541  5.149  3.503  2.759  H21 P2J 52 
P2J H22 H22 H 0 1 N N N N N N -26.703 11.067 -1.695  5.001  5.830  3.604  H22 P2J 53 
P2J H23 H23 H 0 1 N N N N N N -25.100 10.381 -2.124  5.472  5.802  1.888  H23 P2J 54 
P2J H24 H24 H 0 1 N N N N N N -25.288 11.355 -0.627  3.801  6.210  2.345  H24 P2J 55 
P2J H26 H26 H 0 1 N N N N N N -26.958 21.807 -10.022 -5.527 -2.405 2.740  H26 P2J 56 
P2J H27 H27 H 0 1 N N N N N N -27.184 21.112 -8.562  -7.068 -1.737 2.713  H27 P2J 57 
P2J H28 H28 H 0 1 N N N N N N -21.336 11.308 -6.559  5.541  -3.548 -1.183 H28 P2J 58 
P2J H29 H29 H 0 1 N N N N N N -20.573 10.490 -7.748  4.027  -3.300 -1.826 H29 P2J 59 
P2J H31 H31 H 0 1 N N N N N N -18.361 16.426 -6.965  -1.185 2.069  -4.386 H31 P2J 60 
P2J H32 H32 H 0 1 N N N N N N -22.783 17.123 -9.501  -1.796 -1.367 -3.228 H32 P2J 61 
P2J H33 H33 H 0 1 N N N N N N -17.043 9.267  -6.561  3.211  -5.042 2.328  H33 P2J 62 
# 
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 
P2J C4  N5  DOUB Y N 1  
P2J C4  N3  SING Y N 2  
P2J N5  C6  SING Y N 3  
P2J N3  C2  DOUB Y N 4  
P2J C6  N17 SING N N 5  
P2J C6  C1  DOUB Y N 6  
P2J O23 C14 SING N N 7  
P2J C2  C1  SING Y N 8  
P2J C2  N9  SING Y N 9  
P2J C14 C13 SING N N 10 
P2J C14 C10 SING N N 11 
P2J C1  N7  SING Y N 12 
P2J O77 C75 DOUB N N 13 
P2J C13 O22 SING N N 14 
P2J C13 C12 SING N N 15 
P2J N9  C10 SING N N 16 
P2J N9  C8  SING Y N 17 
P2J C10 O11 SING N N 18 
P2J N7  C8  DOUB Y N 19 
P2J C75 C20 SING N N 20 
P2J C75 O76 SING N N 21 
P2J N21 C20 SING N N 22 
P2J C15 C12 SING N N 23 
P2J C15 N16 SING N N 24 
P2J C12 O11 SING N N 25 
P2J C20 C19 SING N N 26 
P2J N16 C18 SING N N 27 
P2J N16 C24 SING N N 28 
P2J C19 C18 SING N N 29 
P2J C24 C25 SING N N 30 
P2J C25 C26 SING N N 31 
P2J C27 C26 SING N N 32 
P2J C27 C28 SING N N 33 
P2J C4  H1  SING N N 34 
P2J C8  H2  SING N N 35 
P2J C10 H3  SING N N 36 
P2J C12 H4  SING N N 37 
P2J C13 H5  SING N N 38 
P2J C14 H6  SING N N 39 
P2J C15 H7  SING N N 40 
P2J C15 H8  SING N N 41 
P2J C18 H9  SING N N 42 
P2J C18 H10 SING N N 43 
P2J C19 H11 SING N N 44 
P2J C19 H12 SING N N 45 
P2J C20 H13 SING N N 46 
P2J C24 H14 SING N N 47 
P2J C24 H15 SING N N 48 
P2J C25 H16 SING N N 49 
P2J C25 H17 SING N N 50 
P2J C26 H18 SING N N 51 
P2J C26 H19 SING N N 52 
P2J C27 H20 SING N N 53 
P2J C27 H21 SING N N 54 
P2J C28 H22 SING N N 55 
P2J C28 H23 SING N N 56 
P2J C28 H24 SING N N 57 
P2J N17 H26 SING N N 58 
P2J N17 H27 SING N N 59 
P2J N21 H28 SING N N 60 
P2J N21 H29 SING N N 61 
P2J O22 H31 SING N N 62 
P2J O23 H32 SING N N 63 
P2J O76 H33 SING N N 64 
# 
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 
P2J SMILES           ACDLabs              12.01 "c2nc(N)c3ncn(C1OC(C(O)C1O)CN(CCC(C(O)=O)N)CCCCC)c3n2"                                                                                                                                                   
P2J InChI            InChI                1.03  "InChI=1S/C19H31N7O5/c1-2-3-4-6-25(7-5-11(20)19(29)30)8-12-14(27)15(28)18(31-12)26-10-24-13-16(21)22-9-23-17(13)26/h9-12,14-15,18,27-28H,2-8,20H2,1H3,(H,29,30)(H2,21,22,23)/t11-,12-,14-,15+,18-/m0/s1" 
P2J InChIKey         InChI                1.03  IZQBBTVZUZUZGN-VQYVRKMMSA-N                                                                                                                                                                              
P2J SMILES_CANONICAL CACTVS               3.385 "CCCCCN(CC[C@H](N)C(O)=O)C[C@@H]1O[C@@H]([C@H](O)[C@H]1O)n2cnc3c(N)ncnc23"                                                                                                                               
P2J SMILES           CACTVS               3.385 "CCCCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                                                      
P2J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCCN(CC[C@@H](C(=O)O)N)C[C@H]1[C@@H]([C@H]([C@H](O1)n2cnc3c2ncnc3N)O)O"                                                                                                                               
P2J SMILES           "OpenEye OEToolkits" 2.0.7 "CCCCCN(CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)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 
P2J "SYSTEMATIC NAME" ACDLabs              12.01 "9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine"                                 
P2J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-4-[[(2~{S},3~{R},4~{R},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-pentyl-amino]-2-azanyl-butanoic 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 
P2J "Create component" 2019-07-25 RCSB 
P2J "Initial release"  2020-08-19 RCSB 
P2J "Modify PCM"       2024-09-27 PDBE 
# 
