data_PJ3
# 
_chem_comp.id                                    PJ3 
_chem_comp.name                                  "(2~{S})-2-azanyl-3-[1-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-4-yl]propanoic acid" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C17 H25 N8 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               HIS 
_chem_comp.pdbx_synonyms                         "7GMP capped histidine" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-10-04 
_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                        516.402 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     PJ3 
_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        8APX 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
PJ3 N     N1  N 0 1 N N N N N N 124.873 203.969 139.387 -5.873 2.418  0.044  N     PJ3 1  
PJ3 CA    C1  C 0 1 N N S N N N 123.765 203.344 139.622 -6.646 1.472  -0.772 CA    PJ3 2  
PJ3 C     C2  C 0 1 N N N N N N 123.409 202.995 137.826 -8.089 1.907  -0.813 C     PJ3 3  
PJ3 O     O1  O 0 1 N N N N N N 123.020 203.769 137.104 -8.518 2.656  0.032  O     PJ3 4  
PJ3 CB    C3  C 0 1 N N N N N N 122.538 204.013 140.262 -6.552 0.074  -0.159 CB    PJ3 5  
PJ3 CG    C4  C 0 1 Y N N N N N 122.284 205.298 139.489 -5.127 -0.411 -0.230 CG    PJ3 6  
PJ3 N2    N2  N 0 1 N N N N N N 112.911 207.745 144.680 2.746  1.470  3.284  N2    PJ3 7  
PJ3 C2    C5  C 0 1 N N N N N N 113.004 208.297 143.408 3.364  1.717  2.084  C2    PJ3 8  
PJ3 N1    N3  N 0 1 N N N N N N 112.308 209.477 143.168 4.023  2.894  1.906  N1    PJ3 9  
PJ3 ND1   N4  N 0 1 Y N N N N N 123.117 206.444 139.368 -4.376 -0.492 -1.338 ND1   PJ3 10 
PJ3 CD2   C6  C 0 1 Y N N N N N 121.150 205.601 138.741 -4.382 -0.834 0.809  CD2   PJ3 11 
PJ3 CE1   C7  C 0 1 Y N N N N N 122.467 207.378 138.561 -3.196 -0.953 -1.026 CE1   PJ3 12 
PJ3 NE2   N5  N 0 1 Y N N N N N 121.254 206.882 138.162 -3.158 -1.180 0.305  NE2   PJ3 13 
PJ3 "C1'" C8  C 0 1 N N R N N N 115.268 206.379 139.920 3.356  -1.131 -1.314 "C1'" PJ3 14 
PJ3 "C2'" C9  C 0 1 N N R N N N 114.544 205.489 138.867 4.024  -2.135 -0.341 "C2'" PJ3 15 
PJ3 "C3'" C10 C 0 1 N N S N N N 115.654 205.044 137.846 2.915  -3.199 -0.160 "C3'" PJ3 16 
PJ3 C4    C11 C 0 1 N N N N N N 113.806 208.274 141.218 3.898  1.008  -0.055 C4    PJ3 17 
PJ3 "C4'" C12 C 0 1 N N R N N N 116.992 205.432 138.523 1.620  -2.468 -0.563 "C4'" PJ3 18 
PJ3 C5    C13 C 0 1 N N N N N N 113.142 209.481 140.845 4.577  2.193  -0.288 C5    PJ3 19 
PJ3 "C5'" C14 C 0 1 N N N N N N 118.069 205.936 137.467 0.630  -2.482 0.603  "C5'" PJ3 20 
PJ3 C6    C15 C 0 1 N N N N N N 112.319 210.169 141.866 4.636  3.154  0.732  C6    PJ3 21 
PJ3 C8    C16 C 0 1 N N N N N N 114.129 208.484 138.946 4.734  0.905  -2.201 C8    PJ3 22 
PJ3 CM7   C17 C 0 1 N N N N N N 114.192 210.918 138.827 5.898  3.255  -2.221 CM7   PJ3 23 
PJ3 N3    N6  N 0 1 N N N N N N 113.765 207.668 142.463 3.309  0.810  1.135  N3    PJ3 24 
PJ3 N7    N7  N 0 1 N N N N N N 113.463 209.762 139.444 5.114  2.188  -1.594 N7    PJ3 25 
PJ3 N9    N8  N 0 1 N N N N N N 114.565 207.731 140.147 3.956  0.198  -1.178 N9    PJ3 26 
PJ3 O1A   O2  O 0 1 N N N N N N 120.291 207.230 135.716 -2.225 -3.081 1.724  O1A   PJ3 27 
PJ3 "O2'" O3  O 0 1 N N N N N N 114.032 204.381 139.528 5.194  -2.711 -0.926 "O2'" PJ3 28 
PJ3 "O3'" O4  O 0 1 N N N N N N 115.611 203.661 137.654 3.148  -4.315 -1.021 "O3'" PJ3 29 
PJ3 O3A   O5  O 0 1 N N N N N N 120.237 209.214 137.358 -1.528 -0.737 2.351  O3A   PJ3 30 
PJ3 "O4'" O6  O 0 1 N N N N N N 116.616 206.465 139.454 1.977  -1.113 -0.885 "O4'" PJ3 31 
PJ3 "O5'" O7  O 0 1 N N N N N N 118.439 207.285 137.585 -0.608 -1.906 0.183  "O5'" PJ3 32 
PJ3 O6    O8  O 0 1 N N N N N N 111.646 211.175 141.879 5.231  4.207  0.561  O6    PJ3 33 
PJ3 PA    P1  P 0 1 N N N N N N 120.014 207.781 137.065 -1.882 -1.758 1.157  PA    PJ3 34 
PJ3 H     H1  H 0 1 N N N N N N 125.529 203.340 138.969 -5.866 3.336  -0.375 H     PJ3 35 
PJ3 H2    H2  H 0 1 N Y N N N N 124.700 204.732 138.764 -6.227 2.454  0.988  H2    PJ3 36 
PJ3 HA    H4  H 0 1 N N N N N N 123.921 202.360 140.089 -6.244 1.453  -1.785 HA    PJ3 37 
PJ3 HB2   H6  H 0 1 N N N N N N 121.664 203.349 140.190 -6.872 0.111  0.883  HB2   PJ3 38 
PJ3 HB3   H7  H 0 1 N N N N N N 122.739 204.241 141.319 -7.197 -0.610 -0.712 HB3   PJ3 39 
PJ3 H8    H8  H 0 1 N N N N N N 113.397 206.898 144.894 2.783  2.131  3.994  H8    PJ3 40 
PJ3 H9    H9  H 0 1 N N N N N N 112.358 208.195 145.381 2.273  0.635  3.423  H9    PJ3 41 
PJ3 H10   H10 H 0 1 N N N N N N 111.775 209.875 143.914 4.053  3.547  2.623  H10   PJ3 42 
PJ3 HD2   H11 H 0 1 N N N N N N 120.303 204.942 138.620 -4.692 -0.889 1.843  HD2   PJ3 43 
PJ3 HE1   H12 H 0 1 N N N N N N 122.861 208.347 138.291 -2.384 -1.124 -1.717 HE1   PJ3 44 
PJ3 H13   H13 H 0 1 N N N N N N 115.254 205.834 140.875 3.436  -1.483 -2.343 H13   PJ3 45 
PJ3 H14   H14 H 0 1 N N N N N N 113.768 206.071 138.348 4.262  -1.655 0.609  H14   PJ3 46 
PJ3 H15   H15 H 0 1 N N N N N N 115.535 205.599 136.904 2.863  -3.523 0.880  H15   PJ3 47 
PJ3 H16   H16 H 0 1 N N N N N N 117.398 204.558 139.053 1.176  -2.953 -1.433 H16   PJ3 48 
PJ3 H17   H17 H 0 1 N N N N N N 118.975 205.323 137.587 0.462  -3.510 0.924  H17   PJ3 49 
PJ3 H18   H18 H 0 1 N N N N N N 117.654 205.784 136.460 1.037  -1.904 1.432  H18   PJ3 50 
PJ3 H19   H19 H 0 1 N N N N N N 113.413 207.886 138.364 4.120  1.075  -3.086 H19   PJ3 51 
PJ3 H20   H20 H 0 1 N N N N N N 114.998 208.730 138.317 5.625  0.335  -2.464 H20   PJ3 52 
PJ3 H21   H21 H 0 1 N N N N N N 114.240 210.782 137.736 6.015  4.081  -1.519 H21   PJ3 53 
PJ3 H22   H22 H 0 1 N N N N N N 113.659 211.852 139.057 6.880  2.870  -2.496 H22   PJ3 54 
PJ3 H23   H23 H 0 1 N N N N N N 115.212 210.968 139.235 5.382  3.607  -3.114 H23   PJ3 55 
PJ3 H24   H24 H 0 1 N N N N N N 113.584 203.820 138.906 5.648  -3.345 -0.355 H24   PJ3 56 
PJ3 H25   H25 H 0 1 N N N N N N 116.286 203.406 137.036 3.980  -4.778 -0.849 H25   PJ3 57 
PJ3 H26   H26 H 0 1 N N N N N N 120.560 209.651 136.578 -1.293 0.152  2.052  H26   PJ3 58 
PJ3 OXT   OXT O 0 1 N Y N N N N ?       ?       ?       -8.896 1.461  -1.788 OXT   PJ3 59 
PJ3 HXT   H3  H 0 1 N Y N N N N ?       ?       ?       -9.814 1.768  -1.773 HXT   PJ3 60 
# 
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 
PJ3 N     CA    SING N N 1  
PJ3 CA    CB    SING N N 2  
PJ3 C     O     DOUB N N 3  
PJ3 CB    CG    SING N N 4  
PJ3 CG    ND1   SING Y N 5  
PJ3 CG    CD2   DOUB Y N 6  
PJ3 N2    C2    SING N N 7  
PJ3 C2    N1    SING N N 8  
PJ3 C2    N3    DOUB N N 9  
PJ3 N1    C6    SING N N 10 
PJ3 ND1   CE1   DOUB Y N 11 
PJ3 CD2   NE2   SING Y N 12 
PJ3 CE1   NE2   SING Y N 13 
PJ3 NE2   PA    SING N N 14 
PJ3 "C1'" "C2'" SING N N 15 
PJ3 "C1'" N9    SING N N 16 
PJ3 "C1'" "O4'" SING N N 17 
PJ3 "C2'" "C3'" SING N N 18 
PJ3 "C2'" "O2'" SING N N 19 
PJ3 "C3'" "C4'" SING N N 20 
PJ3 "C3'" "O3'" SING N N 21 
PJ3 C4    C5    DOUB N N 22 
PJ3 C4    N3    SING N N 23 
PJ3 C4    N9    SING N N 24 
PJ3 "C4'" "C5'" SING N N 25 
PJ3 "C4'" "O4'" SING N N 26 
PJ3 C5    C6    SING N N 27 
PJ3 C5    N7    SING N N 28 
PJ3 "C5'" "O5'" SING N N 29 
PJ3 C6    O6    DOUB N N 30 
PJ3 C8    N7    SING N N 31 
PJ3 C8    N9    SING N N 32 
PJ3 CM7   N7    SING N N 33 
PJ3 O1A   PA    DOUB N N 34 
PJ3 O3A   PA    SING N N 35 
PJ3 "O5'" PA    SING N N 36 
PJ3 CA    C     SING N N 37 
PJ3 N     H     SING N N 38 
PJ3 N     H2    SING N N 39 
PJ3 CA    HA    SING N N 40 
PJ3 CB    HB2   SING N N 41 
PJ3 CB    HB3   SING N N 42 
PJ3 N2    H8    SING N N 43 
PJ3 N2    H9    SING N N 44 
PJ3 N1    H10   SING N N 45 
PJ3 CD2   HD2   SING N N 46 
PJ3 CE1   HE1   SING N N 47 
PJ3 "C1'" H13   SING N N 48 
PJ3 "C2'" H14   SING N N 49 
PJ3 "C3'" H15   SING N N 50 
PJ3 "C4'" H16   SING N N 51 
PJ3 "C5'" H17   SING N N 52 
PJ3 "C5'" H18   SING N N 53 
PJ3 C8    H19   SING N N 54 
PJ3 C8    H20   SING N N 55 
PJ3 CM7   H21   SING N N 56 
PJ3 CM7   H22   SING N N 57 
PJ3 CM7   H23   SING N N 58 
PJ3 "O2'" H24   SING N N 59 
PJ3 "O3'" H25   SING N N 60 
PJ3 O3A   H26   SING N N 61 
PJ3 C     OXT   SING N N 62 
PJ3 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 
PJ3 InChI            InChI                1.06    "InChI=1S/C17H25N8O9P/c1-23-6-25(13-10(23)14(28)22-17(19)21-13)15-12(27)11(26)9(34-15)4-33-35(31,32)24-3-7(20-5-24)2-8(18)16(29)30/h3,5,8-9,11-12,15,26-27H,2,4,6,18H2,1H3,(H,29,30)(H,31,32)(H3,19,21,22,28)/t8-,9+,11+,12+,15+/m0/s1" 
PJ3 InChIKey         InChI                1.06    GHFKLICNYXEREV-OPYVMVOTSA-N                                                                                                                                                                                                             
PJ3 SMILES_CANONICAL CACTVS               3.385   "CN1CN([C@@H]2O[C@H](CO[P](O)(=O)n3cnc(C[C@H](N)C(O)=O)c3)[C@@H](O)[C@H]2O)C4=C1C(=O)NC(=N4)N"                                                                                                                                          
PJ3 SMILES           CACTVS               3.385   "CN1CN([CH]2O[CH](CO[P](O)(=O)n3cnc(C[CH](N)C(O)=O)c3)[CH](O)[CH]2O)C4=C1C(=O)NC(=N4)N"                                                                                                                                                 
PJ3 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CN1CN(C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(n4cc(nc4)C[C@@H](C(=O)O)N)O)O)O"                                                                                                                                         
PJ3 SMILES           "OpenEye OEToolkits" 3.1.0.0 "CN1CN(C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(n4cc(nc4)CC(C(=O)O)N)O)O)O"                                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           PJ3 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   3.1.0.0 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-2-azanyl-3-[1-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-4-yl]propanoic 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 
PJ3 "Create component"    2022-10-04 PDBE 
PJ3 "Modify linking type" 2022-10-11 PDBE 
PJ3 "Initial release"     2023-05-03 RCSB 
PJ3 "Modify PCM"          2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      PJ3 
_pdbx_chem_comp_synonyms.name         "7GMP capped histidine" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
