data_OBX
# 
_chem_comp.id                                    OBX 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-2-(4-carbamimidamidobutylamino)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H27 N7 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         agmatidine 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2023-01-30 
_chem_comp.pdbx_modified_date                    2024-03-29 
_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                        436.381 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OBX 
_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        8HTZ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
OBX P     P1  P 0 1 N N N N N N 171.752 189.166 265.812 -6.342 1.249  0.919  P     OBX 1  
OBX N1    N1  N 1 1 Y N N N N N 175.982 186.558 266.503 -0.377 -1.668 -0.170 N1    OBX 2  
OBX C2    C1  C 0 1 Y N N N N N 177.197 186.303 266.020 0.911  -1.936 -0.012 C2    OBX 3  
OBX N2    N2  N 0 1 N N N N N N 178.340 186.096 266.893 1.817  -0.891 0.027  N2    OBX 4  
OBX N3    N3  N 0 1 Y N N N N N 177.417 186.240 264.720 1.353  -3.178 0.109  N3    OBX 5  
OBX C4    C2  C 0 1 Y N N N N N 176.447 186.412 263.849 0.507  -4.204 0.076  C4    OBX 6  
OBX N4    N4  N 0 1 N N N N N N 176.729 186.336 262.430 0.973  -5.503 0.198  N4    OBX 7  
OBX C5    C3  C 0 1 Y N N N N N 175.173 186.675 264.315 -0.856 -3.953 -0.090 C5    OBX 8  
OBX C6    C4  C 0 1 Y N N N N N 174.960 186.744 265.682 -1.275 -2.642 -0.208 C6    OBX 9  
OBX CA    C5  C 0 1 N N N N N N 179.549 185.454 266.397 3.246  -1.166 0.201  CA    OBX 10 
OBX CB    C6  C 0 1 N N N N N N 179.312 183.962 266.156 4.022  0.153  0.211  CB    OBX 11 
OBX CD    C7  C 0 1 N N N N N N 179.081 181.729 267.399 6.289  1.184  0.401  CD    OBX 12 
OBX NE    N5  N 0 1 N N N N N N 178.466 181.376 266.134 7.718  0.909  0.576  NE    OBX 13 
OBX CG    C8  C 0 1 N N N N N N 179.736 183.110 267.349 5.513  -0.135 0.392  CG    OBX 14 
OBX CZ    C9  C 0 1 N N N N N N 177.024 181.232 266.043 8.618  1.947  0.615  CZ    OBX 15 
OBX "C1'" C10 C 0 1 N N R N N N 175.730 186.613 267.967 -0.815 -0.276 -0.300 "C1'" OBX 16 
OBX OP2   O1  O 0 1 N N N N N N 171.212 187.837 265.360 -6.993 -0.160 0.491  OP2   OBX 17 
OBX "C2'" C11 C 0 1 N N R N N N 176.298 187.858 268.639 -0.773 0.165  -1.779 "C2'" OBX 18 
OBX "O2'" O2  O 0 1 N N N N N N 176.604 187.529 269.985 0.425  0.897  -2.050 "O2'" OBX 19 
OBX OP3   O3  O 0 1 N Y N N N N 170.801 190.179 266.387 -6.625 1.518  2.481  OP3   OBX 20 
OBX "C3'" C12 C 0 1 N N S N N N 175.105 188.800 268.582 -2.011 1.077  -1.934 "C3'" OBX 21 
OBX "O3'" O4  O 0 1 N N N N N N 175.157 189.847 269.538 -1.615 2.399  -2.305 "O3'" OBX 22 
OBX "C4'" C13 C 0 1 N N R N N N 173.919 187.865 268.787 -2.654 1.078  -0.530 "C4'" OBX 23 
OBX "O4'" O5  O 0 1 N N N N N N 174.339 186.607 268.192 -2.201 -0.148 0.085  "O4'" OBX 24 
OBX "C5'" C14 C 0 1 N N N N N N 172.637 188.311 268.139 -4.180 1.088  -0.643 "C5'" OBX 25 
OBX "O5'" O6  O 0 1 N N N N N N 172.903 188.902 266.878 -4.753 1.207  0.660  "O5'" OBX 26 
OBX NH1   N6  N 0 1 N N N N N N 176.204 181.442 267.220 8.178  3.244  0.491  NH1   OBX 27 
OBX NH2   N7  N 0 1 N N N N N N 176.490 180.927 264.951 9.889  1.702  0.770  NH2   OBX 28 
OBX H1    H1  H 0 1 N N N N N N 178.296 186.398 267.845 1.507  0.024  -0.060 H1    OBX 29 
OBX H2    H2  H 0 1 N N N N N N 177.701 186.148 262.293 0.350  -6.246 0.170  H2    OBX 30 
OBX H3    H3  H 0 1 N N N N N N 176.187 185.602 262.021 1.922  -5.669 0.313  H3    OBX 31 
OBX H4    H4  H 0 1 N N N N N N 174.356 186.824 263.624 -1.567 -4.765 -0.121 H4    OBX 32 
OBX H5    H5  H 0 1 N N N N N N 173.974 186.947 266.073 -2.323 -2.413 -0.336 H5    OBX 33 
OBX H6    H6  H 0 1 N N N N N N 180.352 185.576 267.138 3.403  -1.687 1.146  H6    OBX 34 
OBX H7    H7  H 0 1 N N N N N N 179.847 185.929 265.451 3.598  -1.789 -0.621 H7    OBX 35 
OBX H8    H8  H 0 1 N N N N N N 178.240 183.800 265.968 3.864  0.674  -0.734 H8    OBX 36 
OBX H9    H9  H 0 1 N N N N N N 179.891 183.649 265.274 3.669  0.776  1.032  H9    OBX 37 
OBX H10   H10 H 0 1 N N N N N N 178.308 181.730 268.182 5.937  1.807  1.223  H10   OBX 38 
OBX H11   H11 H 0 1 N N N N N N 179.849 180.980 267.642 6.132  1.705  -0.543 H11   OBX 39 
OBX H12   H12 H 0 1 N N N N N N 179.035 181.232 265.324 8.028  -0.006 0.663  H12   OBX 40 
OBX H13   H13 H 0 1 N N N N N N 180.827 182.973 267.305 5.671  -0.655 1.337  H13   OBX 41 
OBX H14   H14 H 0 1 N N N N N N 179.472 183.650 268.270 5.866  -0.758 -0.430 H14   OBX 42 
OBX H15   H15 H 0 1 N N N N N N 176.187 185.730 268.437 -0.190 0.375  0.311  H15   OBX 43 
OBX H16   H16 H 0 1 N N N N N N 171.454 187.688 264.453 -6.645 -0.919 0.979  H16   OBX 44 
OBX H17   H17 H 0 1 N N N N N N 177.158 188.260 268.084 -0.848 -0.700 -2.438 H17   OBX 45 
OBX H18   H18 H 0 1 N N N N N N 176.960 188.292 270.425 0.503  1.199  -2.965 H18   OBX 46 
OBX H19   H19 H 0 1 N Y N N N N 170.862 190.988 265.892 -7.563 1.556  2.710  H19   OBX 47 
OBX H20   H20 H 0 1 N N N N N N 175.043 189.223 267.568 -2.700 0.663  -2.670 H20   OBX 48 
OBX H21   H21 H 0 1 N N N N N N 174.387 190.396 269.449 -1.152 2.448  -3.152 H21   OBX 49 
OBX H22   H22 H 0 1 N N N N N N 173.752 187.732 269.866 -2.311 1.939  0.044  H22   OBX 50 
OBX H23   H23 H 0 1 N N N N N N 172.140 189.047 268.787 -4.493 1.933  -1.256 H23   OBX 51 
OBX H24   H24 H 0 1 N N N N N N 171.979 187.441 268.000 -4.516 0.160  -1.105 H24   OBX 52 
OBX H25   H25 H 0 1 N N N N N N 176.632 181.685 268.091 7.232  3.426  0.376  H25   OBX 53 
OBX H26   H26 H 0 1 N N N N N N 175.211 181.344 267.161 8.813  3.976  0.518  H26   OBX 54 
OBX H27   H27 H 0 1 N N N N N N 175.495 180.860 265.026 10.524 2.435  0.797  H27   OBX 55 
OBX OP1   OP1 O 0 1 N N N N N N 172.534 189.814 264.564 -6.944 2.335  0.114  OP1   OBX 56 
# 
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 
OBX N4    C4    SING N N 1  
OBX C4    C5    DOUB Y N 2  
OBX C4    N3    SING Y N 3  
OBX C5    C6    SING Y N 4  
OBX N3    C2    DOUB Y N 5  
OBX NH2   CZ    DOUB N N 6  
OBX OP2   P     SING N N 7  
OBX C6    N1    DOUB Y N 8  
OBX P     OP3   SING N N 9  
OBX P     "O5'" SING N N 10 
OBX C2    N1    SING Y N 11 
OBX C2    N2    SING N N 12 
OBX CZ    NE    SING N N 13 
OBX CZ    NH1   SING N N 14 
OBX NE    CD    SING N N 15 
OBX CB    CA    SING N N 16 
OBX CB    CG    SING N N 17 
OBX CA    N2    SING N N 18 
OBX N1    "C1'" SING N N 19 
OBX "O5'" "C5'" SING N N 20 
OBX CG    CD    SING N N 21 
OBX "C1'" "O4'" SING N N 22 
OBX "C1'" "C2'" SING N N 23 
OBX "C5'" "C4'" SING N N 24 
OBX "O4'" "C4'" SING N N 25 
OBX "C3'" "C2'" SING N N 26 
OBX "C3'" "C4'" SING N N 27 
OBX "C3'" "O3'" SING N N 28 
OBX "C2'" "O2'" SING N N 29 
OBX N2    H1    SING N N 30 
OBX N4    H2    SING N N 31 
OBX N4    H3    SING N N 32 
OBX C5    H4    SING N N 33 
OBX C6    H5    SING N N 34 
OBX CA    H6    SING N N 35 
OBX CA    H7    SING N N 36 
OBX CB    H8    SING N N 37 
OBX CB    H9    SING N N 38 
OBX CD    H10   SING N N 39 
OBX CD    H11   SING N N 40 
OBX NE    H12   SING N N 41 
OBX CG    H13   SING N N 42 
OBX CG    H14   SING N N 43 
OBX "C1'" H15   SING N N 44 
OBX OP2   H16   SING N N 45 
OBX "C2'" H17   SING N N 46 
OBX "O2'" H18   SING N N 47 
OBX OP3   H19   SING N N 48 
OBX "C3'" H20   SING N N 49 
OBX "O3'" H21   SING N N 50 
OBX "C4'" H22   SING N N 51 
OBX "C5'" H23   SING N N 52 
OBX "C5'" H24   SING N N 53 
OBX NH1   H25   SING N N 54 
OBX NH1   H26   SING N N 55 
OBX NH2   H27   SING N N 56 
OBX P     OP1   DOUB N N 57 
# 
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 
OBX InChI            InChI                1.06  "InChI=1S/C14H26N7O7P/c15-9-3-6-21(14(20-9)19-5-2-1-4-18-13(16)17)12-11(23)10(22)8(28-12)7-27-29(24,25)26/h3,6,8,10-12,22-23H,1-2,4-5,7H2,(H8,15,16,17,18,19,20,24,25,26)/p+1/t8-,10-,11-,12-/m1/s1" 
OBX InChIKey         InChI                1.06  IIGUQJFGJGKMTR-HJQYOEGKSA-O                                                                                                                                                                          
OBX SMILES_CANONICAL CACTVS               3.385 "NC(=N)NCCCCNc1nc(N)cc[n+]1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"                                                                                                                             
OBX SMILES           CACTVS               3.385 "NC(=N)NCCCCNc1nc(N)cc[n+]1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O"                                                                                                                                   
OBX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\N)/NCCCCNc1nc(cc[n+]1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N"                                                                                                                       
OBX SMILES           "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1N)NCCCCNC(=N)N)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           OBX 
_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-[4-azanyl-2-(4-carbamimidamidobutylamino)pyrimidin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      OBX 
_pdbx_chem_comp_synonyms.name         agmatidine 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
OBX "Create component" 2023-01-30 PDBJ 
OBX "Initial release"  2024-04-03 RCSB 
# 
