data_5DD
# 
_chem_comp.id                                    5DD 
_chem_comp.name                                  "[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H24 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-10-31 
_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                        457.372 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     5DD 
_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        6I25 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_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 
5DD O3P   O1  O 0 1 N N N N N N -37.754 46.138 5.330  7.490  0.352  -1.669 O3P   5DD 1  
5DD P     P1  P 0 1 N N N N N N -37.105 45.034 4.530  6.675  0.090  -0.306 P     5DD 2  
5DD O1P   O2  O 0 1 N N N N N N -35.646 44.869 4.930  7.129  -1.318 0.329  O1P   5DD 3  
5DD O2P   O3  O 0 1 N N N N N N -37.196 45.363 3.051  6.959  1.179  0.655  O2P   5DD 4  
5DD "O5'" O4  O 0 1 N N N N N N -37.915 43.666 4.825  5.097  0.052  -0.622 "O5'" 5DD 5  
5DD "C5'" C1  C 0 1 N N N N N N -37.504 42.399 4.328  4.101  -0.059 0.397  "C5'" 5DD 6  
5DD "C4'" C2  C 0 1 N N R N N N -36.389 41.825 5.197  2.712  -0.066 -0.245 "C4'" 5DD 7  
5DD "O4'" O5  O 0 1 N N N N N N -35.224 42.662 5.122  2.565  -1.240 -1.047 "O4'" 5DD 8  
5DD "C3'" C3  C 0 1 N N S N N N -36.867 41.692 6.643  1.644  -0.059 0.850  "C3'" 5DD 9  
5DD "O3'" O6  O 0 1 N N N N N N -38.124 41.002 6.625  1.791  1.114  1.652  "O3'" 5DD 10 
5DD "C2'" C4  C 0 1 N N S N N N -35.859 40.942 7.528  0.255  -0.067 0.207  "C2'" 5DD 11 
5DD "O2'" O7  O 0 1 N N N N N N -36.354 40.772 8.855  0.108  -1.240 -0.595 "O2'" 5DD 12 
5DD "C1'" C5  C 0 1 N N N N N N -35.566 39.582 6.918  -0.813 -0.060 1.302  "C1'" 5DD 13 
5DD N10   N1  N 0 1 N N N N N N -35.118 38.620 7.912  -2.143 -0.036 0.687  N10   5DD 14 
5DD C9A   C6  C 0 1 Y N N N N N -36.048 37.928 8.677  -2.707 1.181  0.294  C9A   5DD 15 
5DD C9    C7  C 0 1 Y N N N N N -37.314 38.451 8.912  -2.172 2.374  0.762  C9    5DD 16 
5DD C8    C8  C 0 1 Y N N N N N -38.220 37.713 9.663  -2.721 3.578  0.367  C8    5DD 17 
5DD C8M   C9  C 0 1 N N N N N N -39.586 38.250 9.959  -2.141 4.872  0.876  C8M   5DD 18 
5DD C7    C10 C 0 1 Y N N N N N -37.847 36.376 10.184 -3.803 3.598  -0.495 C7    5DD 19 
5DD C7M   C11 C 0 1 N N N N N N -38.834 35.584 10.993 -4.396 4.915  -0.927 C7M   5DD 20 
5DD C6    C12 C 0 1 Y N N N N N -36.592 35.857 9.924  -4.341 2.412  -0.961 C6    5DD 21 
5DD C5A   C13 C 0 1 Y N N N N N -35.677 36.577 9.175  -3.800 1.206  -0.565 C5A   5DD 22 
5DD C10   C14 C 0 1 N N N N N N -33.802 38.179 7.888  -2.820 -1.194 0.496  C10   5DD 23 
5DD N1    N2  N 0 1 N N N N N N -33.037 38.732 6.928  -2.220 -2.337 0.700  N1    5DD 24 
5DD C4A   C15 C 0 1 N N R N N N -33.289 37.119 8.846  -4.252 -1.139 0.043  C4A   5DD 25 
5DD C4    C16 C 0 1 N N N N N N -31.919 36.714 8.439  -4.723 -2.483 -0.421 C4    5DD 26 
5DD O4    O8  O 0 1 N N N N N N -31.379 35.828 9.132  -5.777 -2.576 -1.013 O4    5DD 27 
5DD N3    N3  N 0 1 N N N N N N -31.229 37.371 7.490  -3.992 -3.587 -0.190 N3    5DD 28 
5DD C2    C17 C 0 1 N N N N N N -31.773 38.340 6.743  -2.799 -3.511 0.423  C2    5DD 29 
5DD O2    O9  O 0 1 N N N N N N -31.106 38.905 5.855  -2.228 -4.539 0.735  O2    5DD 30 
5DD C1    C18 C 0 1 N N N N N N -34.305 35.985 8.907  -4.403 -0.089 -1.053 C1    5DD 31 
5DD H1    H1  H 0 1 N N N N N N -38.083 46.806 4.740  8.449  0.387  -1.554 H1    5DD 32 
5DD H2    H2  H 0 1 N N N N N N -35.092 45.006 4.171  6.972  -2.078 -0.247 H2    5DD 33 
5DD H3    H3  H 0 1 N N N N N N -38.362 41.710 4.337  4.250  -0.985 0.951  H3    5DD 34 
5DD H4    H4  H 0 1 N N N N N N -37.137 42.515 3.297  4.182  0.789  1.078  H4    5DD 35 
5DD H5    H5  H 0 1 N N N N N N -36.143 40.820 4.822  2.597  0.819  -0.871 H5    5DD 36 
5DD H6    H6  H 0 1 N N N N N N -34.536 42.297 5.666  2.656  -2.067 -0.555 H6    5DD 37 
5DD H7    H7  H 0 1 N N N N N N -37.005 42.702 7.057  1.759  -0.944 1.476  H7    5DD 38 
5DD H8    H8  H 0 1 N N N N N N -38.445 40.905 7.514  1.700  1.941  1.159  H8    5DD 39 
5DD H9    H9  H 0 1 N N N N N N -34.924 41.521 7.552  0.140  0.818  -0.419 H9    5DD 40 
5DD H10   H10 H 0 1 N N N N N N -35.710 40.307 9.376  0.204  -2.067 -0.103 H10   5DD 41 
5DD H11   H11 H 0 1 N N N N N N -36.483 39.201 6.444  -0.712 -0.956 1.914  H11   5DD 42 
5DD H12   H12 H 0 1 N N N N N N -34.780 39.697 6.157  -0.687 0.824  1.928  H12   5DD 43 
5DD H13   H13 H 0 1 N N N N N N -37.589 39.417 8.516  -1.327 2.361  1.434  H13   5DD 44 
5DD H14   H14 H 0 1 N N N N N N -40.282 37.943 9.164  -1.361 5.213  0.195  H14   5DD 45 
5DD H15   H15 H 0 1 N N N N N N -39.934 37.854 10.924 -2.927 5.625  0.933  H15   5DD 46 
5DD H16   H16 H 0 1 N N N N N N -39.546 39.348 10.006 -1.715 4.715  1.867  H16   5DD 47 
5DD H17   H17 H 0 1 N N N N N N -39.435 34.952 10.323 -3.898 5.257  -1.834 H17   5DD 48 
5DD H18   H18 H 0 1 N N N N N N -38.294 34.948 11.709 -5.461 4.786  -1.122 H18   5DD 49 
5DD H19   H19 H 0 1 N N N N N N -39.496 36.272 11.540 -4.258 5.652  -0.137 H19   5DD 50 
5DD H20   H20 H 0 1 N N N N N N -36.324 34.884 10.308 -5.185 2.430  -1.634 H20   5DD 51 
5DD H21   H21 H 0 1 N N N N N N -33.231 37.571 9.847  -4.869 -0.842 0.891  H21   5DD 52 
5DD H22   H22 H 0 1 N N N N N N -30.272 37.126 7.336  -4.331 -4.452 -0.468 H22   5DD 53 
5DD H23   H23 H 0 1 N N N N N N -34.315 35.445 7.949  -5.459 0.059  -1.276 H23   5DD 54 
5DD H24   H24 H 0 1 N N N N N N -34.037 35.290 9.717  -3.879 -0.419 -1.950 H24   5DD 55 
# 
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 
5DD O2P   P     DOUB N N 1  
5DD "C5'" "O5'" SING N N 2  
5DD "C5'" "C4'" SING N N 3  
5DD P     "O5'" SING N N 4  
5DD P     O1P   SING N N 5  
5DD P     O3P   SING N N 6  
5DD "O4'" "C4'" SING N N 7  
5DD "C4'" "C3'" SING N N 8  
5DD O2    C2    DOUB N N 9  
5DD "O3'" "C3'" SING N N 10 
5DD "C3'" "C2'" SING N N 11 
5DD C2    N1    SING N N 12 
5DD C2    N3    SING N N 13 
5DD "C1'" "C2'" SING N N 14 
5DD "C1'" N10   SING N N 15 
5DD N1    C10   DOUB N N 16 
5DD N3    C4    SING N N 17 
5DD "C2'" "O2'" SING N N 18 
5DD C10   N10   SING N N 19 
5DD C10   C4A   SING N N 20 
5DD N10   C9A   SING N N 21 
5DD C4    C4A   SING N N 22 
5DD C4    O4    DOUB N N 23 
5DD C9A   C9    DOUB Y N 24 
5DD C9A   C5A   SING Y N 25 
5DD C4A   C1    SING N N 26 
5DD C1    C5A   SING N N 27 
5DD C9    C8    SING Y N 28 
5DD C5A   C6    DOUB Y N 29 
5DD C8    C8M   SING N N 30 
5DD C8    C7    DOUB Y N 31 
5DD C6    C7    SING Y N 32 
5DD C7    C7M   SING N N 33 
5DD O3P   H1    SING N N 34 
5DD O1P   H2    SING N N 35 
5DD "C5'" H3    SING N N 36 
5DD "C5'" H4    SING N N 37 
5DD "C4'" H5    SING N N 38 
5DD "O4'" H6    SING N N 39 
5DD "C3'" H7    SING N N 40 
5DD "O3'" H8    SING N N 41 
5DD "C2'" H9    SING N N 42 
5DD "O2'" H10   SING N N 43 
5DD "C1'" H11   SING N N 44 
5DD "C1'" H12   SING N N 45 
5DD C9    H13   SING N N 46 
5DD C8M   H14   SING N N 47 
5DD C8M   H15   SING N N 48 
5DD C8M   H16   SING N N 49 
5DD C7M   H17   SING N N 50 
5DD C7M   H18   SING N N 51 
5DD C7M   H19   SING N N 52 
5DD C6    H20   SING N N 53 
5DD C4A   H21   SING N N 54 
5DD N3    H22   SING N N 55 
5DD C1    H23   SING N N 56 
5DD C1    H24   SING 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 
5DD InChI            InChI                1.03  "InChI=1S/C18H24N3O9P/c1-8-3-10-5-11-16(19-18(26)20-17(11)25)21(12(10)4-9(8)2)6-13(22)15(24)14(23)7-30-31(27,28)29/h3-4,11,13-15,22-24H,5-7H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,13+,14-,15+/m1/s1" 
5DD InChIKey         InChI                1.03  MPTDYDRCOLGCLP-BEAPCOKYSA-N                                                                                                                                                                           
5DD SMILES_CANONICAL CACTVS               3.385 "Cc1cc2C[C@H]3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C"                                                                                                                         
5DD SMILES           CACTVS               3.385 "Cc1cc2C[CH]3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C"                                                                                                                             
5DD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@H]3C2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O"                                                                                                                     
5DD SMILES           "OpenEye OEToolkits" 2.0.6 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3C2)CC(C(C(COP(=O)(O)O)O)O)O"                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           5DD 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.6 
_pdbx_chem_comp_identifier.identifier        "[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen 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 
5DD "Create component" 2018-10-31 EBI  
5DD "Initial release"  2019-05-29 RCSB 
5DD "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            5DD 
_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               C4A 
_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      ? 
# 
