data_05K
# 
_chem_comp.id                                    05K 
_chem_comp.name                                  "[(2S,3R,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-[2-[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C22 H30 N5 O12 P" 
_chem_comp.mon_nstd_parent_comp_id               "DT, DT" 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-05-28 
_chem_comp.pdbx_modified_date                    2023-03-09 
_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                        587.474 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     05K 
_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        7OOS 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.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 
05K C1     C1  C 0 1 N N N -18.818 0.515  -9.147  0.251  0.635  -0.911 C1     05K 1  
05K "C1'"  C2  C 0 1 N N R -20.409 3.242  -5.766  5.822  1.383  -0.489 "C1'"  05K 2  
05K C5A    C3  C 0 1 N N N -25.594 -1.838 -8.702  -4.927 -5.955 1.368  C5A    05K 3  
05K C2     C4  C 0 1 N N N -22.481 2.531  -4.554  6.453  -0.880 0.138  C2     05K 4  
05K "C2'"  C5  C 0 1 N N N -19.441 3.344  -4.604  6.205  1.255  -1.976 "C2'"  05K 5  
05K C21    C6  C 0 1 N N N -24.346 2.198  -8.474  -4.406 -2.362 -0.802 C21    05K 6  
05K "C3'"  C7  C 0 1 N N S -18.244 2.542  -5.043  4.876  0.885  -2.679 "C3'"  05K 7  
05K C4     C8  C 0 1 N N N -23.430 0.443  -4.879  8.063  -1.332 1.770  C4     05K 8  
05K "C4'"  C9  C 0 1 N N R -18.249 2.690  -6.540  3.820  1.368  -1.653 "C4'"  05K 9  
05K C41    C10 C 0 1 N N N -25.697 0.519  -7.636  -5.222 -4.550 -0.724 C41    05K 10 
05K C5     C11 C 0 1 N N N -22.368 0.127  -5.849  8.245  0.060  1.959  C5     05K 11 
05K "C5'"  C12 C 0 1 N N N -17.642 1.467  -7.195  2.508  0.601  -1.828 "C5'"  05K 12 
05K C51    C13 C 0 1 N N N -25.145 -0.407 -8.638  -4.738 -4.672 0.601  C51    05K 13 
05K C6     C14 C 0 1 N N N -21.412 1.081  -6.100  7.508  0.924  1.229  C6     05K 14 
05K C61    C15 C 0 1 N N N -24.194 0.072  -9.510  -4.109 -3.621 1.169  C61    05K 15 
05K C5M    C16 C 0 1 N N N -22.310 -1.197 -6.550  9.240  0.569  2.970  C5M    05K 16 
05K C11    C17 C 0 1 N N N -19.281 0.784  -10.552 -0.791 1.203  0.018  C11    05K 17 
05K N1     N1  N 0 1 N N N -21.450 2.256  -5.473  6.613  0.445  0.312  N1     05K 18 
05K N11    N2  N 0 1 N N N -23.805 1.345  -9.442  -3.946 -2.463 0.459  N11    05K 19 
05K N3     N3  N 0 1 N N N -23.424 1.631  -4.287  7.167  -1.764 0.860  N3     05K 20 
05K N31    N4  N 0 1 N N N -25.265 1.773  -7.613  -5.041 -3.392 -1.391 N31    05K 21 
05K "N5'"  N5  N 0 1 N N N -18.172 1.499  -8.541  1.494  1.157  -0.929 "N5'"  05K 22 
05K O2     O1  O 0 1 N N N -22.529 3.616  -3.951  5.649  -1.284 -0.680 O2     05K 23 
05K O21    O2  O 0 1 N N N -23.962 3.378  -8.431  -4.250 -1.324 -1.415 O21    05K 24 
05K O1     O3  O 0 1 N N N -19.043 -0.555 -8.611  -0.027 -0.294 -1.639 O1     05K 25 
05K "O3'"  O4  O 0 1 N N N -17.011 3.011  -4.456  4.742  1.587  -3.917 "O3'"  05K 26 
05K O4     O5  O 0 1 N N N -24.316 -0.389 -4.618  8.709  -2.130 2.424  O4     05K 27 
05K "O4'"  O6  O 0 1 N N N -19.629 2.803  -6.881  4.425  1.062  -0.378 "O4'"  05K 28 
05K O41    O7  O 0 1 N N N -26.554 0.130  -6.824  -5.797 -5.483 -1.256 O41    05K 29 
05K "O5'"  O8  O 0 1 N N N -22.102 -1.548 -11.790 -4.917 2.647  1.074  "O5'"  05K 30 
05K OP1    O9  O 0 1 N N N -23.604 -3.680 -11.337 -6.594 3.626  -0.539 OP1    05K 31 
05K OP2    O10 O 0 1 N N N -21.859 -3.689 -13.345 -6.953 4.080  1.918  OP2    05K 32 
05K P      P1  P 0 1 N N N -22.841 -2.806 -12.441 -5.882 3.890  0.731  P      05K 33 
05K "C1'1" C18 C 0 0 N N R -22.794 1.886  -10.346 -3.264 -1.323 1.076  "C1'1" 05K 34 
05K "C2'1" C19 C 0 0 N N N -21.445 1.647  -9.705  -1.949 -1.032 0.327  "C2'1" 05K 35 
05K "C3'1" C20 C 0 0 N N R -20.783 0.586  -10.551 -2.101 0.432  -0.154 "C3'1" 05K 36 
05K "C4'1" C21 C 0 0 N N S -21.443 0.751  -11.902 -3.192 0.976  0.803  "C4'1" 05K 37 
05K "C5'1" C22 C 0 0 N N N -21.504 -0.577 -12.636 -3.927 2.158  0.167  "C5'1" 05K 38 
05K "O4'1" O11 O 0 0 N N N -22.764 1.206  -11.600 -4.084 -0.147 0.970  "O4'1" 05K 39 
05K "H1'"  H1  H 0 1 N N N -20.857 4.227  -5.963  5.999  2.402  -0.147 "H1'"  05K 40 
05K H5A1   H2  H 0 0 N N N -26.353 -2.020 -7.927  -5.456 -6.676 0.745  H5A1   05K 41 
05K H5A2   H3  H 0 0 N N N -26.026 -2.043 -9.693  -3.953 -6.359 1.645  H5A2   05K 42 
05K H5A3   H4  H 0 0 N N N -24.732 -2.500 -8.534  -5.508 -5.757 2.269  H5A3   05K 43 
05K "H2'1" H5  H 0 0 N N N -19.162 4.392  -4.421  6.587  2.203  -2.354 "H2'1" 05K 44 
05K "H2'2" H6  H 0 0 N N N -19.882 2.917  -3.691  6.944  0.465  -2.113 "H2'2" 05K 45 
05K "H3'"  H7  H 0 1 N N N -18.405 1.485  -4.785  4.805  -0.191 -2.835 "H3'"  05K 46 
05K "H4'"  H8  H 0 1 N N N -17.690 3.591  -6.833  3.652  2.441  -1.750 "H4'"  05K 47 
05K "H5'1" H9  H 0 0 N N N -17.951 0.549  -6.674  2.169  0.693  -2.860 "H5'1" 05K 48 
05K "H5'2" H10 H 0 0 N N N -16.544 1.532  -7.204  2.668  -0.451 -1.590 "H5'2" 05K 49 
05K H6     H11 H 0 1 N N N -20.624 0.877  -6.810  7.634  1.989  1.360  H6     05K 50 
05K H61    H12 H 0 1 N N N -23.762 -0.585 -10.251 -3.736 -3.694 2.180  H61    05K 51 
05K H52    H13 H 0 1 N N N -23.153 -1.823 -6.222  9.725  -0.275 3.460  H52    05K 52 
05K H53    H14 H 0 1 N N N -22.372 -1.039 -7.637  9.992  1.177  2.466  H53    05K 53 
05K H51    H15 H 0 1 N N N -21.363 -1.700 -6.306  8.724  1.174  3.715  H51    05K 54 
05K H2     H16 H 0 1 N N N -18.805 0.081  -11.251 -0.448 1.111  1.048  H2     05K 55 
05K H3     H17 H 0 1 N N N -19.033 1.815  -10.844 -0.954 2.254  -0.218 H3     05K 56 
05K HN3    H18 H 0 1 N N N -24.142 1.854  -3.628  7.036  -2.715 0.725  HN3    05K 57 
05K H31    H19 H 0 1 N N N -25.637 2.409  -6.937  -5.371 -3.301 -2.299 H31    05K 58 
05K "HN5'" H20 H 0 0 N N N -18.038 2.342  -9.062  1.716  1.900  -0.347 "HN5'" 05K 59 
05K "HO3'" H21 H 0 0 N Y N -17.047 2.901  -3.513  5.435  1.385  -4.561 "HO3'" 05K 60 
05K HOP2   H23 H 0 0 N N N -21.900 -4.596 -13.065 -7.569 4.813  1.778  HOP2   05K 61 
05K H1     H24 H 0 1 N N N -22.948 2.966  -10.490 -3.054 -1.539 2.123  H1     05K 62 
05K HC22   H25 H 0 0 N N N -21.567 1.294  -8.670  -1.097 -1.125 1.002  HC22   05K 63 
05K HC21   H26 H 0 0 N N N -20.848 2.571  -9.709  -1.836 -1.705 -0.523 HC21   05K 64 
05K "H3'1" H27 H 0 0 N N N -21.021 -0.409 -10.146 -2.439 0.468  -1.189 "H3'1" 05K 65 
05K HC41   H28 H 0 0 N N N -20.893 1.489  -12.504 -2.755 1.264  1.759  HC41   05K 66 
05K HC51   H29 H 0 0 N N N -22.105 -0.465 -13.551 -4.408 1.832  -0.755 HC51   05K 67 
05K HC52   H30 H 0 0 N N N -20.486 -0.898 -12.903 -3.214 2.951  -0.055 HC52   05K 68 
05K OP3    OP3 O 0 1 N Y N ?       ?      ?       -5.000 5.229  0.584  OP3    05K 69 
05K HOP3   H22 H 0 0 N Y N ?       ?      ?       -4.505 5.463  1.381  HOP3   05K 70 
# 
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 
05K OP2    P      SING N N 1  
05K "C5'1" "C4'1" SING N N 2  
05K "C5'1" "O5'"  SING N N 3  
05K P      "O5'"  SING N N 4  
05K P      OP1    DOUB N N 5  
05K "C4'1" "O4'1" SING N N 6  
05K "C4'1" "C3'1" SING N N 7  
05K "O4'1" "C1'1" SING N N 8  
05K C11    "C3'1" SING N N 9  
05K C11    C1     SING N N 10 
05K "C3'1" "C2'1" SING N N 11 
05K "C1'1" "C2'1" SING N N 12 
05K "C1'1" N11    SING N N 13 
05K C61    N11    SING N N 14 
05K C61    C51    DOUB N N 15 
05K N11    C21    SING N N 16 
05K C1     O1     DOUB N N 17 
05K C1     "N5'"  SING N N 18 
05K C5A    C51    SING N N 19 
05K C51    C41    SING N N 20 
05K "N5'"  "C5'"  SING N N 21 
05K C21    O21    DOUB N N 22 
05K C21    N31    SING N N 23 
05K C41    N31    SING N N 24 
05K C41    O41    DOUB N N 25 
05K "C5'"  "C4'"  SING N N 26 
05K "O4'"  "C4'"  SING N N 27 
05K "O4'"  "C1'"  SING N N 28 
05K C5M    C5     SING N N 29 
05K "C4'"  "C3'"  SING N N 30 
05K C6     C5     DOUB N N 31 
05K C6     N1     SING N N 32 
05K C5     C4     SING N N 33 
05K "C1'"  N1     SING N N 34 
05K "C1'"  "C2'"  SING N N 35 
05K N1     C2     SING N N 36 
05K "C3'"  "C2'"  SING N N 37 
05K "C3'"  "O3'"  SING N N 38 
05K C4     O4     DOUB N N 39 
05K C4     N3     SING N N 40 
05K C2     N3     SING N N 41 
05K C2     O2     DOUB N N 42 
05K "C1'"  "H1'"  SING N N 43 
05K C5A    H5A1   SING N N 44 
05K C5A    H5A2   SING N N 45 
05K C5A    H5A3   SING N N 46 
05K "C2'"  "H2'1" SING N N 47 
05K "C2'"  "H2'2" SING N N 48 
05K "C3'"  "H3'"  SING N N 49 
05K "C4'"  "H4'"  SING N N 50 
05K "C5'"  "H5'1" SING N N 51 
05K "C5'"  "H5'2" SING N N 52 
05K C6     H6     SING N N 53 
05K C61    H61    SING N N 54 
05K C5M    H52    SING N N 55 
05K C5M    H53    SING N N 56 
05K C5M    H51    SING N N 57 
05K C11    H2     SING N N 58 
05K C11    H3     SING N N 59 
05K N3     HN3    SING N N 60 
05K N31    H31    SING N N 61 
05K "N5'"  "HN5'" SING N N 62 
05K "O3'"  "HO3'" SING N N 63 
05K OP2    HOP2   SING N N 64 
05K "C1'1" H1     SING N N 65 
05K "C2'1" HC22   SING N N 66 
05K "C2'1" HC21   SING N N 67 
05K "C3'1" "H3'1" SING N N 68 
05K "C4'1" HC41   SING N N 69 
05K "C5'1" HC51   SING N N 70 
05K "C5'1" HC52   SING N N 71 
05K P      OP3    SING N N 72 
05K OP3    HOP3   SING N N 73 
# 
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 
05K InChI            InChI                1.06  "InChI=1S/C22H30N5O12P/c1-10-7-26(21(32)24-19(10)30)17-4-12(15(39-17)9-37-40(34,35)36)3-16(29)23-6-14-13(28)5-18(38-14)27-8-11(2)20(31)25-22(27)33/h7-8,12-15,17-18,28H,3-6,9H2,1-2H3,(H,23,29)(H,24,30,32)(H,25,31,33)(H2,34,35,36)/t12-,13-,14+,15+,17+,18+/m0/s1" 
05K InChIKey         InChI                1.06  LKZCDFBGSPSCDT-LVBQRNIJSA-N                                                                                                                                                                                                                                          
05K SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CNC(=O)C[C@H]3C[C@@H](O[C@@H]3CO[P](O)(O)=O)N4C=C(C)C(=O)NC4=O)O2)C(=O)NC1=O"                                                                                                                                                          
05K SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CNC(=O)C[CH]3C[CH](O[CH]3CO[P](O)(O)=O)N4C=C(C)C(=O)NC4=O)O2)C(=O)NC1=O"                                                                                                                                                                   
05K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)CC(=O)NC[C@@H]3[C@H](C[C@@H](O3)N4C=C(C(=O)NC4=O)C)O"                                                                                                                                                          
05K SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)CC(=O)NCC3C(CC(O3)N4C=C(C(=O)NC4=O)C)O"                                                                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           05K 
_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},3~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-[2-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]oxolan-2-yl]methyl 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 
05K "Create component"         2021-05-28 PDBE 
05K "Initial release"          2022-08-03 RCSB 
05K "Modify leaving atom flag" 2023-03-09 PDBE 
# 
