data_D4B
# 
_chem_comp.id                                    D4B 
_chem_comp.name                                  "[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C19 H18 N3 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-12-19 
_chem_comp.pdbx_modified_date                    2018-09-21 
_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                        431.336 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     D4B 
_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        6FBF 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
D4B O      O1  O 0 1 N N N 32.389 -14.632 3.438  -2.536 0.109  0.469  O      D4B 1  
D4B "C1'"  C1  C 0 1 N N R 31.502 -14.983 2.418  -1.391 0.758  1.065  "C1'"  D4B 2  
D4B C10    C2  C 0 1 Y N N 28.639 -18.518 8.564  6.081  -0.942 1.227  C10    D4B 3  
D4B C11    C3  C 0 1 Y N N 28.074 -18.821 9.785  7.375  -1.321 1.445  C11    D4B 4  
D4B C12    C4  C 0 1 Y N N 26.744 -19.534 7.433  6.698  -0.108 -0.963 C12    D4B 5  
D4B C13    C5  C 0 1 Y N N 26.182 -19.834 8.670  7.994  -0.477 -0.738 C13    D4B 6  
D4B C14    C6  C 0 1 Y N N 26.847 -19.486 9.848  8.346  -1.093 0.466  C14    D4B 7  
D4B C15    C7  C 0 1 N N N 26.365 -19.785 11.138 9.702  -1.491 0.697  C15    D4B 8  
D4B C16    C8  C 0 1 N N N 25.853 -20.097 12.155 10.814 -1.817 0.886  C16    D4B 9  
D4B C2     C9  C 0 1 N N N 31.522 -17.507 1.817  -0.665 1.560  -1.106 C2     D4B 10 
D4B "C2'"  C10 C 0 1 N N N 30.269 -14.030 2.639  -1.930 2.111  1.581  "C2'"  D4B 11 
D4B "C3'"  C11 C 0 1 N N S 31.013 -12.716 2.892  -3.442 1.862  1.779  "C3'"  D4B 12 
D4B C4     C12 C 0 1 N N N 30.348 -16.735 3.772  0.927  0.580  0.325  C4     D4B 13 
D4B "C4'"  C13 C 0 1 N N R 32.304 -13.219 3.626  -3.638 0.389  1.359  "C4'"  D4B 14 
D4B C5     C14 C 0 1 N N N 29.962 -18.054 4.050  1.902  0.790  -0.631 C5     D4B 15 
D4B "C5'"  C15 C 0 1 N N N 32.131 -12.834 5.141  -4.970 0.217  0.627  "C5'"  D4B 16 
D4B C6     C16 C 0 1 N N N 30.389 -19.071 3.137  1.506  1.433  -1.890 C6     D4B 17 
D4B C7     C17 C 0 1 N N N 29.227 -18.337 5.192  3.258  0.393  -0.401 C7     D4B 18 
D4B C8     C18 C 0 1 N N N 28.613 -18.595 6.171  4.370  0.067  -0.212 C8     D4B 19 
D4B C9     C19 C 0 1 Y N N 27.974 -18.882 7.381  5.727  -0.330 0.019  C9     D4B 20 
D4B N1     N1  N 0 1 N N N 31.143 -18.837 2.060  0.239  1.783  -2.057 N1     D4B 21 
D4B N3     N2  N 0 1 N N N 31.097 -16.441 2.700  -0.347 0.975  0.060  N3     D4B 22 
D4B N6     N3  N 0 1 N N N 30.010 -20.379 3.328  2.433  1.667  -2.876 N6     D4B 23 
D4B O1     O2  O 0 1 N N N 31.029 -13.396 5.677  -5.152 -1.159 0.285  O1     D4B 24 
D4B O2     O3  O 0 1 N N N 32.230 -17.238 0.859  -1.819 1.903  -1.298 O2     D4B 25 
D4B OP1    O4  O 0 1 N N N 29.218 -13.676 7.501  -6.619 -0.951 -1.758 OP1    D4B 26 
D4B "O3'"  O5  O 0 1 N N N 31.313 -12.027 1.721  -3.804 2.045  3.149  "O3'"  D4B 27 
D4B P      P1  P 0 1 N N N 30.657 -13.236 7.430  -6.450 -1.705 -0.496 P      D4B 28 
D4B OP2    O6  O 0 1 N N N 30.815 -11.702 7.499  -6.259 -3.269 -0.827 OP2    D4B 29 
D4B "H1'"  H1  H 0 1 N N N 31.917 -14.866 1.406  -1.005 0.163  1.893  "H1'"  D4B 30 
D4B H2     H2  H 0 1 N N N 29.588 -18.004 8.517  5.331  -1.118 1.984  H2     D4B 31 
D4B H11    H3  H 0 1 N N N 28.582 -18.543 10.696 7.648  -1.796 2.376  H11    D4B 32 
D4B H14    H4  H 0 1 N N N 26.231 -19.804 6.522  6.426  0.368  -1.894 H14    D4B 33 
D4B H15    H5  H 0 1 N N N 25.228 -20.338 8.720  8.746  -0.294 -1.491 H15    D4B 34 
D4B H16    H6  H 0 1 N N N 25.393 -20.377 13.068 11.808 -2.108 1.054  H16    D4B 35 
D4B "H2'A" H7  H 0 0 N N N 29.628 -13.974 1.747  -1.459 2.373  2.529  "H2'A" D4B 36 
D4B "H2'B" H8  H 0 0 N N N 29.665 -14.334 3.507  -1.765 2.895  0.842  "H2'B" D4B 37 
D4B "H3'"  H9  H 0 1 N N N 30.429 -12.094 3.586  -4.025 2.523  1.137  "H3'"  D4B 38 
D4B H4     H10 H 0 1 N N N 30.036 -15.941 4.434  1.172  0.111  1.266  H4     D4B 39 
D4B "H4'"  H11 H 0 1 N N N 33.185 -12.704 3.215  -3.597 -0.263 2.231  "H4'"  D4B 40 
D4B "H5'B" H12 H 0 0 N N N 33.014 -13.179 5.699  -5.785 0.541  1.274  "H5'B" D4B 41 
D4B "H5'A" H13 H 0 0 N N N 32.049 -11.740 5.223  -4.966 0.819  -0.282 "H5'A" D4B 42 
D4B HN2    H14 H 0 1 N N N 30.300 -21.083 2.680  3.358  1.408  -2.744 HN2    D4B 43 
D4B HN1    H15 H 0 1 N N N 29.444 -20.626 4.115  2.162  2.093  -3.705 HN1    D4B 44 
D4B H3     H17 H 0 1 N N N 31.772 -11.223 1.935  -3.644 2.938  3.483  H3     D4B 45 
D4B HP2    HP2 H 0 1 N N N 29.959 -11.298 7.576  -7.005 -3.665 -1.298 HP2    D4B 46 
D4B OP3    OP3 O 0 1 N Y N 31.909 -13.926 8.142  -7.754 -1.507 0.427  OP3    D4B 47 
D4B HP3    HP3 H 0 1 N N N 31.615 -14.682 8.637  -7.712 -1.974 1.272  HP3    D4B 48 
# 
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 
D4B O2    C2     DOUB N N 1  
D4B "O3'" "C3'"  SING N N 2  
D4B C2    N1     SING N N 3  
D4B C2    N3     SING N N 4  
D4B N1    C6     DOUB N N 5  
D4B "C1'" "C2'"  SING N N 6  
D4B "C1'" N3     SING N N 7  
D4B "C1'" O      SING N N 8  
D4B "C2'" "C3'"  SING N N 9  
D4B N3    C4     SING N N 10 
D4B "C3'" "C4'"  SING N N 11 
D4B C6    N6     SING N N 12 
D4B C6    C5     SING N N 13 
D4B O     "C4'"  SING N N 14 
D4B "C4'" "C5'"  SING N N 15 
D4B C4    C5     DOUB N N 16 
D4B C5    C7     SING N N 17 
D4B "C5'" O1     SING N N 18 
D4B C7    C8     TRIP N N 19 
D4B O1    P      SING N N 20 
D4B C8    C9     SING N N 21 
D4B C9    C12    DOUB Y N 22 
D4B C9    C10    SING Y N 23 
D4B P     OP2    SING N N 24 
D4B P     OP1    DOUB N N 25 
D4B C12   C13    SING Y N 26 
D4B C10   C11    DOUB Y N 27 
D4B C13   C14    DOUB Y N 28 
D4B C11   C14    SING Y N 29 
D4B C14   C15    SING N N 30 
D4B C15   C16    TRIP N N 31 
D4B "C1'" "H1'"  SING N N 32 
D4B C10   H2     SING N N 33 
D4B C11   H11    SING N N 34 
D4B C12   H14    SING N N 35 
D4B C13   H15    SING N N 36 
D4B C16   H16    SING N N 37 
D4B "C2'" "H2'A" SING N N 38 
D4B "C2'" "H2'B" SING N N 39 
D4B "C3'" "H3'"  SING N N 40 
D4B C4    H4     SING N N 41 
D4B "C4'" "H4'"  SING N N 42 
D4B "C5'" "H5'B" SING N N 43 
D4B "C5'" "H5'A" SING N N 44 
D4B N6    HN2    SING N N 45 
D4B N6    HN1    SING N N 46 
D4B "O3'" H3     SING N N 47 
D4B OP2   HP2    SING N N 48 
D4B P     OP3    SING N N 49 
D4B OP3   HP3    SING N N 50 
# 
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 
D4B InChI            InChI                1.03  "InChI=1S/C19H18N3O7P/c1-2-12-3-5-13(6-4-12)7-8-14-10-22(19(24)21-18(14)20)17-9-15(23)16(29-17)11-28-30(25,26)27/h1,3-6,10,15-17,23H,9,11H2,(H2,20,21,24)(H2,25,26,27)/t15-,16+,17+/m0/s1" 
D4B InChIKey         InChI                1.03  JCGCLKWMRGKZTM-GVDBMIGSSA-N                                                                                                                                                                
D4B SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3"                                                                                                                  
D4B SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3"                                                                                                                      
D4B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O"                                                                                                                    
D4B SMILES           "OpenEye OEToolkits" 2.0.6 "C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)C3CC(C(O3)COP(=O)(O)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 
D4B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-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 
D4B "Create component"   2017-12-19 RCSB 
D4B "Other modification" 2018-01-18 EBI  
D4B "Initial release"    2018-09-26 RCSB 
# 
