data_77Y
# 
_chem_comp.id                                    77Y 
_chem_comp.name                                  
; 5-(3-(2-(1H-indol-3-yl)acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C22 H25 N4 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               DU 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-09-12 
_chem_comp.pdbx_modified_date                    2016-09-23 
_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                        520.429 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     77Y 
_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        5LUW 
_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 
77Y C6    C1  C 0 1 N N N -29.328 37.751 6.750  1.230   -1.073 0.935  C6    77Y 1  
77Y C1    C2  C 0 1 N N N -28.193 35.784 8.842  -2.199  -1.618 -0.243 C1    77Y 2  
77Y C29   C3  C 0 1 Y N N -30.791 30.792 6.827  -8.808  3.053  1.523  C29   77Y 3  
77Y C28   C4  C 0 1 Y N N -30.854 29.423 6.635  -10.148 2.728  1.683  C28   77Y 4  
77Y C27   C5  C 0 1 Y N N -30.480 28.508 7.624  -10.699 1.663  1.003  C27   77Y 5  
77Y C30   C6  C 0 1 Y N N -30.345 31.191 8.087  -8.011  2.322  0.687  C30   77Y 6  
77Y C5    C7  C 0 1 N N N -29.265 37.955 8.140  0.194   -1.381 0.101  C5    77Y 7  
77Y C4    C8  C 0 1 N N N -30.162 38.978 8.675  0.509   -1.887 -1.243 C4    77Y 8  
77Y C3    C9  C 0 1 N N N -27.525 34.914 9.838  -3.622  -1.549 0.249  C3    77Y 9  
77Y C2    C10 C 0 1 N N N -31.010 39.458 6.584  2.781   -1.706 -0.729 C2    77Y 10 
77Y C14   C11 C 0 1 Y N N -30.003 28.902 8.862  -9.906  0.906  0.147  C14   77Y 11 
77Y C16   C12 C 0 1 Y N N -29.183 29.208 10.897 -9.005  -0.554 -1.304 C16   77Y 12 
77Y O34   O1  O 0 1 N N N -27.089 32.146 10.001 -6.256  -1.051 0.530  O34   77Y 13 
77Y C32   C13 C 0 1 N N N -28.108 32.690 10.464 -5.744  -0.591 -0.469 C32   77Y 14 
77Y C33   C14 C 0 1 N N N -29.197 31.787 11.100 -6.577  0.195  -1.448 C33   77Y 15 
77Y C12   C15 C 0 1 Y N N -29.382 30.507 10.345 -7.999  0.264  -0.956 C12   77Y 16 
77Y N15   N1  N 0 1 Y N N -29.586 28.296 9.981  -10.151 -0.188 -0.652 N15   77Y 17 
77Y C13   C16 C 0 1 Y N N -29.957 30.317 9.052  -8.547  1.237  -0.007 C13   77Y 18 
77Y N9    N2  N 0 1 N N N -28.479 33.938 10.423 -4.431  -0.785 -0.703 N9    77Y 19 
77Y C7    C17 C 0 1 N N N -28.521 37.092 9.045  -1.207  -1.210 0.537  C7    77Y 20 
77Y O4    O2  O 0 1 N N N -30.125 39.179 9.944  -0.381  -2.175 -2.023 O4    77Y 21 
77Y N3    N3  N 0 1 N N N -30.967 39.681 7.897  1.804   -2.026 -1.595 N3    77Y 22 
77Y O2    O3  O 0 1 N N N -31.756 40.084 5.846  3.941   -1.839 -1.070 O2    77Y 23 
77Y N1    N4  N 0 1 N N N -30.167 38.517 6.031  2.514   -1.236 0.501  N1    77Y 24 
77Y "C1'" C18 C 0 1 N N R -30.258 38.231 4.575  3.623   -0.905 1.399  "C1'" 77Y 25 
77Y "C2'" C19 C 0 1 N N N -28.870 38.343 3.758  4.413   -2.181 1.748  "C2'" 77Y 26 
77Y "C3'" C20 C 0 1 N N S -29.298 37.371 2.713  5.854   -1.878 1.269  "C3'" 77Y 27 
77Y "O3'" O4  O 0 1 N N N -30.050 38.141 1.857  6.817   -2.356 2.210  "O3'" 77Y 28 
77Y "O4'" O5  O 0 1 N N N -30.602 36.852 4.452  4.530   -0.003 0.743  "O4'" 77Y 29 
77Y "C4'" C21 C 0 1 N N R -29.963 36.180 3.360  5.858   -0.329 1.212  "C4'" 77Y 30 
77Y "C5'" C22 C 0 1 N N N -29.081 35.084 3.768  6.916   0.171  0.227  "C5'" 77Y 31 
77Y "O5'" O6  O 0 1 N N N -27.966 35.629 4.509  6.979   1.598  0.279  "O5'" 77Y 32 
77Y P     P1  P 0 1 N N N -26.573 35.038 4.024  7.987   2.465  -0.629 P     77Y 33 
77Y OP1   O7  O 0 1 N N N -26.465 34.858 2.556  7.784   2.124  -2.055 OP1   77Y 34 
77Y OP2   O8  O 0 1 N N N -25.602 35.970 4.776  7.695   4.033  -0.406 OP2   77Y 35 
77Y H1    H1  H 0 1 N N N -28.718 36.998 6.272  1.036   -0.698 1.929  H1    77Y 36 
77Y H2    H2  H 0 1 N N N -28.438 35.350 7.884  -1.987  -2.000 -1.231 H2    77Y 37 
77Y H3    H3  H 0 1 N N N -31.067 31.499 6.058  -8.393  3.893  2.060  H3    77Y 38 
77Y H4    H4  H 0 1 N N N -31.205 29.047 5.685  -10.765 3.315  2.348  H4    77Y 39 
77Y H5    H5  H 0 1 N N N -30.567 27.452 7.414  -11.742 1.418  1.135  H5    77Y 40 
77Y H6    H6  H 0 1 N N N -30.306 32.248 8.306  -6.971  2.584  0.564  H6    77Y 41 
77Y H7    H7  H 0 1 N N N -26.708 34.366 9.346  -4.024  -2.558 0.339  H7    77Y 42 
77Y H8    H8  H 0 1 N N N -27.113 35.540 10.643 -3.646  -1.059 1.222  H8    77Y 43 
77Y H9    H9  H 0 1 N N N -28.781 28.989 11.875 -8.922  -1.380 -1.995 H9    77Y 44 
77Y H10   H10 H 0 1 N N N -30.151 32.335 11.108 -6.174  1.204  -1.539 H10   77Y 45 
77Y H11   H11 H 0 1 N N N -28.902 31.550 12.133 -6.552  -0.295 -2.421 H11   77Y 46 
77Y H12   H12 H 0 1 N N N -29.574 27.306 10.121 -11.008 -0.634 -0.739 H12   77Y 47 
77Y H13   H13 H 0 1 N N N -29.371 34.227 10.772 -4.022  -0.417 -1.502 H13   77Y 48 
77Y H14   H14 H 0 1 N N N -28.194 37.534 9.975  -1.423  -0.754 1.492  H14   77Y 49 
77Y H15   H15 H 0 1 N N N -31.550 40.388 8.298  2.032   -2.362 -2.476 H15   77Y 50 
77Y H16   H16 H 0 1 N N N -31.007 38.879 4.098  3.237   -0.447 2.310  H16   77Y 51 
77Y H17   H17 H 0 1 N N N -27.997 38.004 4.335  4.398   -2.357 2.823  H17   77Y 52 
77Y H18   H18 H 0 1 N N N -28.679 39.351 3.362  4.005   -3.040 1.215  H18   77Y 53 
77Y H19   H19 H 0 1 N N N -28.398 37.012 2.192  6.032   -2.304 0.282  H19   77Y 54 
77Y H20   H20 H 0 1 N N N -29.518 38.853 1.520  6.852   -3.320 2.281  H20   77Y 55 
77Y H21   H21 H 0 1 N N N -30.727 35.790 2.671  6.029   0.091  2.203  H21   77Y 56 
77Y H22   H22 H 0 1 N N N -29.638 34.380 4.404  7.887   -0.245 0.493  H22   77Y 57 
77Y H23   H23 H 0 1 N N N -28.709 34.558 2.876  6.650   -0.143 -0.783 H23   77Y 58 
77Y H25   H25 H 0 1 N N N -24.992 36.357 4.159  8.267   4.617  -0.923 H25   77Y 59 
77Y OP3   OP3 O 0 1 N Y N -26.412 33.648 4.706  9.505   2.137  -0.208 OP3   77Y 60 
77Y H27   H27 H 0 1 N N N -26.279 32.982 4.041  9.710   2.336  0.715  H27   77Y 61 
# 
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 
77Y "O3'" "C3'" SING N N 1  
77Y OP1   P     DOUB N N 2  
77Y "C3'" "C4'" SING N N 3  
77Y "C3'" "C2'" SING N N 4  
77Y "C4'" "C5'" SING N N 5  
77Y "C4'" "O4'" SING N N 6  
77Y "C2'" "C1'" SING N N 7  
77Y "C5'" "O5'" SING N N 8  
77Y P     "O5'" SING N N 9  
77Y P     OP2   SING N N 10 
77Y "O4'" "C1'" SING N N 11 
77Y "C1'" N1    SING N N 12 
77Y O2    C2    DOUB N N 13 
77Y N1    C2    SING N N 14 
77Y N1    C6    SING N N 15 
77Y C2    N3    SING N N 16 
77Y C28   C29   DOUB Y N 17 
77Y C28   C27   SING Y N 18 
77Y C6    C5    DOUB N N 19 
77Y C29   C30   SING Y N 20 
77Y C27   C14   DOUB Y N 21 
77Y N3    C4    SING N N 22 
77Y C30   C13   DOUB Y N 23 
77Y C5    C4    SING N N 24 
77Y C5    C7    SING N N 25 
77Y C4    O4    DOUB N N 26 
77Y C1    C7    DOUB N E 27 
77Y C1    C3    SING N N 28 
77Y C14   C13   SING Y N 29 
77Y C14   N15   SING Y N 30 
77Y C13   C12   SING Y N 31 
77Y C3    N9    SING N N 32 
77Y N15   C16   SING Y N 33 
77Y O34   C32   DOUB N N 34 
77Y C12   C16   DOUB Y N 35 
77Y C12   C33   SING N N 36 
77Y N9    C32   SING N N 37 
77Y C32   C33   SING N N 38 
77Y C6    H1    SING N N 39 
77Y C1    H2    SING N N 40 
77Y C29   H3    SING N N 41 
77Y C28   H4    SING N N 42 
77Y C27   H5    SING N N 43 
77Y C30   H6    SING N N 44 
77Y C3    H7    SING N N 45 
77Y C3    H8    SING N N 46 
77Y C16   H9    SING N N 47 
77Y C33   H10   SING N N 48 
77Y C33   H11   SING N N 49 
77Y N15   H12   SING N N 50 
77Y N9    H13   SING N N 51 
77Y C7    H14   SING N N 52 
77Y N3    H15   SING N N 53 
77Y "C1'" H16   SING N N 54 
77Y "C2'" H17   SING N N 55 
77Y "C2'" H18   SING N N 56 
77Y "C3'" H19   SING N N 57 
77Y "O3'" H20   SING N N 58 
77Y "C4'" H21   SING N N 59 
77Y "C5'" H22   SING N N 60 
77Y "C5'" H23   SING N N 61 
77Y OP2   H25   SING N N 62 
77Y P     OP3   SING N N 63 
77Y OP3   H27   SING N N 64 
# 
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 
77Y InChI            InChI                1.03  
"InChI=1S/C22H25N4O9P/c27-17-9-20(35-18(17)12-34-36(31,32)33)26-11-13(21(29)25-22(26)30)4-3-7-23-19(28)8-14-10-24-16-6-2-1-5-15(14)16/h1-6,10-11,17-18,20,24,27H,7-9,12H2,(H,23,28)(H,25,29,30)(H2,31,32,33)/b4-3+/t17-,18+,20+/m0/s1" 
77Y InChIKey         InChI                1.03  DJBPRNKHEIKONB-VGEFNSAVSA-N 
77Y SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(/C=C/CNC(=O)Cc3c[nH]c4ccccc34)C(=O)NC2=O" 
77Y SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C=CCNC(=O)Cc3c[nH]c4ccccc34)C(=O)NC2=O" 
77Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "c1ccc2c(c1)c(c[nH]2)CC(=O)NC/C=C/C3=CN(C(=O)NC3=O)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" 
77Y SMILES           "OpenEye OEToolkits" 2.0.5 "c1ccc2c(c1)c(c[nH]2)CC(=O)NCC=CC3=CN(C(=O)NC3=O)C4CC(C(O4)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 
77Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "[(2~{R},3~{S},5~{R})-5-[5-[(~{E})-3-[2-(1~{H}-indol-3-yl)ethanoylamino]prop-1-enyl]-2,4-bis(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 
77Y "Create component"   2016-09-12 EBI  
77Y "Other modification" 2016-09-13 EBI  
77Y "Initial release"    2016-09-28 RCSB 
# 
