data_D3U # _chem_comp.id D3U _chem_comp.name "2-PCPA derivative" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C36 H41 N9 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-06-20 _chem_comp.pdbx_modified_date 2020-05-15 _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 901.710 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D3U _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 6K3E _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.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 D3U C4 C1 C 0 1 Y N N -4.523 75.669 88.935 10.280 2.460 -0.589 C4 D3U 1 D3U C5 C2 C 0 1 Y N N -3.298 76.171 88.628 10.315 3.277 0.553 C5 D3U 2 D3U C6 C3 C 0 1 Y N N -2.885 77.374 89.090 11.129 4.423 0.525 C6 D3U 3 D3U C8 C4 C 0 1 Y N N -3.485 74.240 87.692 8.967 1.632 0.977 C8 D3U 4 D3U N1 N1 N 0 1 Y N N -3.682 78.121 89.875 11.826 4.677 -0.578 N1 D3U 5 D3U N3 N2 N 0 1 Y N N -5.396 76.357 89.709 11.012 2.796 -1.646 N3 D3U 6 D3U OAL O1 O 0 1 N N N -9.358 56.809 81.550 -7.961 3.793 -2.372 OAL D3U 7 D3U CAK C5 C 0 1 N N N -8.907 57.277 82.611 -7.192 3.400 -1.521 CAK D3U 8 D3U NAM N3 N 0 1 N N N -9.155 56.639 83.883 -5.996 4.003 -1.321 NAM D3U 9 D3U CAN C6 C 0 1 N N N -8.541 57.112 85.091 -5.120 3.491 -0.436 CAN D3U 10 D3U OAO O2 O 0 1 N N N -8.831 56.631 86.203 -4.228 4.201 -0.010 OAO D3U 11 D3U NAP N4 N 0 1 N N N -7.652 58.121 84.970 -5.201 2.222 -0.008 NAP D3U 12 D3U CAQ C7 C 0 1 N N N -7.323 58.616 83.748 -6.291 1.522 -0.214 CAQ D3U 13 D3U CAJ C8 C 0 1 N N S -7.736 57.937 82.536 -7.532 2.234 -0.647 CAJ D3U 14 D3U CCB C9 C 0 1 N N S -7.114 56.482 82.090 -8.383 2.747 0.545 CCB D3U 15 D3U CCE C10 C 0 1 Y N N -6.331 55.724 83.024 -8.375 1.766 1.689 CCE D3U 16 D3U CCF C11 C 0 1 Y N N -5.006 56.022 83.309 -7.889 2.149 2.925 CCF D3U 17 D3U CCG C12 C 0 1 Y N N -4.300 55.227 84.230 -7.882 1.249 3.974 CCG D3U 18 D3U CCH C13 C 0 1 Y N N -4.880 54.119 84.856 -8.362 -0.034 3.787 CCH D3U 19 D3U CCI C14 C 0 1 Y N N -6.195 53.796 84.555 -8.849 -0.417 2.552 CCI D3U 20 D3U CCJ C15 C 0 1 Y N N -6.897 54.585 83.643 -8.860 0.485 1.504 CCJ D3U 21 D3U CCD C16 C 0 1 N N N -6.410 56.566 80.899 -9.754 2.806 -0.132 CCD D3U 22 D3U CCC C17 C 0 1 N N N -6.353 57.813 80.544 -9.732 1.953 -1.157 CCC D3U 23 D3U NAI N5 N 0 1 N N N -7.137 58.577 81.319 -8.509 1.301 -1.219 NAI D3U 24 D3U CAH C18 C 0 1 Y N N -6.800 59.815 81.248 -8.225 -0.019 -1.558 CAH D3U 25 D3U CAG C19 C 0 1 Y N N -6.694 60.482 80.037 -9.007 -0.748 -2.432 CAG D3U 26 D3U CAE C20 C 0 1 Y N N -6.233 61.781 80.005 -8.687 -2.067 -2.703 CAE D3U 27 D3U CAF C21 C 0 1 N N N -6.209 62.409 78.757 -9.535 -2.865 -3.659 CAF D3U 28 D3U CAC C22 C 0 1 Y N N -5.832 62.390 81.201 -7.590 -2.653 -2.098 CAC D3U 29 D3U CAD C23 C 0 1 N N N -5.358 63.713 81.200 -7.259 -4.095 -2.386 CAD D3U 30 D3U CAB C24 C 0 1 Y N N -5.903 61.680 82.410 -6.795 -1.926 -1.232 CAB D3U 31 D3U CAA C25 C 0 1 Y N N -6.306 60.337 82.457 -7.096 -0.600 -0.965 CAA D3U 32 D3U NAR N6 N 0 1 N N N -6.453 59.678 83.660 -6.254 0.173 -0.160 NAR D3U 33 D3U CAS C26 C 0 1 N N N -5.878 60.242 84.962 -5.332 -0.489 0.767 CAS D3U 34 D3U CAT C27 C 0 1 N N S -6.869 61.198 85.744 -3.952 -0.605 0.118 CAT D3U 35 D3U OAU O3 O 0 1 N N N -7.595 62.029 84.835 -4.027 -1.485 -1.006 OAU D3U 36 D3U CAV C28 C 0 1 N N S -6.162 62.165 86.738 -2.955 -1.161 1.136 CAV D3U 37 D3U OAW O4 O 0 1 N N N -5.248 61.487 87.590 -2.880 -0.281 2.259 OAW D3U 38 D3U CAX C29 C 0 1 N N R -7.158 62.863 87.672 -1.574 -1.277 0.486 CAX D3U 39 D3U OAY O5 O 0 1 N N N -8.287 63.370 86.956 -1.649 -2.157 -0.637 OAY D3U 40 D3U CAZ C30 C 0 1 N N N -6.402 64.009 88.362 -0.577 -1.833 1.505 CAZ D3U 41 D3U OBA O6 O 0 1 N N N -7.216 64.853 89.228 0.734 -1.833 0.936 OBA D3U 42 D3U PBB P1 P 0 1 N N N -6.303 65.891 90.167 2.035 -2.353 1.730 PBB D3U 43 D3U OBD O7 O 0 1 N N N -5.171 64.975 90.883 1.802 -3.735 2.205 OBD D3U 44 D3U OBC O8 O 0 1 N N N -7.134 66.666 91.136 2.313 -1.392 2.992 OBC D3U 45 D3U OBE O9 O 0 1 N N N -5.459 66.906 89.171 3.309 -2.330 0.747 OBE D3U 46 D3U PBF P2 P 0 1 N N N -6.248 67.980 88.228 4.742 -3.065 0.756 PBF D3U 47 D3U OBH O10 O 0 1 N N N -7.692 67.189 87.793 4.577 -4.570 0.208 OBH D3U 48 D3U OBG O11 O 0 1 N N N -5.350 68.480 87.140 5.271 -3.098 2.138 OBG D3U 49 D3U "O5'" O12 O 0 1 N N N -6.838 69.202 89.128 5.764 -2.258 -0.191 "O5'" D3U 50 D3U "C5'" C31 C 0 1 N N N -5.989 70.266 89.545 7.147 -2.599 -0.312 "C5'" D3U 51 D3U "C4'" C32 C 0 1 N N R -6.602 71.631 89.254 7.826 -1.635 -1.287 "C4'" D3U 52 D3U "O4'" O13 O 0 1 N N N -5.482 72.566 89.365 7.843 -0.309 -0.732 "O4'" D3U 53 D3U "C3'" C33 C 0 1 N N S -7.120 71.746 87.822 9.291 -2.059 -1.507 "C3'" D3U 54 D3U "O3'" O14 O 0 1 N N N -8.520 72.175 87.835 9.525 -2.353 -2.886 "O3'" D3U 55 D3U "C2'" C34 C 0 1 N N R -6.159 72.792 87.230 10.113 -0.822 -1.071 "C2'" D3U 56 D3U "O2'" O15 O 0 1 N N N -6.779 73.584 86.217 11.205 -0.594 -1.964 "O2'" D3U 57 D3U "C1'" C35 C 0 1 N N R -5.817 73.615 88.460 9.067 0.317 -1.174 "C1'" D3U 58 D3U N9 N7 N 0 1 Y N N -4.623 74.479 88.343 9.426 1.429 -0.290 N9 D3U 59 D3U N7 N8 N 0 1 Y N N -2.668 75.280 87.858 9.491 2.716 1.471 N7 D3U 60 D3U C2 C36 C 0 1 Y N N -4.986 77.615 90.194 11.760 3.879 -1.628 C2 D3U 61 D3U N6 N9 N 0 1 N N N -1.661 77.772 88.709 11.204 5.266 1.620 N6 D3U 62 D3U H1 H1 H 0 1 N N N -3.261 73.350 87.123 8.273 0.988 1.496 H1 D3U 63 D3U H2 H2 H 0 1 N N N -9.768 55.850 83.923 -5.770 4.806 -1.817 H2 D3U 64 D3U H3 H3 H 0 1 N N N -8.004 55.871 81.881 -8.056 3.735 0.871 H3 D3U 65 D3U H4 H4 H 0 1 N N N -4.521 56.858 82.827 -7.514 3.151 3.071 H4 D3U 66 D3U H5 H5 H 0 1 N N N -3.276 55.481 84.461 -7.501 1.548 4.939 H5 D3U 67 D3U H6 H6 H 0 1 N N N -4.315 53.526 85.560 -8.356 -0.737 4.607 H6 D3U 68 D3U H7 H7 H 0 1 N N N -6.669 52.945 85.021 -9.223 -1.419 2.405 H7 D3U 69 D3U H8 H8 H 0 1 N N N -7.914 54.315 83.400 -9.244 0.187 0.539 H8 D3U 70 D3U H9 H9 H 0 1 N N N -5.982 55.735 80.358 -10.587 3.424 0.166 H9 D3U 71 D3U H10 H10 H 0 1 N N N -5.751 58.188 79.729 -10.552 1.792 -1.842 H10 D3U 72 D3U H11 H11 H 0 1 N N N -6.972 59.984 79.120 -9.864 -0.290 -2.903 H11 D3U 73 D3U H12 H12 H 0 1 N N N -7.169 62.917 78.583 -9.146 -2.753 -4.671 H12 D3U 74 D3U H13 H13 H 0 1 N N N -5.394 63.147 78.734 -9.511 -3.917 -3.375 H13 D3U 75 D3U H14 H14 H 0 1 N N N -6.045 61.657 77.971 -10.562 -2.503 -3.623 H14 D3U 76 D3U H15 H15 H 0 1 N N N -6.200 64.405 81.347 -6.588 -4.149 -3.243 H15 D3U 77 D3U H16 H16 H 0 1 N N N -4.631 63.842 82.015 -6.773 -4.537 -1.516 H16 D3U 78 D3U H17 H17 H 0 1 N N N -4.871 63.927 80.237 -8.176 -4.641 -2.607 H17 D3U 79 D3U H18 H18 H 0 1 N N N -5.640 62.182 83.330 -5.940 -2.391 -0.763 H18 D3U 80 D3U H19 H19 H 0 1 N N N -5.620 59.399 85.620 -5.255 0.097 1.683 H19 D3U 81 D3U H20 H20 H 0 1 N N N -4.968 60.811 84.720 -5.708 -1.484 1.004 H20 D3U 82 D3U H21 H21 H 0 1 N N N -7.567 60.568 86.315 -3.622 0.380 -0.213 H21 D3U 83 D3U H22 H22 H 0 1 N N N -8.183 62.594 85.322 -4.323 -2.379 -0.786 H22 D3U 84 D3U H23 H23 H 0 1 N N N -5.634 62.933 86.154 -3.284 -2.146 1.467 H23 D3U 85 D3U H24 H24 H 0 1 N N N -4.840 62.111 88.178 -2.592 0.616 2.038 H24 D3U 86 D3U H25 H25 H 0 1 N N N -7.486 62.145 88.438 -1.244 -0.292 0.155 H25 D3U 87 D3U H26 H26 H 0 1 N N N -8.882 63.795 87.562 -1.936 -3.053 -0.416 H26 D3U 88 D3U H27 H27 H 0 1 N N N -5.599 63.569 88.972 -0.585 -1.210 2.399 H27 D3U 89 D3U H28 H28 H 0 1 N N N -5.962 64.646 87.581 -0.858 -2.852 1.769 H28 D3U 90 D3U H29 H29 H 0 1 N N N -6.845 66.480 92.022 2.474 -0.468 2.755 H29 D3U 91 D3U H30 H30 H 0 1 N N N -7.763 67.156 86.846 4.234 -4.624 -0.694 H30 D3U 92 D3U H31 H31 H 0 1 N N N -5.815 70.178 90.628 7.626 -2.525 0.664 H31 D3U 93 D3U H32 H32 H 0 1 N N N -5.030 70.186 89.011 7.238 -3.618 -0.686 H32 D3U 94 D3U H33 H33 H 0 1 N N N -7.399 71.863 89.976 7.292 -1.632 -2.237 H33 D3U 95 D3U H34 H34 H 0 1 N N N -7.004 70.786 87.297 9.536 -2.921 -0.887 H34 D3U 96 D3U H35 H35 H 0 1 N N N -9.059 71.488 88.210 10.432 -2.625 -3.082 H35 D3U 97 D3U H36 H36 H 0 1 N N N -5.256 72.292 86.850 10.468 -0.933 -0.046 H36 D3U 98 D3U H37 H37 H 0 1 N N N -6.153 74.214 85.880 11.841 -1.321 -2.002 H37 D3U 99 D3U H38 H38 H 0 1 N N N -6.692 74.189 88.798 8.973 0.659 -2.204 H38 D3U 100 D3U H39 H39 H 0 1 N N N -5.655 78.200 90.808 12.343 4.123 -2.503 H39 D3U 101 D3U H40 H40 H 0 1 N N N -1.468 78.673 89.096 10.691 5.069 2.419 H40 D3U 102 D3U H41 H41 H 0 1 N N N -0.981 77.116 89.036 11.770 6.053 1.588 H41 D3U 103 # # 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 D3U CAF CAE SING N N 1 D3U CAE CAG DOUB Y N 2 D3U CAE CAC SING Y N 3 D3U CAG CAH SING Y N 4 D3U CCC CCD DOUB N N 5 D3U CCC NAI SING N N 6 D3U CCD CCB SING N N 7 D3U CAD CAC SING N N 8 D3U CAC CAB DOUB Y N 9 D3U CAH NAI SING N N 10 D3U CAH CAA DOUB Y N 11 D3U NAI CAJ SING N N 12 D3U OAL CAK DOUB N N 13 D3U CCB CAJ SING N N 14 D3U CCB CCE SING N N 15 D3U CAB CAA SING Y N 16 D3U CAA NAR SING N N 17 D3U CAJ CAK SING N N 18 D3U CAJ CAQ SING N N 19 D3U CAK NAM SING N N 20 D3U CCE CCF DOUB Y N 21 D3U CCE CCJ SING Y N 22 D3U CCF CCG SING Y N 23 D3U CCJ CCI DOUB Y N 24 D3U NAR CAQ SING N N 25 D3U NAR CAS SING N N 26 D3U CAQ NAP DOUB N N 27 D3U NAM CAN SING N N 28 D3U CCG CCH DOUB Y N 29 D3U CCI CCH SING Y N 30 D3U OAU CAT SING N N 31 D3U CAS CAT SING N N 32 D3U NAP CAN SING N N 33 D3U CAN OAO DOUB N N 34 D3U CAT CAV SING N N 35 D3U "O2'" "C2'" SING N N 36 D3U CAV OAW SING N N 37 D3U CAV CAX SING N N 38 D3U OAY CAX SING N N 39 D3U OBG PBF DOUB N N 40 D3U "C2'" "C3'" SING N N 41 D3U "C2'" "C1'" SING N N 42 D3U CAX CAZ SING N N 43 D3U C8 N7 DOUB Y N 44 D3U C8 N9 SING Y N 45 D3U OBH PBF SING N N 46 D3U "C3'" "O3'" SING N N 47 D3U "C3'" "C4'" SING N N 48 D3U N7 C5 SING Y N 49 D3U PBF "O5'" SING N N 50 D3U PBF OBE SING N N 51 D3U N9 "C1'" SING N N 52 D3U N9 C4 SING Y N 53 D3U CAZ OBA SING N N 54 D3U "C1'" "O4'" SING N N 55 D3U C5 C4 DOUB Y N 56 D3U C5 C6 SING Y N 57 D3U N6 C6 SING N N 58 D3U C4 N3 SING Y N 59 D3U C6 N1 DOUB Y N 60 D3U "O5'" "C5'" SING N N 61 D3U OBE PBB SING N N 62 D3U OBA PBB SING N N 63 D3U "C4'" "O4'" SING N N 64 D3U "C4'" "C5'" SING N N 65 D3U N3 C2 DOUB Y N 66 D3U N1 C2 SING Y N 67 D3U PBB OBD DOUB N N 68 D3U PBB OBC SING N N 69 D3U C8 H1 SING N N 70 D3U NAM H2 SING N N 71 D3U CCB H3 SING N N 72 D3U CCF H4 SING N N 73 D3U CCG H5 SING N N 74 D3U CCH H6 SING N N 75 D3U CCI H7 SING N N 76 D3U CCJ H8 SING N N 77 D3U CCD H9 SING N N 78 D3U CCC H10 SING N N 79 D3U CAG H11 SING N N 80 D3U CAF H12 SING N N 81 D3U CAF H13 SING N N 82 D3U CAF H14 SING N N 83 D3U CAD H15 SING N N 84 D3U CAD H16 SING N N 85 D3U CAD H17 SING N N 86 D3U CAB H18 SING N N 87 D3U CAS H19 SING N N 88 D3U CAS H20 SING N N 89 D3U CAT H21 SING N N 90 D3U OAU H22 SING N N 91 D3U CAV H23 SING N N 92 D3U OAW H24 SING N N 93 D3U CAX H25 SING N N 94 D3U OAY H26 SING N N 95 D3U CAZ H27 SING N N 96 D3U CAZ H28 SING N N 97 D3U OBC H29 SING N N 98 D3U OBH H30 SING N N 99 D3U "C5'" H31 SING N N 100 D3U "C5'" H32 SING N N 101 D3U "C4'" H33 SING N N 102 D3U "C3'" H34 SING N N 103 D3U "O3'" H35 SING N N 104 D3U "C2'" H36 SING N N 105 D3U "O2'" H37 SING N N 106 D3U "C1'" H38 SING N N 107 D3U C2 H39 SING N N 108 D3U N6 H40 SING N N 109 D3U N6 H41 SING N N 110 # # 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 D3U InChI InChI 1.03 "InChI=1S/C36H41N9O15P2/c1-17-10-21-22(11-18(17)2)45-9-8-20(19-6-4-3-5-7-19)36(45)33(41-35(52)42-34(36)51)43(21)12-23(46)27(48)24(47)13-57-61(53,54)60-62(55,56)58-14-25-28(49)29(50)32(59-25)44-16-40-26-30(37)38-15-39-31(26)44/h3-11,15-16,20,23-25,27-29,32,46-50H,12-14H2,1-2H3,(H,53,54)(H,55,56)(H2,37,38,39)(H,42,51,52)/t20-,23-,24+,25+,27-,28+,29+,32+,36-/m0/s1" D3U InChIKey InChI 1.03 LTYXJNFFNLDHFB-VXYXFEBYSA-N D3U SMILES_CANONICAL CACTVS 3.385 "Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)[C@]67[C@@H](C=CN7c2cc1C)c8ccccc8" D3U SMILES CACTVS 3.385 "Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)[C]67[CH](C=CN7c2cc1C)c8ccccc8" D3U SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@]34N2C=C[C@H]4c5ccccc5)C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]6[C@H]([C@H]([C@@H](O6)n7cnc8c7ncnc8N)O)O)O)O)O" D3U SMILES "OpenEye OEToolkits" 2.0.7 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C34N2C=CC4c5ccccc5)CC(C(C(COP(=O)(O)OP(=O)(O)OCC6C(C(C(O6)n7cnc8c7ncnc8N)O)O)O)O)O" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D3U "Create component" 2019-06-20 PDBJ D3U "Initial release" 2020-05-20 RCSB ##