data_8ML # _chem_comp.id 8ML _chem_comp.name "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-2-[(2S,3S,4R,5R)-1,2,3,4,5-pentakis(oxidanyl)-6-phosphonooxy-hexan-2-yl]-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H33 N4 O16 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-08-04 _chem_comp.pdbx_modified_date 2018-06-22 _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 686.458 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8ML _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 5XTX _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 8ML O2A O1 O 0 1 N N N -15.159 40.926 -23.934 -4.945 -1.742 -1.560 O2A 8ML 1 8ML PA P1 P 0 1 N N N -16.139 41.288 -22.914 -5.585 -0.842 -0.574 PA 8ML 2 8ML O1A O2 O 0 1 N N N -16.042 42.641 -22.370 -6.475 0.254 -1.347 O1A 8ML 3 8ML O3A O3 O 0 1 N N N -17.611 41.018 -23.498 -6.526 -1.704 0.407 O3A 8ML 4 8ML PB P2 P 0 1 N N N -19.018 41.685 -23.165 -7.531 -2.942 0.191 PB 8ML 5 8ML O3B O4 O 0 1 N N N -20.021 40.876 -23.799 -6.890 -3.952 -0.682 O3B 8ML 6 8ML O2B O5 O 0 1 N N N -18.973 43.089 -23.437 -7.879 -3.607 1.615 O2B 8ML 7 8ML O1B O6 O 0 1 N N N -19.214 41.547 -21.614 -8.887 -2.418 -0.502 O1B 8ML 8 8ML O7 O7 O 0 1 N N N -16.066 40.291 -21.716 -4.448 -0.098 0.289 O7 8ML 9 8ML C7 C1 C 0 1 N N N -15.899 38.920 -22.206 -3.392 0.661 -0.304 C7 8ML 10 8ML C6 C2 C 0 1 N N N -15.802 37.996 -21.155 -2.493 1.230 0.795 C6 8ML 11 8ML C5 C3 C 0 1 N N R -15.635 36.614 -21.595 -1.363 2.043 0.160 C5 8ML 12 8ML S1 S1 S 0 1 N N N -16.795 35.886 -22.732 -0.128 0.943 -0.639 S1 8ML 13 8ML C2 C4 C 0 1 N N S -16.282 34.282 -22.348 1.324 1.947 -0.144 C2 8ML 14 8ML CF2 C5 C 0 1 N N S -17.224 33.056 -22.559 2.416 1.054 0.447 CF2 8ML 15 8ML OF2 O8 O 0 1 N N N -16.467 31.887 -22.540 2.093 0.741 1.804 OF2 8ML 16 8ML CF1 C6 C 0 1 N N N -17.912 33.245 -23.870 3.758 1.788 0.398 CF1 8ML 17 8ML OF1 O9 O 0 1 N N N -17.004 33.145 -24.967 3.984 2.279 -0.924 OF1 8ML 18 8ML CF3 C7 C 0 1 N N S -18.217 33.049 -21.399 2.512 -0.240 -0.365 CF3 8ML 19 8ML OF3 O10 O 0 1 N N N -19.200 34.043 -21.522 2.819 0.074 -1.725 OF3 8ML 20 8ML CF4 C8 C 0 1 N N R -18.901 31.742 -21.095 3.616 -1.125 0.216 CF4 8ML 21 8ML OF4 O11 O 0 1 N N N -19.840 31.477 -22.161 4.893 -0.590 -0.140 OF4 8ML 22 8ML CF5 C9 C 0 1 N N R -19.630 31.714 -19.764 3.483 -2.542 -0.347 CF5 8ML 23 8ML OF5 O12 O 0 1 N N N -18.750 32.105 -18.734 2.206 -3.077 0.009 OF5 8ML 24 8ML CF6 C10 C 0 1 N N N -20.201 30.332 -19.489 4.587 -3.428 0.234 CF6 8ML 25 8ML OF6 O13 O 0 1 N N N -21.004 30.372 -18.300 4.534 -4.718 -0.379 OF6 8ML 26 8ML PF P3 P 0 1 N N N -21.514 29.173 -17.487 5.552 -5.908 -0.006 PF 8ML 27 8ML OF8 O14 O 0 1 N N N -20.994 29.396 -16.051 5.322 -6.352 1.524 OF8 8ML 28 8ML OF7 O15 O 0 1 N N N -23.006 29.148 -17.535 5.286 -7.165 -0.976 OF7 8ML 29 8ML OF9 O16 O 0 1 N N N -20.929 27.938 -18.112 6.945 -5.437 -0.179 OF9 8ML 30 8ML N3 N1 N 0 1 N N N -15.209 34.342 -21.460 0.802 2.865 0.877 N3 8ML 31 8ML C4 C11 C 0 1 N N N -14.925 35.637 -20.954 -0.519 2.725 1.223 C4 8ML 32 8ML CM4 C12 C 0 1 N N N -13.942 35.860 -19.937 -1.011 3.145 2.374 CM4 8ML 33 8ML "C7'" C13 C 0 1 N N N -14.283 33.236 -21.206 1.653 3.883 1.499 C7, 8ML 34 8ML "C5'" C14 C 0 1 Y N N -13.011 33.267 -21.971 1.720 5.095 0.606 C5, 8ML 35 8ML "C4'" C15 C 0 1 Y N N -12.919 33.116 -23.410 0.687 6.035 0.596 C4, 8ML 36 8ML "N4'" N2 N 0 1 N N N -13.985 32.991 -24.170 -0.424 5.867 1.407 N4, 8ML 37 8ML "N3'" N3 N 0 1 Y N N -11.706 33.118 -24.052 0.787 7.093 -0.202 N3, 8ML 38 8ML "C2'" C16 C 0 1 Y N N -10.598 33.192 -23.340 1.843 7.255 -0.974 C2, 8ML 39 8ML CM2 C17 C 0 1 N N N -9.287 33.094 -23.969 1.920 8.469 -1.865 CM2 8ML 40 8ML "N1'" N4 N 0 1 Y N N -10.631 33.343 -21.991 2.834 6.387 -0.988 N1, 8ML 41 8ML "C6'" C18 C 0 1 Y N N -11.819 33.375 -21.312 2.806 5.307 -0.220 C6, 8ML 42 8ML H1 H1 H 0 1 N N N -15.320 43.099 -22.785 -6.925 0.879 -0.762 H1 8ML 43 8ML H2 H2 H 0 1 N N N -19.665 43.316 -24.047 -8.481 -4.362 1.561 H2 8ML 44 8ML H3 H3 H 0 1 N N N -19.944 40.966 -21.437 -9.361 -1.753 0.015 H3 8ML 45 8ML H4 H4 H 0 1 N N N -16.766 38.658 -22.831 -2.804 0.018 -0.958 H4 8ML 46 8ML H5 H5 H 0 1 N N N -14.982 38.868 -22.811 -3.816 1.480 -0.886 H5 8ML 47 8ML H6 H6 H 0 1 N N N -14.936 38.268 -20.533 -3.081 1.874 1.449 H6 8ML 48 8ML H7 H7 H 0 1 N N N -16.720 38.059 -20.553 -2.069 0.411 1.377 H7 8ML 49 8ML H8 H8 H 0 1 N N N -16.044 31.797 -21.694 1.253 0.274 1.910 H8 8ML 50 8ML H9 H9 H 0 1 N N N -18.380 34.240 -23.886 3.741 2.623 1.099 H9 8ML 51 8ML H10 H10 H 0 1 N N N -18.688 32.473 -23.979 4.558 1.100 0.673 H10 8ML 52 8ML H11 H11 H 0 1 N N N -17.476 33.270 -25.782 4.819 2.756 -1.029 H11 8ML 53 8ML H12 H12 H 0 1 N N N -17.626 33.292 -20.504 1.561 -0.769 -0.319 H12 8ML 54 8ML H13 H13 H 0 1 N N N -19.791 33.998 -20.780 3.702 0.446 -1.853 H13 8ML 55 8ML H14 H14 H 0 1 N N N -18.139 30.949 -21.083 3.525 -1.156 1.301 H14 8ML 56 8ML H15 H15 H 0 1 N N N -20.287 30.655 -21.993 5.044 -0.534 -1.093 H15 8ML 57 8ML H16 H16 H 0 1 N N N -20.468 32.424 -19.820 3.574 -2.512 -1.433 H16 8ML 58 8ML H17 H17 H 0 1 N N N -19.208 32.087 -17.902 2.055 -3.133 0.962 H17 8ML 59 8ML H18 H18 H 0 1 N N N -20.822 30.016 -20.340 5.558 -2.973 0.039 H18 8ML 60 8ML H19 H19 H 0 1 N N N -19.377 29.616 -19.351 4.443 -3.530 1.309 H19 8ML 61 8ML H20 H20 H 0 1 N N N -20.389 28.700 -15.821 4.429 -6.673 1.710 H20 8ML 62 8ML H21 H21 H 0 1 N N N -23.296 28.347 -17.956 5.866 -7.921 -0.808 H21 8ML 63 8ML H22 H22 H 0 1 N N N -13.388 35.027 -19.529 -2.078 3.145 2.538 H22 8ML 64 8ML H23 H23 H 0 1 N N N -13.754 36.861 -19.578 -0.345 3.490 3.152 H23 8ML 65 8ML H25 H25 H 0 1 N N N -14.802 32.298 -21.453 1.234 4.166 2.465 H25 8ML 66 8ML H26 H26 H 0 1 N N N -14.033 33.245 -20.135 2.656 3.480 1.641 H26 8ML 67 8ML H27 H27 H 0 1 N N N -13.706 32.916 -25.127 -0.390 5.253 2.156 H27 8ML 68 8ML H28 H28 H 0 1 N N N -14.489 32.169 -23.905 -1.237 6.365 1.224 H28 8ML 69 8ML H29 H29 H 0 1 N N N -9.409 32.959 -25.054 2.407 9.283 -1.328 H29 8ML 70 8ML H30 H30 H 0 1 N N N -8.718 34.016 -23.776 2.495 8.227 -2.759 H30 8ML 71 8ML H31 H31 H 0 1 N N N -8.744 32.234 -23.552 0.913 8.773 -2.151 H31 8ML 72 8ML H32 H32 H 0 1 N N N -11.814 33.487 -20.238 3.626 4.603 -0.236 H32 8ML 73 8ML H33 H33 H 0 1 N N N -14.877 36.830 -22.362 -1.759 2.769 -0.550 H33 8ML 74 8ML H34 H34 H 0 1 N N N -15.690 34.136 -23.263 1.709 2.507 -0.997 H34 8ML 75 # 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 8ML OF1 CF1 SING N N 1 8ML "N4'" "C4'" SING N N 2 8ML "N3'" "C4'" DOUB Y N 3 8ML "N3'" "C2'" SING Y N 4 8ML CM2 "C2'" SING N N 5 8ML O2A PA DOUB N N 6 8ML CF1 CF2 SING N N 7 8ML O3B PB DOUB N N 8 8ML O3A PB SING N N 9 8ML O3A PA SING N N 10 8ML O2B PB SING N N 11 8ML "C4'" "C5'" SING Y N 12 8ML "C2'" "N1'" DOUB Y N 13 8ML PB O1B SING N N 14 8ML PA O1A SING N N 15 8ML PA O7 SING N N 16 8ML S1 C2 SING N N 17 8ML S1 C5 SING N N 18 8ML CF2 OF2 SING N N 19 8ML CF2 C2 SING N N 20 8ML CF2 CF3 SING N N 21 8ML C2 N3 SING N N 22 8ML C7 O7 SING N N 23 8ML C7 C6 SING N N 24 8ML OF4 CF4 SING N N 25 8ML "N1'" "C6'" SING Y N 26 8ML "C5'" "C6'" DOUB Y N 27 8ML "C5'" "C7'" SING N N 28 8ML C5 C6 SING N N 29 8ML C5 C4 SING N N 30 8ML OF3 CF3 SING N N 31 8ML N3 "C7'" SING N N 32 8ML N3 C4 SING N N 33 8ML CF3 CF4 SING N N 34 8ML CF4 CF5 SING N N 35 8ML C4 CM4 DOUB N N 36 8ML CF5 CF6 SING N N 37 8ML CF5 OF5 SING N N 38 8ML CF6 OF6 SING N N 39 8ML OF6 PF SING N N 40 8ML OF9 PF DOUB N N 41 8ML OF7 PF SING N N 42 8ML PF OF8 SING N N 43 8ML O1A H1 SING N N 44 8ML O2B H2 SING N N 45 8ML O1B H3 SING N N 46 8ML C7 H4 SING N N 47 8ML C7 H5 SING N N 48 8ML C6 H6 SING N N 49 8ML C6 H7 SING N N 50 8ML OF2 H8 SING N N 51 8ML CF1 H9 SING N N 52 8ML CF1 H10 SING N N 53 8ML OF1 H11 SING N N 54 8ML CF3 H12 SING N N 55 8ML OF3 H13 SING N N 56 8ML CF4 H14 SING N N 57 8ML OF4 H15 SING N N 58 8ML CF5 H16 SING N N 59 8ML OF5 H17 SING N N 60 8ML CF6 H18 SING N N 61 8ML CF6 H19 SING N N 62 8ML OF8 H20 SING N N 63 8ML OF7 H21 SING N N 64 8ML CM4 H22 SING N N 65 8ML CM4 H23 SING N N 66 8ML "C7'" H25 SING N N 67 8ML "C7'" H26 SING N N 68 8ML "N4'" H27 SING N N 69 8ML "N4'" H28 SING N N 70 8ML CM2 H29 SING N N 71 8ML CM2 H30 SING N N 72 8ML CM2 H31 SING N N 73 8ML "C6'" H32 SING N N 74 8ML C5 H33 SING N N 75 8ML C2 H34 SING N N 76 # 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 8ML InChI InChI 1.03 ;InChI=1S/C18H33N4O16P3S/c1-9-13(3-4-36-41(34,35)38-40(31,32)33)42-17(22(9)6-11-5-20-10(2)21-16(11)19)18(27,8-23)15(26)14(25)12(24)7-37-39(28,29)30/h5,12-15,17,23-27H,1,3-4,6-8H2,2H3,(H,34,35)(H2,19,20,21)(H2,28,29,30)(H2,31,32,33)/t12-,13-,14-,15+,17?,18+/m1/s1 ; 8ML InChIKey InChI 1.03 MJHVDDPQXKRRMA-OYVLIZFGSA-N 8ML SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CN2[C@@H](S[C@H](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)[C@](O)(CO)[C@@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c(N)n1" 8ML SMILES CACTVS 3.385 "Cc1ncc(CN2[CH](S[CH](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)[C](O)(CO)[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c(N)n1" 8ML SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2C(SC(C2=C)CCOP(=O)(O)OP(=O)(O)O)[C@](CO)([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O" 8ML SMILES "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2C(SC(C2=C)CCOP(=O)(O)OP(=O)(O)O)C(CO)(C(C(C(COP(=O)(O)O)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 8ML "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-2-[(2~{S},3~{S},4~{R},5~{R})-1,2,3,4,5-pentakis(oxidanyl)-6-phosphonooxy-hexan-2-yl]-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen 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 8ML "Create component" 2017-08-04 PDBJ 8ML "Initial release" 2018-06-27 RCSB #