data_ULP # _chem_comp.id ULP _chem_comp.name ;(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name) ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H34 N5 O22 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-16 _chem_comp.pdbx_modified_date 2011-06-04 _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 849.479 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ULP _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 3NYT _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 ULP P P P 0 1 N N N 5.414 -9.004 7.809 3.373 -5.559 -1.648 P ULP 1 ULP N1 N1 N 0 1 N N N 12.917 -19.656 8.386 -6.553 -1.852 1.213 N1 ULP 2 ULP C2 C2 C 0 1 N N N 12.682 -20.737 7.641 -6.319 -2.975 1.916 C2 ULP 3 ULP O2 O2 O 0 1 N N N 13.183 -21.922 8.032 -5.762 -3.913 1.379 O2 ULP 4 ULP C3 C3 C 0 1 Y N N 8.236 -6.937 12.474 6.668 -0.898 1.130 C3 ULP 5 ULP N3 N3 N 0 1 N N N 11.981 -20.721 6.469 -6.693 -3.074 3.205 N3 ULP 6 ULP O3 O3 O 0 1 N N N 9.283 -7.598 13.013 6.723 0.359 1.638 O3 ULP 7 ULP C4 C4 C 0 1 N N N 11.444 -19.548 6.077 -7.311 -2.043 3.815 C4 ULP 8 ULP O4 O4 O 0 1 N N N 10.726 -19.599 4.934 -7.649 -2.132 4.982 O4 ULP 9 ULP C5 C5 C 0 1 N N N 11.640 -18.372 6.803 -7.563 -0.855 3.087 C5 ULP 10 ULP C6 C6 C 0 1 N N N 12.403 -18.492 7.950 -7.173 -0.781 1.796 C6 ULP 11 ULP PA PA P 0 1 N N N 14.374 -14.883 8.171 -2.869 2.707 -2.092 PA ULP 12 ULP PB PB P 0 1 N N N 14.042 -12.560 9.857 -0.226 3.666 -1.155 PB ULP 13 ULP "O'P" "O'P" O 0 1 N N N 9.795 -10.189 6.088 0.681 2.314 4.679 "O'P" ULP 14 ULP "O'Q" "O'Q" O 0 1 N N N 11.845 -10.873 5.752 1.186 4.379 4.076 "O'Q" ULP 15 ULP "C1'" "C1'" C 0 1 N N R 12.659 -10.324 9.653 2.067 3.603 0.215 "C1'" ULP 16 ULP "N1'" N1* N 0 1 Y N N 6.650 -5.195 12.538 7.743 -2.935 0.651 N1* ULP 17 ULP O1A O1A O 0 1 N N N 13.871 -15.175 6.786 -3.567 3.753 -1.312 O1A ULP 18 ULP O1B O1B O 0 1 N N N 14.123 -13.433 11.087 0.353 4.402 -2.465 O1B ULP 19 ULP C1C C1C C 0 1 N N R 13.718 -19.763 9.633 -6.135 -1.773 -0.189 C1C ULP 20 ULP "C2'" "C2'" C 0 1 N N R 11.670 -9.605 10.567 3.314 2.717 0.178 "C2'" ULP 21 ULP "N2'" "N2'" N 0 1 N N N 12.049 -10.023 11.914 3.613 2.350 -1.209 "N2'" ULP 22 ULP "C2'A" C2* C 0 0 Y N N 7.671 -5.840 13.120 7.791 -1.714 1.142 C2* ULP 23 ULP C2A C2A C 0 1 N N N 8.158 -5.381 14.482 9.081 -1.197 1.725 C2A ULP 24 ULP O2A O2A O 0 1 N N N 15.890 -14.805 8.289 -2.895 3.095 -3.655 O2A ULP 25 ULP O2B O2B O 0 1 N N N 15.193 -11.675 9.434 -0.834 4.670 -0.253 O2B ULP 26 ULP C2C C2C C 0 1 N N R 15.208 -19.792 9.347 -7.362 -1.572 -1.106 C2C ULP 27 ULP O2C O2C O 0 1 N N N 15.847 -20.469 10.453 -7.772 -2.818 -1.675 O2C ULP 28 ULP "C3'" "C3'" C 0 1 N N R 10.217 -10.016 10.280 3.055 1.449 0.998 "C3'" ULP 29 ULP "N3'" "N3'" N 0 1 N N N 9.441 -8.979 10.973 4.269 0.630 1.030 "N3'" ULP 30 ULP O3A O3A O 0 1 N N N 13.626 -13.517 8.612 -1.343 2.592 -1.593 O3A ULP 31 ULP O3B O3B O 0 1 N N N 12.631 -11.721 9.919 0.972 2.912 -0.389 O3B ULP 32 ULP C3C C3C C 0 1 N N S 15.625 -18.344 9.418 -6.855 -0.614 -2.207 C3C ULP 33 ULP O3C O3C O 0 1 N N N 17.012 -18.125 9.662 -6.936 -1.239 -3.490 O3C ULP 34 ULP "C4'" "C4'" C 0 1 N N S 9.932 -9.975 8.765 2.668 1.849 2.425 "C4'" ULP 35 ULP "O4'" "O4'" O 0 1 N N N 8.720 -10.744 8.674 2.355 0.677 3.181 "O4'" ULP 36 ULP "C4'A" C4* C 0 0 Y N N 7.787 -7.320 11.219 5.473 -1.398 0.588 C4* ULP 37 ULP C4A C4A C 0 1 N N N 8.430 -8.402 10.447 4.250 -0.573 0.555 C4A ULP 38 ULP C4C C4C C 0 1 N N R 14.789 -17.795 10.545 -5.382 -0.350 -1.826 C4C ULP 39 ULP O4C O4C O 0 1 N N N 13.584 -18.531 10.341 -5.318 -0.603 -0.405 O4C ULP 40 ULP "C5'" "C5'" C 0 1 N N S 11.011 -10.742 7.998 1.446 2.769 2.376 "C5'" ULP 41 ULP "O5'" "O5'" O 0 1 N N N 12.294 -10.171 8.280 1.744 3.912 1.573 "O5'" ULP 42 ULP "C5'A" C5* C 0 0 Y N N 6.716 -6.649 10.648 5.476 -2.703 0.079 C5* ULP 43 ULP C5A C5A C 0 1 N N N 6.094 -6.913 9.264 4.223 -3.293 -0.515 C5A ULP 44 ULP C5C C5C C 0 1 N N N 14.423 -16.325 10.404 -5.005 1.102 -2.128 C5C ULP 45 ULP O5C O5C O 0 1 N N N 13.815 -16.041 9.138 -3.612 1.294 -1.879 O5C ULP 46 ULP "C6'" "C6'" C 0 1 N N N 10.887 -10.597 6.503 1.095 3.213 3.773 "C6'" ULP 47 ULP "C6'A" C6* C 0 0 Y N N 6.165 -5.578 11.339 6.641 -3.439 0.129 C6* ULP 48 ULP "C7'" "C7'" C 0 1 N N N 12.365 -9.078 12.793 4.338 3.180 -1.984 "C7'" ULP 49 ULP "O7'" "O7'" O 0 1 N N N 12.376 -7.874 12.576 4.744 4.231 -1.534 "O7'" ULP 50 ULP "C8'" "C8'" C 0 1 N N N 12.794 -9.572 14.151 4.645 2.803 -3.410 "C8'" ULP 51 ULP OP1 OP1 O 0 1 N N N 5.022 -7.978 6.779 2.792 -4.856 -2.813 OP1 ULP 52 ULP OP2 OP2 O 0 1 N N N 4.397 -10.045 8.071 2.211 -5.882 -0.581 OP2 ULP 53 ULP OP3 OP3 O 0 1 N N N 6.839 -9.500 7.519 4.051 -6.935 -2.135 OP3 ULP 54 ULP OP4 OP4 O 0 1 N N N 5.456 -8.215 9.241 4.489 -4.625 -0.959 OP4 ULP 55 ULP HO3 HO3 H 0 1 N N N 9.482 -7.234 13.868 6.973 1.034 0.992 HO3 ULP 56 ULP H5 H5 H 0 1 N N N 11.222 -17.427 6.488 -8.057 -0.019 3.558 H5 ULP 57 ULP H6 H6 H 0 1 N N N 12.597 -17.601 8.528 -7.357 0.117 1.225 H6 ULP 58 ULP "HO'P" "HO'P" H 0 0 N N N 9.819 -10.128 5.140 0.467 2.647 5.562 "HO'P" ULP 59 ULP "H1'" "H1'" H 0 1 N N N 13.652 -9.889 9.841 2.260 4.526 -0.331 "H1'" ULP 60 ULP HO1B HO1B H 0 0 N N N 14.971 -13.320 11.501 0.766 3.804 -3.102 HO1B ULP 61 ULP H1C H1C H 0 1 N N N 13.374 -20.667 10.157 -5.591 -2.674 -0.473 H1C ULP 62 ULP "H2'" "H2'" H 0 1 N N N 11.710 -8.515 10.421 4.160 3.260 0.601 "H2'" ULP 63 ULP "HN2'" "HN2'" H 0 0 N N N 12.070 -10.990 12.167 3.289 1.510 -1.569 "HN2'" ULP 64 ULP H2A H2A H 0 1 N N N 7.557 -4.523 14.817 9.120 -1.432 2.788 H2A ULP 65 ULP H2AA H2AA H 0 0 N N N 8.055 -6.204 15.204 9.923 -1.667 1.217 H2AA ULP 66 ULP H2AB H2AB H 0 0 N N N 9.215 -5.084 14.412 9.133 -0.116 1.589 H2AB ULP 67 ULP HO2A HO2A H 0 0 N N N 16.283 -14.959 7.438 -2.455 2.453 -4.227 HO2A ULP 68 ULP H2C H2C H 0 1 N N N 15.459 -20.279 8.393 -8.183 -1.116 -0.551 H2C ULP 69 ULP HO2C HO2C H 0 0 N N N 16.785 -20.504 10.304 -8.539 -2.749 -2.259 HO2C ULP 70 ULP "H3'" "H3'" H 0 1 N N N 9.980 -11.038 10.611 2.244 0.881 0.544 "H3'" ULP 71 ULP H3C H3C H 0 1 N N N 15.467 -17.852 8.447 -7.426 0.314 -2.199 H3C ULP 72 ULP HO3C HO3C H 0 0 N N N 17.185 -17.191 9.691 -7.834 -1.482 -3.753 HO3C ULP 73 ULP "H4'" "H4'" H 0 1 N N N 9.886 -8.952 8.363 3.500 2.373 2.895 "H4'" ULP 74 ULP "HO4'" "HO4'" H 0 0 N N N 8.441 -10.790 7.767 2.101 0.855 4.096 "HO4'" ULP 75 ULP H4A H4A H 0 1 N N N 8.060 -8.694 9.475 3.340 -0.973 0.135 H4A ULP 76 ULP H4C H4C H 0 1 N N N 15.310 -17.879 11.510 -4.723 -1.032 -2.362 H4C ULP 77 ULP "H5'" "H5'" H 0 1 N N N 10.897 -11.791 8.307 0.603 2.230 1.943 "H5'" ULP 78 ULP H5A H5A H 0 1 N N N 5.343 -6.138 9.051 3.437 -3.311 0.239 H5A ULP 79 ULP H5AA H5AA H 0 0 N N N 6.885 -6.884 8.500 3.901 -2.686 -1.361 H5AA ULP 80 ULP H5C H5C H 0 1 N N N 13.713 -16.062 11.202 -5.221 1.322 -3.174 H5C ULP 81 ULP H5CA H5CA H 0 0 N N N 15.340 -15.724 10.496 -5.584 1.768 -1.490 H5CA ULP 82 ULP "H6'" H6* H 0 1 N N N 5.332 -5.042 10.908 6.650 -4.446 -0.262 H6* ULP 83 ULP "H8'" "H8'" H 0 1 N N N 13.070 -8.715 14.783 3.857 3.177 -4.063 "H8'" ULP 84 ULP "H8'A" "H8'A" H 0 0 N N N 11.964 -10.121 14.620 5.599 3.241 -3.705 "H8'A" ULP 85 ULP "H8'B" "H8'B" H 0 0 N N N 13.660 -10.241 14.041 4.702 1.718 -3.495 "H8'B" ULP 86 ULP HOP2 HOP2 H 0 0 N N N 3.635 -9.889 7.525 2.520 -6.344 0.210 HOP2 ULP 87 ULP HOP3 HOP3 H 0 0 N N N 7.179 -9.057 6.750 3.436 -7.548 -2.561 HOP3 ULP 88 ULP HN3 HN3 H 0 1 N N N 11.870 -21.550 5.921 -6.517 -3.891 3.697 HN3 ULP 89 # 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 ULP OP1 P DOUB N N 1 ULP OP3 P SING N N 2 ULP P OP2 SING N N 3 ULP P OP4 SING N N 4 ULP C2 N1 SING N N 5 ULP C6 N1 SING N N 6 ULP N1 C1C SING N N 7 ULP N3 C2 SING N N 8 ULP C2 O2 DOUB N N 9 ULP "C4'A" C3 DOUB Y N 10 ULP C3 O3 SING N N 11 ULP C3 "C2'A" SING Y N 12 ULP C4 N3 SING N N 13 ULP O3 HO3 SING N N 14 ULP O4 C4 DOUB N N 15 ULP C4 C5 SING N N 16 ULP C5 C6 DOUB N N 17 ULP C5 H5 SING N N 18 ULP C6 H6 SING N N 19 ULP O1A PA DOUB N N 20 ULP PA O2A SING N N 21 ULP PA O3A SING N N 22 ULP PA O5C SING N N 23 ULP O3A PB SING N N 24 ULP O2B PB DOUB N N 25 ULP PB O3B SING N N 26 ULP PB O1B SING N N 27 ULP "O'P" "C6'" SING N N 28 ULP "O'P" "HO'P" SING N N 29 ULP "O'Q" "C6'" DOUB N N 30 ULP "O5'" "C1'" SING N N 31 ULP "C1'" O3B SING N N 32 ULP "C1'" "C2'" SING N N 33 ULP "C1'" "H1'" SING N N 34 ULP "C6'A" "N1'" SING Y N 35 ULP "N1'" "C2'A" DOUB Y N 36 ULP O1B HO1B SING N N 37 ULP C2C C1C SING N N 38 ULP C1C O4C SING N N 39 ULP C1C H1C SING N N 40 ULP "C3'" "C2'" SING N N 41 ULP "C2'" "N2'" SING N N 42 ULP "C2'" "H2'" SING N N 43 ULP "N2'" "C7'" SING N N 44 ULP "N2'" "HN2'" SING N N 45 ULP "C2'A" C2A SING N N 46 ULP C2A H2A SING N N 47 ULP C2A H2AA SING N N 48 ULP C2A H2AB SING N N 49 ULP O2A HO2A SING N N 50 ULP C2C C3C SING N N 51 ULP C2C O2C SING N N 52 ULP C2C H2C SING N N 53 ULP O2C HO2C SING N N 54 ULP "C4'" "C3'" SING N N 55 ULP "C3'" "N3'" SING N N 56 ULP "C3'" "H3'" SING N N 57 ULP C4A "N3'" DOUB N N 58 ULP C3C O3C SING N N 59 ULP C3C C4C SING N N 60 ULP C3C H3C SING N N 61 ULP O3C HO3C SING N N 62 ULP "C5'" "C4'" SING N N 63 ULP "O4'" "C4'" SING N N 64 ULP "C4'" "H4'" SING N N 65 ULP "O4'" "HO4'" SING N N 66 ULP C4A "C4'A" SING N N 67 ULP "C5'A" "C4'A" SING Y N 68 ULP C4A H4A SING N N 69 ULP O4C C4C SING N N 70 ULP C5C C4C SING N N 71 ULP C4C H4C SING N N 72 ULP "C6'" "C5'" SING N N 73 ULP "C5'" "O5'" SING N N 74 ULP "C5'" "H5'" SING N N 75 ULP C5A "C5'A" SING N N 76 ULP "C5'A" "C6'A" DOUB Y N 77 ULP OP4 C5A SING N N 78 ULP C5A H5A SING N N 79 ULP C5A H5AA SING N N 80 ULP O5C C5C SING N N 81 ULP C5C H5C SING N N 82 ULP C5C H5CA SING N N 83 ULP "C6'A" "H6'" SING N N 84 ULP "O7'" "C7'" DOUB N N 85 ULP "C7'" "C8'" SING N N 86 ULP "C8'" "H8'" SING N N 87 ULP "C8'" "H8'A" SING N N 88 ULP "C8'" "H8'B" SING N N 89 ULP OP2 HOP2 SING N N 90 ULP OP3 HOP3 SING N N 91 ULP N3 HN3 SING N N 92 # 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 ULP SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC4OC(C(=O)O)C(O)C(/N=C/c3c(cnc(c3O)C)COP(=O)(O)O)C4NC(=O)C)O)O" ULP SMILES_CANONICAL CACTVS 3.370 "CC(=O)N[C@H]1[C@H](O[C@@H]([C@@H](O)[C@@H]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O" ULP SMILES CACTVS 3.370 "CC(=O)N[CH]1[CH](O[CH]([CH](O)[CH]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O" ULP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]2[C@H]([C@H](O[C@@H]([C@H]2O)C(=O)O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O" ULP SMILES "OpenEye OEToolkits" 1.7.0 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(C(OC(C2O)C(=O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O" ULP InChI InChI 1.03 ;InChI=1S/C25H34N5O22P3/c1-9-17(33)12(11(5-26-9)7-47-53(40,41)42)6-27-15-16(28-10(2)31)24(50-21(19(15)35)23(37)38)51-55(45,46)52-54(43,44)48-8-13-18(34)20(36)22(49-13)30-4-3-14(32)29-25(30)39/h3-6,13,15-16,18-22,24,33-36H,7-8H2,1-2H3,(H,28,31)(H,37,38)(H,43,44)(H,45,46)(H,29,32,39)(H2,40,41,42)/b27-6+/t13-,15-,16-,18-,19+,20-,21+,22-,24-/m1/s1 ; ULP InChIKey InChI 1.03 IGKBPIFLZAFLLV-IOECPDIJSA-N # 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 ULP "SYSTEMATIC NAME" ACDLabs 12.01 ;(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name) ; ULP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 ;(2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3-hydroxy-4-[(E)-[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxane-2-carboxylic acid ; # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ULP "Create component" 2010-07-16 RCSB ULP "Modify aromatic_flag" 2011-06-04 RCSB ULP "Modify descriptor" 2011-06-04 RCSB #