data_SOS # _chem_comp.id SOS _chem_comp.name "[(1R,2S,4R)-4-({2-AMINO-5-[BENZYL(FORMYL)AMINO]-6-OXO-1,6-DIHYDROPYRIMIDIN-4-YL}AMINO)-2-HYDROXYCYCLOPENTYL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C18 H24 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-01-23 _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 453.386 _chem_comp.one_letter_code N _chem_comp.three_letter_code SOS _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye OEToolkits" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 SOS OP3 O3P O 0 1 N Y N -4.738 21.868 46.925 3.912 4.663 -3.442 OP3 SOS 1 SOS C15 C15 C 0 1 Y N N -6.141 16.440 45.164 0.691 -1.131 -0.937 C15 SOS 2 SOS C14 C14 C 0 1 Y N N -6.550 17.729 45.568 1.783 -0.732 -1.707 C14 SOS 3 SOS C13 C13 C 0 1 Y N N -5.660 18.799 45.449 3.076 -0.845 -1.197 C13 SOS 4 SOS C12 C12 C 0 1 Y N N -4.363 18.604 44.949 3.277 -1.358 0.085 C12 SOS 5 SOS C11 C11 C 0 1 Y N N -3.969 17.321 44.529 2.185 -1.757 0.856 C11 SOS 6 SOS C10 C10 C 0 1 Y N N -4.866 16.258 44.634 0.900 -1.641 0.339 C10 SOS 7 SOS C9 C9 C 0 1 N N N -4.450 14.863 44.174 -0.275 -2.071 1.169 C9 SOS 8 SOS N7 N7 N 0 1 N N N -3.799 14.097 45.248 -0.796 -0.979 1.984 N7 SOS 9 SOS C8 C8 C 0 1 N N N -2.531 13.678 45.004 -0.305 -0.764 3.268 C8 SOS 10 SOS O8 O8 O 0 1 N N N -1.841 13.019 45.786 0.563 -1.403 3.855 O8 SOS 11 SOS C5 C5 C 0 1 N N N -4.370 13.782 46.440 -1.773 -0.163 1.484 C5 SOS 12 SOS C6 C6 C 0 1 N N N -5.305 12.745 46.529 -3.048 -0.828 1.104 C6 SOS 13 SOS O6 O6 O 0 1 N N N -5.638 12.158 45.503 -3.218 -2.037 1.230 O6 SOS 14 SOS N1 N1 N 0 1 N N N -5.879 12.387 47.758 -3.996 0.036 0.606 N1 SOS 15 SOS C2 C2 C 0 1 N N N -5.517 13.026 48.910 -3.786 1.396 0.473 C2 SOS 16 SOS N2 N2 N 0 1 N N N -6.056 12.718 50.111 -4.836 2.112 -0.040 N2 SOS 17 SOS N3 N3 N 0 1 N N N -4.612 14.015 48.801 -2.661 1.954 0.813 N3 SOS 18 SOS C4 C4 C 0 1 N N N -4.034 14.418 47.642 -1.633 1.176 1.327 C4 SOS 19 SOS N9 N9 N 0 1 N N N -3.129 15.427 47.664 -0.496 1.770 1.666 N9 SOS 20 SOS "C1'" C1* C 0 1 N N R -3.010 16.350 48.815 -0.289 3.191 1.521 "C1'" SOS 21 SOS "C6'" C6* C 0 1 N N N -4.397 17.017 49.191 0.092 3.545 0.075 "C6'" SOS 22 SOS "C2'" C2* C 0 1 N N N -2.070 17.567 48.537 0.876 3.672 2.386 "C2'" SOS 23 SOS "C3'" C3* C 0 1 N N S -2.566 18.220 49.755 2.076 3.601 1.451 "C3'" SOS 24 SOS "O3'" O3* O 0 1 N N N -1.964 17.860 50.990 3.142 4.408 1.914 "O3'" SOS 25 SOS "C4'" C4* C 0 1 N N R -4.048 18.455 49.686 1.505 4.141 0.142 "C4'" SOS 26 SOS "C5'" C5* C 0 1 N N N -4.558 19.437 48.625 2.359 3.795 -1.069 "C5'" SOS 27 SOS "O5'" O5* O 0 1 N N N -4.149 20.738 48.955 1.720 4.291 -2.233 "O5'" SOS 28 SOS P P P 0 1 N N N -4.930 22.068 48.552 2.432 4.051 -3.667 P SOS 29 SOS OP2 O2P O 0 1 N N N -4.163 23.265 48.726 2.691 2.455 -3.704 OP2 SOS 30 SOS OP1 O1P O 0 1 N N N -6.399 21.971 48.536 1.688 4.608 -4.845 OP1 SOS 31 SOS H15 H15 H 0 1 N N N -6.812 15.600 45.265 -0.313 -1.039 -1.343 H15 SOS 32 SOS H14 H14 H 0 1 N N N -7.542 17.887 45.965 1.626 -0.333 -2.705 H14 SOS 33 SOS H13 H13 H 0 1 N N N -5.974 19.789 45.745 3.926 -0.534 -1.797 H13 SOS 34 SOS H12 H12 H 0 1 N N N -3.673 19.433 44.887 4.284 -1.446 0.482 H12 SOS 35 SOS H11 H11 H 0 1 N N N -2.979 17.160 44.128 2.352 -2.155 1.853 H11 SOS 36 SOS H91 1H9 H 0 1 N N N -5.349 14.318 43.849 -1.088 -2.432 0.529 H91 SOS 37 SOS H92 2H9 H 0 1 N N N -3.728 14.977 43.352 -0.002 -2.891 1.842 H92 SOS 38 SOS H8 H8 H 0 1 N N N -2.093 13.942 44.053 -0.793 0.094 3.760 H8 SOS 39 SOS HN1 HN1 H 0 1 N N N -6.561 11.656 47.791 -4.894 -0.343 0.324 HN1 SOS 40 SOS HN21 1HN2 H 0 0 N N N -6.713 11.973 49.999 -4.646 2.991 -0.463 HN21 SOS 41 SOS HN22 2HN2 H 0 0 N N N -5.832 13.166 50.977 -5.749 1.726 0.031 HN22 SOS 42 SOS HN9 HN9 H 0 1 N N N -2.235 14.986 47.582 0.253 1.191 2.042 HN9 SOS 43 SOS "H1'" H1* H 0 1 N N N -2.615 15.708 49.616 -1.214 3.698 1.814 "H1'" SOS 44 SOS "H6'1" 1H6* H 0 0 N N N -5.062 17.056 48.316 -0.602 4.285 -0.340 "H6'1" SOS 45 SOS "H6'2" 2H6* H 0 0 N N N -4.929 16.440 49.962 0.057 2.666 -0.580 "H6'2" SOS 46 SOS "H2'" 1H2* H 0 1 N N N -0.991 17.358 48.494 0.712 4.708 2.710 "H2'" SOS 47 SOS "H2''" 2H2* H 0 0 N N N -2.112 18.091 47.571 1.029 3.073 3.290 "H2''" SOS 48 SOS "H3'" H3* H 0 1 N N N -2.144 19.236 49.766 2.432 2.570 1.343 "H3'" SOS 49 SOS "HO3'" H3T H 0 0 N Y N -1.025 17.780 50.873 3.059 4.465 2.881 "HO3'" SOS 50 SOS "H4'" H4* H 0 1 N N N -4.462 18.876 50.614 1.438 5.235 0.194 "H4'" SOS 51 SOS "H5'" 1H5* H 0 1 N N N -5.657 19.397 48.587 2.469 2.712 -1.155 "H5'" SOS 52 SOS "H5''" 2H5* H 0 0 N N N -4.146 19.162 47.643 3.345 4.255 -0.978 "H5''" SOS 53 SOS HOP2 2HOP H 0 0 N N N -3.993 23.401 49.651 3.060 2.054 -4.520 HOP2 SOS 54 SOS HOP3 3HOP H 0 0 N N N -4.701 22.718 46.503 4.523 4.721 -4.207 HOP3 SOS 55 # 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 SOS OP3 P SING N N 1 SOS OP3 HOP3 SING N N 2 SOS C15 C10 SING Y N 3 SOS C15 C14 DOUB Y N 4 SOS C15 H15 SING N N 5 SOS C14 C13 SING Y N 6 SOS C14 H14 SING N N 7 SOS C13 C12 DOUB Y N 8 SOS C13 H13 SING N N 9 SOS C12 C11 SING Y N 10 SOS C12 H12 SING N N 11 SOS C11 C10 DOUB Y N 12 SOS C11 H11 SING N N 13 SOS C10 C9 SING N N 14 SOS C9 N7 SING N N 15 SOS C9 H91 SING N N 16 SOS C9 H92 SING N N 17 SOS N7 C8 SING N N 18 SOS N7 C5 SING N N 19 SOS C8 O8 DOUB N N 20 SOS C8 H8 SING N N 21 SOS C5 C6 SING N N 22 SOS C5 C4 DOUB N N 23 SOS C6 O6 DOUB N N 24 SOS C6 N1 SING N N 25 SOS N1 C2 SING N N 26 SOS N1 HN1 SING N N 27 SOS C2 N3 DOUB N N 28 SOS C2 N2 SING N N 29 SOS N2 HN21 SING N N 30 SOS N2 HN22 SING N N 31 SOS N3 C4 SING N N 32 SOS C4 N9 SING N N 33 SOS N9 "C1'" SING N N 34 SOS N9 HN9 SING N N 35 SOS "C1'" "C2'" SING N N 36 SOS "C1'" "C6'" SING N N 37 SOS "C1'" "H1'" SING N N 38 SOS "C6'" "C4'" SING N N 39 SOS "C6'" "H6'1" SING N N 40 SOS "C6'" "H6'2" SING N N 41 SOS "C2'" "C3'" SING N N 42 SOS "C2'" "H2'" SING N N 43 SOS "C2'" "H2''" SING N N 44 SOS "C3'" "C4'" SING N N 45 SOS "C3'" "O3'" SING N N 46 SOS "C3'" "H3'" SING N N 47 SOS "O3'" "HO3'" SING N N 48 SOS "C4'" "C5'" SING N N 49 SOS "C4'" "H4'" SING N N 50 SOS "C5'" "O5'" SING N N 51 SOS "C5'" "H5'" SING N N 52 SOS "C5'" "H5''" SING N N 53 SOS "O5'" P SING N N 54 SOS P OP1 DOUB N N 55 SOS P OP2 SING N N 56 SOS OP2 HOP2 SING N N 57 # 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 SOS SMILES ACDLabs 10.04 "O=C2C(N(C=O)Cc1ccccc1)=C(N=C(N)N2)NC3CC(COP(=O)(O)O)C(O)C3" SOS SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=C(N(Cc2ccccc2)C=O)C(=O)N1)N[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)C3" SOS SMILES CACTVS 3.341 "NC1=NC(=C(N(Cc2ccccc2)C=O)C(=O)N1)N[CH]3C[CH](O)[CH](CO[P](O)(O)=O)C3" SOS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CN(C=O)C2=C(N=C(NC2=O)N)N[C@@H]3C[C@@H]([C@H](C3)O)COP(=O)(O)O" SOS SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CN(C=O)C2=C(N=C(NC2=O)N)NC3CC(C(C3)O)COP(=O)(O)O" SOS InChI InChI 1.03 "InChI=1S/C18H24N5O7P/c19-18-21-16(20-13-6-12(14(25)7-13)9-30-31(27,28)29)15(17(26)22-18)23(10-24)8-11-4-2-1-3-5-11/h1-5,10,12-14,25H,6-9H2,(H2,27,28,29)(H4,19,20,21,22,26)/t12-,13-,14+/m1/s1" SOS InChIKey InChI 1.03 ULUAJGLRYKCHQG-MCIONIFRSA-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 SOS "SYSTEMATIC NAME" ACDLabs 10.04 "[(1R,2S,4R)-4-({2-amino-5-[benzyl(formyl)amino]-6-oxo-1,6-dihydropyrimidin-4-yl}amino)-2-hydroxycyclopentyl]methyl dihydrogen phosphate" SOS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,2S,4R)-4-[[2-amino-5-(methanoyl-(phenylmethyl)amino)-6-oxo-1H-pyrimidin-4-yl]amino]-2-hydroxy-cyclopentyl]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 SOS "Create component" 2007-01-23 RCSB SOS "Modify descriptor" 2011-06-04 RCSB #