data_63H # _chem_comp.id 63H _chem_comp.name "(6R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H18 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-04-15 _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 403.284 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 63H _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 2KDA _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 63H O3P O3P O 0 1 N Y N -7.459 -4.200 13.979 7.215 0.438 -0.071 O3P 63H 1 63H "C1'" "C1'" C 0 1 N N R -6.584 -1.482 18.925 0.409 0.747 -0.199 "C1'" 63H 2 63H C10 C10 C 0 1 N N R -5.002 0.306 12.769 -6.275 1.159 -1.187 C10 63H 3 63H C11 C11 C 0 1 N N N -3.512 0.534 12.695 -6.720 -0.310 -1.133 C11 63H 4 63H C12 C12 C 0 1 N N N -2.750 -0.018 13.872 -6.030 -0.975 0.058 C12 63H 5 63H C2 C2 C 0 1 N N N -4.775 -0.439 15.106 -4.036 0.317 -0.630 C2 63H 6 63H "C2'" "C2'" C 0 1 N N N -7.552 -0.411 18.469 0.472 1.898 0.824 "C2'" 63H 7 63H "C3'" "C3'" C 0 1 N N S -8.840 -1.137 18.116 1.960 1.946 1.249 "C3'" 63H 8 63H C4 C4 C 0 1 Y N N -4.714 -0.934 17.289 -1.895 -0.264 0.045 C4 63H 9 63H "C4'" "C4'" C 0 1 N N R -8.405 -2.591 17.987 2.659 1.225 0.068 "C4'" 63H 10 63H C5 C5 C 0 1 Y N N -3.353 -0.862 17.385 -2.389 -1.420 0.660 C5 63H 11 63H "C5'" "C5'" C 0 1 N N N -8.762 -3.194 16.635 3.994 0.627 0.515 "C5'" 63H 12 63H C6 C6 C 0 1 N N N -2.580 -0.546 16.239 -3.780 -1.664 0.616 C6 63H 13 63H C8 C8 C 0 1 Y N N -4.060 -1.355 19.327 -0.243 -1.398 0.963 C8 63H 14 63H N1 N1 N 0 1 N N N -3.381 -0.343 15.105 -4.582 -0.758 0.003 N1 63H 15 63H N2 N2 N 0 1 N N N -5.517 -0.230 13.960 -4.819 1.169 -1.378 N2 63H 16 63H N3 N3 N 0 1 N N N -5.480 -0.738 16.198 -2.740 0.558 -0.584 N3 63H 17 63H N7 N7 N 0 1 Y N N -2.948 -1.131 18.685 -1.330 -2.072 1.199 N7 63H 18 63H N9 N9 N 0 1 Y N N -5.176 -1.256 18.545 -0.543 -0.270 0.255 N9 63H 19 63H O10 O10 O 0 1 N N N -5.358 -0.650 11.771 -6.608 1.813 0.039 O10 63H 20 63H O1P O1P O 0 1 N N N -9.806 -3.307 13.802 6.503 -1.263 -1.945 O1P 63H 21 63H O2P O2P O 0 1 N N N -7.771 -1.861 13.171 6.049 -1.728 0.494 O2P 63H 22 63H "O3'" "O3'" O 0 1 N N N -9.814 -1.120 19.162 2.415 3.296 1.364 "O3'" 63H 23 63H "O4'" "O4'" O 0 1 N N N -6.996 -2.656 18.223 1.727 0.181 -0.288 "O4'" 63H 24 63H "O5'" "O5'" O 0 1 N N N -8.232 -2.423 15.549 4.669 0.071 -0.615 "O5'" 63H 25 63H O6 O6 O 0 1 N N N -1.354 -0.450 16.179 -4.250 -2.670 1.119 O6 63H 26 63H P P P 0 1 N N N -8.400 -2.894 14.024 6.108 -0.644 -0.512 P 63H 27 63H "H1'" "H1'" H 0 1 N N N -6.611 -1.523 20.024 0.104 1.132 -1.171 "H1'" 63H 28 63H H10 H10 H 0 1 N N N -5.419 1.318 12.657 -6.762 1.664 -2.021 H10 63H 29 63H HO10 HO10 H 0 0 N N N -5.437 -0.216 10.930 -6.324 2.737 0.082 HO10 63H 30 63H H11 H11 H 0 1 N N N -3.137 0.041 11.786 -7.801 -0.362 -1.008 H11 63H 31 63H H11A H11A H 0 0 N N N -3.353 1.622 12.691 -6.431 -0.815 -2.055 H11A 63H 32 63H H12 H12 H 0 1 N N N -2.305 -0.959 13.516 -6.421 -0.552 0.983 H12 63H 33 63H H12A H12A H 0 0 N N N -2.107 0.829 14.153 -6.234 -2.046 0.039 H12A 63H 34 63H HN2 HN2 H 0 1 N N N -6.486 -0.477 13.980 -4.412 1.768 -2.024 HN2 63H 35 63H "H2'" "H2'" H 0 1 N N N -7.726 0.322 19.271 0.176 2.838 0.360 "H2'" 63H 36 63H "H2'A" "H2'A" H 0 0 N N N -7.157 0.149 17.608 -0.163 1.680 1.683 "H2'A" 63H 37 63H "H3'" "H3'" H 0 1 N N N -9.295 -0.669 17.231 2.116 1.404 2.182 "H3'" 63H 38 63H "H4'" "H4'" H 0 1 N N N -8.948 -3.190 18.732 2.805 1.911 -0.767 "H4'" 63H 39 63H "H5'" "H5'" H 0 1 N N N -9.858 -3.205 16.544 4.611 1.407 0.960 "H5'" 63H 40 63H "H5''" "H5''" H 0 0 N N N -8.345 -4.210 16.582 3.812 -0.157 1.251 "H5''" 63H 41 63H H8 H8 H 0 1 N N N -4.096 -1.596 20.379 0.748 -1.687 1.280 H8 63H 42 63H HO3P HO3P H 0 0 N Y N -7.274 -4.426 13.075 7.308 1.178 -0.686 HO3P 63H 43 63H HO1P HO1P H 0 0 N N N -10.246 -3.395 14.639 7.360 -1.711 -1.957 HO1P 63H 44 63H "HO3'" "HO3'" H 0 0 N N N -9.375 -1.116 20.004 1.943 3.814 2.030 "HO3'" 63H 45 # 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 63H O3P P SING N N 1 63H O3P HO3P SING N N 2 63H "O4'" "C1'" SING N N 3 63H "C2'" "C1'" SING N N 4 63H N9 "C1'" SING N N 5 63H "C1'" "H1'" SING N N 6 63H O10 C10 SING N N 7 63H H10 C10 SING N N 8 63H C11 C10 SING N N 9 63H C10 N2 SING N N 10 63H H11 C11 SING N N 11 63H H11A C11 SING N N 12 63H C11 C12 SING N N 13 63H H12 C12 SING N N 14 63H C12 H12A SING N N 15 63H C12 N1 SING N N 16 63H N2 C2 SING N N 17 63H N1 C2 SING N N 18 63H C2 N3 DOUB N N 19 63H "H2'" "C2'" SING N N 20 63H "C3'" "C2'" SING N N 21 63H "C2'" "H2'A" SING N N 22 63H "H3'" "C3'" SING N N 23 63H "C4'" "C3'" SING N N 24 63H "C3'" "O3'" SING N N 25 63H N3 C4 SING N N 26 63H C4 C5 DOUB Y N 27 63H C4 N9 SING Y N 28 63H "C5'" "C4'" SING N N 29 63H "C4'" "O4'" SING N N 30 63H "C4'" "H4'" SING N N 31 63H C6 C5 SING N N 32 63H C5 N7 SING Y N 33 63H "O5'" "C5'" SING N N 34 63H "H5''" "C5'" SING N N 35 63H "H5'" "C5'" SING N N 36 63H N1 C6 SING N N 37 63H O6 C6 DOUB N N 38 63H N9 C8 SING Y N 39 63H N7 C8 DOUB Y N 40 63H C8 H8 SING N N 41 63H HN2 N2 SING N N 42 63H O10 HO10 SING N N 43 63H O1P P SING N N 44 63H O1P HO1P SING N N 45 63H O2P P DOUB N N 46 63H "O3'" "HO3'" SING N N 47 63H P "O5'" SING N N 48 # 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 63H SMILES ACDLabs 10.04 "O=C2c3ncn(c3N=C1NC(O)CCN12)C4OC(C(O)C4)COP(=O)(O)O" 63H SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1CCN2C(=O)c3ncn([C@H]4C[C@H](O)[C@@H](CO[P](O)(O)=O)O4)c3N=C2N1" 63H SMILES CACTVS 3.341 "O[CH]1CCN2C(=O)c3ncn([CH]4C[CH](O)[CH](CO[P](O)(O)=O)O4)c3N=C2N1" 63H SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C4N[C@@H](CCN4C2=O)O" 63H SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C4NC(CCN4C2=O)O" 63H InChI InChI 1.03 "InChI=1S/C13H18N5O8P/c19-6-3-9(26-7(6)4-25-27(22,23)24)18-5-14-10-11(18)16-13-15-8(20)1-2-17(13)12(10)21/h5-9,19-20H,1-4H2,(H,15,16)(H2,22,23,24)/t6-,7+,8+,9+/m0/s1" 63H InChIKey InChI 1.03 KALRENSTRPIBON-JQCXWYLXSA-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 63H "SYSTEMATIC NAME" ACDLabs 10.04 "(6R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one" 63H "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-[(6R)-6-hydroxy-10-oxo-5,6,7,8-tetrahydropyrimido[1,2-a]purin-3-yl]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 63H "Create component" 2009-04-15 RCSB 63H "Modify aromatic_flag" 2011-06-04 RCSB 63H "Modify descriptor" 2011-06-04 RCSB #