data_63G # _chem_comp.id 63G _chem_comp.name "(6S)-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 2009-01-08 _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 63G _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 2KD9 _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 63G O3P O3P O 0 1 N Y N -8.153 -3.020 14.325 7.224 -0.479 0.142 O3P 63G 1 63G "C1'" "C1'" C 0 1 N N R -7.608 0.396 19.210 0.416 -0.757 -0.000 "C1'" 63G 2 63G C10 C10 C 0 1 N N S -4.944 1.515 13.301 -6.297 -1.273 0.693 C10 63G 3 63G C11 C11 C 0 1 N N N -3.540 0.949 13.202 -6.738 0.190 0.857 C11 63G 4 63G C12 C12 C 0 1 N N N -3.071 0.293 14.482 -6.007 1.030 -0.191 C12 63G 5 63G C2 C2 C 0 1 N N N -5.241 0.560 15.509 -4.040 -0.369 0.349 C2 63G 6 63G "C2'" "C2'" C 0 1 N N N -8.370 1.389 18.345 0.512 -1.733 -1.189 "C2'" 63G 7 63G "C3'" "C3'" C 0 1 N N S -9.700 0.724 18.032 2.013 -1.724 -1.567 "C3'" 63G 8 63G C4 C4 C 0 1 Y N N -5.522 0.286 17.717 -1.877 0.296 -0.156 C4 63G 9 63G "C4'" "C4'" C 0 1 N N R -9.426 -0.768 18.273 2.673 -1.203 -0.266 "C4'" 63G 10 63G C5 C5 C 0 1 Y N N -4.205 -0.004 17.956 -2.348 1.538 -0.597 C5 63G 11 63G "C5'" "C5'" C 0 1 N N N -9.531 -1.678 17.033 4.023 -0.551 -0.570 "C5'" 63G 12 63G C6 C6 C 0 1 N N N -3.282 -0.023 16.882 -3.739 1.781 -0.560 C6 63G 13 63G C8 C8 C 0 1 Y N N -5.175 -0.098 19.837 -0.193 1.548 -0.830 C8 63G 14 63G N1 N1 N 0 1 N N N -3.882 0.275 15.658 -4.563 0.797 -0.124 N1 63G 15 63G N2 N2 N 0 1 N N N -5.741 0.846 14.247 -4.848 -1.323 0.928 N2 63G 16 63G N3 N3 N 0 1 N N N -6.101 0.575 16.529 -2.743 -0.609 0.308 N3 63G 17 63G N7 N7 N 0 1 Y N N -3.993 -0.246 19.307 -1.270 2.260 -0.992 N7 63G 18 63G N9 N9 N 0 1 Y N N -6.161 0.224 18.939 -0.518 0.326 -0.319 N9 63G 19 63G O10 O10 O 0 1 N N N -4.854 2.865 13.763 -6.973 -2.094 1.648 O10 63G 20 63G O1P O1P O 0 1 N N N -10.460 -2.018 14.300 6.453 0.912 2.236 O1P 63G 21 63G O2P O2P O 0 1 N N N -8.427 -0.619 13.563 6.081 1.757 -0.113 O2P 63G 22 63G "O3'" "O3'" O 0 1 N N N -10.778 0.980 18.940 2.468 -3.043 -1.878 "O3'" 63G 23 63G "O4'" "O4'" O 0 1 N N N -8.162 -0.898 18.929 1.732 -0.221 0.220 "O4'" 63G 24 63G "O5'" "O5'" O 0 1 N N N -8.741 -1.191 15.943 4.662 -0.185 0.655 "O5'" 63G 25 63G O6 O6 O 0 1 N N N -2.082 -0.272 16.946 -4.190 2.858 -0.913 O6 63G 26 63G P P P 0 1 N N N -9.022 -1.660 14.433 6.104 0.528 0.712 P 63G 27 63G "H1'" "H1'" H 0 1 N N N -7.705 0.790 20.232 0.079 -1.288 0.890 "H1'" 63G 28 63G H10 H10 H 0 1 N N N -5.396 1.413 12.303 -6.521 -1.617 -0.317 H10 63G 29 63G H010 H010 H 0 0 N N N -4.834 2.874 14.713 -6.715 -3.025 1.618 H010 63G 30 63G H111 H111 H 0 0 N N N -2.860 1.789 12.994 -7.814 0.268 0.706 H111 63G 31 63G H211 H211 H 0 0 N N N -3.529 0.193 12.403 -6.479 0.542 1.856 H211 63G 32 63G H112 H112 H 0 0 N N N -2.224 0.927 14.782 -6.369 0.760 -1.183 H112 63G 33 63G H212 H212 H 0 0 N N N -2.898 -0.763 14.226 -6.209 2.085 -0.010 H212 63G 34 63G HN2 HN2 H 0 1 N N N -6.674 0.575 14.009 -4.465 -2.019 1.483 HN2 63G 35 63G "H2'" "H2'" H 0 1 N N N -8.525 2.336 18.883 0.198 -2.733 -0.887 "H2'" 63G 36 63G "H2''" "H2''" H 0 0 N N N -7.815 1.636 17.428 -0.094 -1.379 -2.023 "H2''" 63G 37 63G "H3'" "H3'" H 0 1 N N N -10.001 1.079 17.035 2.200 -1.044 -2.398 "H3'" 63G 38 63G "H4'" "H4'" H 0 1 N N N -10.239 -1.138 18.914 2.790 -2.012 0.456 "H4'" 63G 39 63G "H5'" "H5'" H 0 1 N N N -10.583 -1.696 16.711 4.653 -1.256 -1.112 "H5'" 63G 40 63G "H5''" "H5''" H 0 0 N N N -9.176 -2.683 17.303 3.867 0.340 -1.179 "H5''" 63G 41 63G H8 H8 H 0 1 N N N -5.362 -0.219 20.894 0.808 1.877 -1.066 H8 63G 42 63G HO3P HO3P H 0 0 N Y N -7.983 -3.216 13.411 7.295 -1.308 0.636 HO3P 63G 43 63G HO1P HO1P H 0 0 N N N -10.849 -2.094 15.163 7.310 1.346 2.346 HO1P 63G 44 63G "HO3'" "HO3'" H 0 0 N N N -10.440 1.037 19.826 2.018 -3.447 -2.632 "HO3'" 63G 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 63G O3P P SING N N 1 63G O3P HO3P SING N N 2 63G "C2'" "C1'" SING N N 3 63G "O4'" "C1'" SING N N 4 63G N9 "C1'" SING N N 5 63G "C1'" "H1'" SING N N 6 63G H10 C10 SING N N 7 63G C11 C10 SING N N 8 63G C10 O10 SING N N 9 63G C10 N2 SING N N 10 63G H211 C11 SING N N 11 63G H111 C11 SING N N 12 63G C11 C12 SING N N 13 63G H212 C12 SING N N 14 63G C12 H112 SING N N 15 63G C12 N1 SING N N 16 63G N2 C2 SING N N 17 63G C2 N1 SING N N 18 63G C2 N3 DOUB N N 19 63G "H2'" "C2'" SING N N 20 63G "C3'" "C2'" SING N N 21 63G "C2'" "H2''" SING N N 22 63G "H3'" "C3'" SING N N 23 63G "C3'" "C4'" SING N N 24 63G "C3'" "O3'" SING N N 25 63G N3 C4 SING N N 26 63G C4 C5 DOUB Y N 27 63G C4 N9 SING Y N 28 63G "C5'" "C4'" SING N N 29 63G "C4'" "O4'" SING N N 30 63G "C4'" "H4'" SING N N 31 63G C6 C5 SING N N 32 63G C5 N7 SING Y N 33 63G "O5'" "C5'" SING N N 34 63G "H5''" "C5'" SING N N 35 63G "C5'" "H5'" SING N N 36 63G N1 C6 SING N N 37 63G C6 O6 DOUB N N 38 63G N9 C8 SING Y N 39 63G N7 C8 DOUB Y N 40 63G C8 H8 SING N N 41 63G HN2 N2 SING N N 42 63G O10 H010 SING N N 43 63G O1P P SING N N 44 63G O1P HO1P SING N N 45 63G O2P P DOUB N N 46 63G "O3'" "HO3'" SING N N 47 63G 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 63G SMILES ACDLabs 10.04 "O=C2c3ncn(c3N=C1NC(O)CCN12)C4OC(C(O)C4)COP(=O)(O)O" 63G 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" 63G SMILES CACTVS 3.341 "O[CH]1CCN2C(=O)c3ncn([CH]4C[CH](O)[CH](CO[P](O)(O)=O)O4)c3N=C2N1" 63G 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" 63G SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C4NC(CCN4C2=O)O" 63G 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" 63G InChIKey InChI 1.03 KALRENSTRPIBON-UYXSQOIJSA-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 63G "SYSTEMATIC NAME" ACDLabs 10.04 "(6S)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one" 63G "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-[(6S)-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 63G "Create component" 2009-01-08 RCSB 63G "Modify aromatic_flag" 2011-06-04 RCSB 63G "Modify descriptor" 2011-06-04 RCSB #