data_HN1 # _chem_comp.id HN1 _chem_comp.name "(6S,8R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-6-[(1S)-1-hydroxyhexyl]-4,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H30 N5 O9 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-08-12 _chem_comp.pdbx_modified_date 2012-02-10 _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 503.443 _chem_comp.one_letter_code ? _chem_comp.three_letter_code HN1 _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 3T5H _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 HN1 C C C 0 1 N N N -17.164 32.769 10.953 -5.088 -2.267 0.303 C HN1 1 HN1 P P P 0 1 N N N -6.274 36.888 14.824 7.495 0.549 -0.353 P HN1 2 HN1 C1 C1 C 0 1 N N R -15.907 32.069 11.052 -4.072 -3.302 -0.185 C1 HN1 3 HN1 N1 N1 N 0 1 N N N -14.756 32.727 11.797 -2.736 -2.698 -0.129 N1 HN1 4 HN1 C2 C2 C 0 1 N N N -14.932 34.011 12.329 -2.563 -1.421 -0.617 C2 HN1 5 HN1 N2 N2 N 0 1 N N N -16.067 34.656 12.194 -3.583 -0.646 -0.814 N2 HN1 6 HN1 C3 C3 C 0 1 N N S -17.205 34.271 11.361 -4.959 -0.980 -0.501 C3 HN1 7 HN1 N3 N3 N 0 1 N N N -14.009 34.703 13.007 -1.294 -0.927 -0.887 N3 HN1 8 HN1 C4 C4 C 0 1 Y N N -12.817 34.042 13.164 -0.253 -1.473 -0.162 C4 HN1 9 HN1 C5 C5 C 0 1 Y N N -12.480 32.785 12.701 -0.421 -2.704 0.488 C5 HN1 10 HN1 C6 C6 C 0 1 N N N -13.488 32.039 11.957 -1.709 -3.401 0.413 C6 HN1 11 HN1 O6 O6 O 0 1 N N N -13.326 30.907 11.485 -1.849 -4.542 0.813 O6 HN1 12 HN1 C7 C7 C 0 1 N N S -18.509 34.665 12.128 -5.575 0.167 0.302 C7 HN1 13 HN1 N7 N7 N 0 1 Y N N -11.159 32.482 13.077 0.737 -2.998 1.098 N7 HN1 14 HN1 C8 C8 C 0 1 Y N N -10.771 33.551 13.736 1.591 -2.035 0.874 C8 HN1 15 HN1 C9 C9 C 0 1 N N N -19.735 34.760 11.177 -5.454 1.469 -0.493 C9 HN1 16 HN1 N9 N9 N 0 1 Y N N -11.727 34.530 13.820 1.004 -1.072 0.097 N9 HN1 17 HN1 "C1'" "C1'" C 0 1 N N R -11.645 35.846 14.476 1.631 0.167 -0.368 "C1'" HN1 18 HN1 C10 C10 C 0 1 N N N -20.880 35.693 11.652 -6.179 2.591 0.252 C10 HN1 19 HN1 O10 O10 O 0 1 N N N -18.311 35.959 12.771 -4.884 0.303 1.546 O10 HN1 20 HN1 C11 C11 C 0 1 N N N -21.576 35.200 12.945 -6.057 3.893 -0.543 C11 HN1 21 HN1 O11 O11 O 0 1 N N N -15.496 31.755 9.728 -4.375 -3.677 -1.530 O11 HN1 22 HN1 C12 C12 C 0 1 N N N -23.095 34.997 12.765 -6.782 5.015 0.203 C12 HN1 23 HN1 C13 C13 C 0 1 N N N -23.755 34.263 13.944 -6.661 6.317 -0.592 C13 HN1 24 HN1 OP1 O1P O 0 1 N N N -5.754 38.228 15.204 7.706 -0.462 0.706 OP1 HN1 25 HN1 "C2'" "C2'" C 0 1 N N N -11.623 35.790 16.003 1.289 1.321 0.594 "C2'" HN1 26 HN1 OP3 OP3 O 0 1 N Y N -5.556 35.659 15.264 8.140 0.025 -1.732 OP3 HN1 27 HN1 "C3'" "C3'" C 0 1 N N S -10.536 36.781 16.391 2.667 1.829 1.083 "C3'" HN1 28 HN1 "O3'" "O3'" O 0 1 N N N -10.966 37.792 17.302 2.691 3.257 1.146 "O3'" HN1 29 HN1 "C4'" "C4'" C 0 1 N N R -10.123 37.421 15.072 3.617 1.309 -0.026 "C4'" HN1 30 HN1 "O4'" "O4'" O 0 1 N N N -10.423 36.430 14.078 3.061 0.021 -0.369 "O4'" HN1 31 HN1 "C5'" "C5'" C 0 1 N N N -8.681 37.850 15.003 5.042 1.160 0.511 "C5'" HN1 32 HN1 "O5'" "O5'" O 0 1 N N N -7.800 36.775 15.304 5.917 0.792 -0.557 "O5'" HN1 33 HN1 OP2 O2P O 0 1 N N N -6.290 36.561 13.135 8.200 1.932 0.076 OP2 HN1 34 HN1 H H H 0 1 N N N -17.469 32.721 9.897 -6.095 -2.666 0.186 H HN1 35 HN1 HA HA H 0 1 N N N -17.870 32.244 11.613 -4.907 -2.053 1.357 HA HN1 36 HN1 H31 H31 H 0 1 N N N -16.125 31.199 11.689 -4.105 -4.181 0.458 H31 HN1 37 HN1 H3 H3 H 0 1 N N N -17.170 34.810 10.403 -5.514 -1.092 -1.433 H3 HN1 38 HN1 HN3 HN3 H 0 1 N N N -14.174 35.621 13.368 -1.145 -0.235 -1.550 HN3 HN1 39 HN1 H7 H7 H 0 1 N N N -18.713 33.881 12.872 -6.627 -0.046 0.492 H7 HN1 40 HN1 H8 H8 H 0 1 N N N -9.788 33.649 14.172 2.605 -2.004 1.244 H8 HN1 41 HN1 H9 H9 H 0 1 N N N -19.375 35.144 10.211 -4.401 1.729 -0.607 H9 HN1 42 HN1 H9A H9A H 0 1 N N N -20.154 33.748 11.075 -5.903 1.337 -1.477 H9A HN1 43 HN1 "H1'" "H1'" H 0 1 N N N -12.543 36.409 14.180 1.281 0.406 -1.372 "H1'" HN1 44 HN1 H10 H10 H 0 1 N N N -20.454 36.688 11.849 -7.231 2.331 0.366 H10 HN1 45 HN1 H10A H10A H 0 0 N N N -21.635 35.745 10.854 -5.729 2.723 1.236 H10A HN1 46 HN1 HO10 HO10 H 0 0 N N N -19.100 36.205 13.239 -3.941 0.493 1.453 HO10 HN1 47 HN1 H11 H11 H 0 1 N N N -21.129 34.237 13.234 -5.005 4.152 -0.656 H11 HN1 48 HN1 H11A H11A H 0 0 N N N -21.417 35.951 13.733 -6.507 3.760 -1.527 H11A HN1 49 HN1 H16 H16 H 0 1 N N N -14.634 31.356 9.750 -3.769 -4.332 -1.902 H16 HN1 50 HN1 H12 H12 H 0 1 N N N -23.565 35.987 12.670 -7.835 4.755 0.316 H12 HN1 51 HN1 H12A H12A H 0 0 N N N -23.257 34.401 11.855 -6.333 5.147 1.187 H12A HN1 52 HN1 H13 H13 H 0 1 N N N -24.832 34.153 13.751 -7.178 7.116 -0.061 H13 HN1 53 HN1 H13A H13A H 0 0 N N N -23.299 33.268 14.058 -5.609 6.576 -0.706 H13A HN1 54 HN1 H13B H13B H 0 0 N N N -23.605 34.843 14.867 -7.111 6.184 -1.576 H13B HN1 55 HN1 HOP3 HOP3 H 0 0 N Y N -4.793 35.903 15.774 9.091 -0.143 -1.683 HOP3 HN1 56 HN1 "H2'" "H2'" H 0 1 N N N -12.596 36.076 16.428 0.755 2.112 0.068 "H2'" HN1 57 HN1 "H2'A" "H2'A" H 0 0 N N N -11.389 34.777 16.363 0.698 0.954 1.434 "H2'A" HN1 58 HN1 "H3'" "H3'" H 0 1 N N N -9.723 36.260 16.918 2.922 1.395 2.049 "H3'" HN1 59 HN1 "HO3'" "HO3'" H 0 0 N Y N -10.239 38.372 17.499 2.048 3.634 1.763 "HO3'" HN1 60 HN1 "H4'" "H4'" H 0 1 N N N -10.669 38.365 14.926 3.601 1.975 -0.889 "H4'" HN1 61 HN1 "H5'" "H5'" H 0 1 N N N -8.467 38.209 13.985 5.369 2.107 0.939 "H5'" HN1 62 HN1 "H5'A" "H5'A" H 0 0 N N N -8.517 38.657 15.732 5.061 0.387 1.279 "H5'A" HN1 63 HN1 HOP2 HO2P H 0 0 N N N -5.951 37.313 12.663 8.102 2.642 -0.573 HOP2 HN1 64 # 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 HN1 C C1 SING N N 1 HN1 C C3 SING N N 2 HN1 P OP1 DOUB N N 3 HN1 P OP3 SING N N 4 HN1 P "O5'" SING N N 5 HN1 C1 N1 SING N N 6 HN1 N1 C6 SING N N 7 HN1 N1 C2 SING N N 8 HN1 C2 N3 SING N N 9 HN1 N2 C2 DOUB N N 10 HN1 C3 N2 SING N N 11 HN1 C3 C7 SING N N 12 HN1 N3 C4 SING N N 13 HN1 C4 N9 SING Y N 14 HN1 C5 C4 DOUB Y N 15 HN1 C5 N7 SING Y N 16 HN1 C6 C5 SING N N 17 HN1 O6 C6 DOUB N N 18 HN1 C7 O10 SING N N 19 HN1 N7 C8 DOUB Y N 20 HN1 C8 N9 SING Y N 21 HN1 C9 C7 SING N N 22 HN1 C9 C10 SING N N 23 HN1 N9 "C1'" SING N N 24 HN1 "C1'" "C2'" SING N N 25 HN1 C10 C11 SING N N 26 HN1 O11 C1 SING N N 27 HN1 C12 C11 SING N N 28 HN1 C12 C13 SING N N 29 HN1 "C2'" "C3'" SING N N 30 HN1 "C3'" "O3'" SING N N 31 HN1 "C4'" "C3'" SING N N 32 HN1 "O4'" "C1'" SING N N 33 HN1 "O4'" "C4'" SING N N 34 HN1 "C5'" "C4'" SING N N 35 HN1 "C5'" "O5'" SING N N 36 HN1 P OP2 SING N N 37 HN1 C H SING N N 38 HN1 C HA SING N N 39 HN1 C1 H31 SING N N 40 HN1 C3 H3 SING N N 41 HN1 N3 HN3 SING N N 42 HN1 C7 H7 SING N N 43 HN1 C8 H8 SING N N 44 HN1 C9 H9 SING N N 45 HN1 C9 H9A SING N N 46 HN1 "C1'" "H1'" SING N N 47 HN1 C10 H10 SING N N 48 HN1 C10 H10A SING N N 49 HN1 O10 HO10 SING N N 50 HN1 C11 H11 SING N N 51 HN1 C11 H11A SING N N 52 HN1 O11 H16 SING N N 53 HN1 C12 H12 SING N N 54 HN1 C12 H12A SING N N 55 HN1 C13 H13 SING N N 56 HN1 C13 H13A SING N N 57 HN1 C13 H13B SING N N 58 HN1 OP3 HOP3 SING N N 59 HN1 "C2'" "H2'" SING N N 60 HN1 "C2'" "H2'A" SING N N 61 HN1 "C3'" "H3'" SING N N 62 HN1 "O3'" "HO3'" SING N N 63 HN1 "C4'" "H4'" SING N N 64 HN1 "C5'" "H5'" SING N N 65 HN1 "C5'" "H5'A" SING N N 66 HN1 OP2 HOP2 SING N N 67 # 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 HN1 SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(n1cnc3c1NC2=NC(C(O)CCCCC)CC(O)N2C3=O)CC4O" HN1 InChI InChI 1.03 "InChI=1S/C19H30N5O9P/c1-2-3-4-5-11(25)10-6-14(27)24-18(28)16-17(22-19(24)21-10)23(9-20-16)15-7-12(26)13(33-15)8-32-34(29,30)31/h9-15,25-27H,2-8H2,1H3,(H,21,22)(H2,29,30,31)/t10-,11-,12-,13+,14+,15+/m0/s1" HN1 InChIKey InChI 1.03 OOIOCUIVTIOESO-PKCACUDHSA-N HN1 SMILES_CANONICAL CACTVS 3.370 "CCCCC[C@H](O)[C@@H]1C[C@@H](O)N2C(=O)c3ncn([C@H]4C[C@H](O)[C@@H](CO[P](O)(O)=O)O4)c3NC2=N1" HN1 SMILES CACTVS 3.370 "CCCCC[CH](O)[CH]1C[CH](O)N2C(=O)c3ncn([CH]4C[CH](O)[CH](CO[P](O)(O)=O)O4)c3NC2=N1" HN1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CCCCC[C@@H]([C@@H]1C[C@H](N2C(=O)c3c(n(cn3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O)NC2=N1)O)O" HN1 SMILES "OpenEye OEToolkits" 1.7.2 "CCCCCC(C1CC(N2C(=O)c3c(n(cn3)C4CC(C(O4)COP(=O)(O)O)O)NC2=N1)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 HN1 "SYSTEMATIC NAME" ACDLabs 12.01 "(6S,8R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-6-[(1S)-1-hydroxyhexyl]-4,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one" HN1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5R)-3-oxidanyl-5-[(6S,8R)-8-oxidanyl-6-[(1S)-1-oxidanylhexyl]-10-oxidanylidene-4,6,7,8-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 HN1 "Create component" 2011-08-12 RCSB HN1 "Modify model coordinates code" 2011-08-25 RCSB #