data_SDE # _chem_comp.id SDE _chem_comp.name "(S,S)-N6,N6-(2,3-dihydroxy-1,4-butadiyl)-2'-deoxyadenosine-5'-monophosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H22 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-01-07 _chem_comp.pdbx_modified_date 2014-05-23 _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 419.327 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SDE _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2MHZ _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 SDE P P P 0 1 N N N 3.988 -7.952 17.163 5.996 -1.769 -0.375 P SDE 1 SDE O1P O1P O 0 1 N N N 4.613 -8.781 18.225 7.206 -0.636 -0.831 O1P SDE 2 SDE O2P O2P O 0 1 N N N 4.404 -8.158 15.754 6.625 -1.796 1.226 O2P SDE 3 SDE "O5'" "O5'" O 0 1 N N N 2.374 -8.095 17.247 4.774 -0.635 -0.799 "O5'" SDE 4 SDE "C5'" "C5'" C 0 1 N N N 1.681 -8.175 18.487 4.378 0.221 0.274 "C5'" SDE 5 SDE "C4'" "C4'" C 0 1 N N R 0.181 -7.843 18.382 3.335 1.221 -0.230 "C4'" SDE 6 SDE "O4'" "O4'" O 0 1 N N N -0.012 -6.431 18.394 2.113 0.542 -0.592 "O4'" SDE 7 SDE "C1'" "C1'" C 0 1 N N R -0.477 -5.991 17.126 1.062 1.523 -0.558 "C1'" SDE 8 SDE N9 N9 N 0 1 Y N N 0.409 -4.897 16.664 -0.187 0.899 -0.114 N9 SDE 9 SDE C8 C8 C 0 1 Y N N 1.673 -4.974 16.127 -0.301 -0.232 0.637 C8 SDE 10 SDE N7 N7 N 0 1 Y N N 2.250 -3.819 15.930 -1.556 -0.499 0.852 N7 SDE 11 SDE C5 C5 C 0 1 Y N N 1.280 -2.907 16.349 -2.326 0.442 0.254 C5 SDE 12 SDE C6 C6 C 0 1 Y N N 1.234 -1.498 16.436 -3.709 0.667 0.149 C6 SDE 13 SDE N6 N6 N 0 1 N N N 2.271 -0.688 16.162 -4.614 -0.193 0.746 N6 SDE 14 SDE CA CA C 0 1 N N N 2.899 0.177 17.160 -6.000 0.245 0.501 CA SDE 15 SDE CB CB C 0 1 N N S 4.155 0.657 16.429 -6.736 -0.929 -0.178 CB SDE 16 SDE OB OB O 0 1 N N N 4.562 1.923 16.938 -8.071 -1.044 0.321 OB SDE 17 SDE CG CG C 0 1 N N S 3.689 0.733 14.966 -5.888 -2.160 0.235 CG SDE 18 SDE OG OG O 0 1 N N N 4.804 0.778 14.080 -6.012 -3.213 -0.723 OG SDE 19 SDE CD CD C 0 1 N N N 2.881 -0.560 14.832 -4.456 -1.569 0.230 CD SDE 20 SDE N1 N1 N 0 1 Y N N 0.119 -0.901 16.901 -4.128 1.726 -0.537 N1 SDE 21 SDE C2 C2 C 0 1 Y N N -0.916 -1.661 17.248 -3.272 2.553 -1.109 C2 SDE 22 SDE N3 N3 N 0 1 Y N N -1.009 -2.984 17.216 -1.968 2.381 -1.037 N3 SDE 23 SDE C4 C4 C 0 1 Y N N 0.143 -3.553 16.769 -1.456 1.351 -0.373 C4 SDE 24 SDE "C3'" "C3'" C 0 1 N N S -0.519 -8.409 17.135 2.895 2.173 0.911 "C3'" SDE 25 SDE "C2'" "C2'" C 0 1 N N N -0.517 -7.206 16.192 1.489 2.617 0.440 "C2'" SDE 26 SDE "O3'" "O3'" O 0 1 N N N -1.813 -8.869 17.501 3.778 3.293 1.009 "O3'" SDE 27 SDE H1 H1 H 0 1 N N N 4.251 -8.540 19.070 7.765 -0.930 -1.563 H1 SDE 28 SDE H3 H3 H 0 1 N N N 5.348 -8.077 15.687 6.147 -2.385 1.827 H3 SDE 29 SDE "H5'2" "H5'2" H 0 0 N N N 1.783 -9.199 18.876 3.948 -0.378 1.077 "H5'2" SDE 30 SDE "H5'1" "H5'1" H 0 0 N N N 2.145 -7.467 19.190 5.247 0.761 0.648 "H5'1" SDE 31 SDE "H4'" "H4'" H 0 1 N N N -0.314 -8.277 19.263 3.725 1.786 -1.077 "H4'" SDE 32 SDE "H1'" "H1'" H 0 1 N N N -1.501 -5.600 17.223 0.928 1.957 -1.549 "H1'" SDE 33 SDE H8 H8 H 0 1 N N N 2.150 -5.913 15.888 0.529 -0.821 1.001 H8 SDE 34 SDE HA2 HA2 H 0 1 N N N 2.245 1.021 17.425 -6.484 0.490 1.446 HA2 SDE 35 SDE HA1 HA1 H 0 1 N N N 3.157 -0.386 18.069 -6.003 1.116 -0.154 HA1 SDE 36 SDE HB HB H 0 1 N N N 4.955 -0.092 16.527 -6.741 -0.807 -1.261 HB SDE 37 SDE HOB HOB H 0 1 N N N 4.840 1.827 17.841 -8.621 -0.267 0.155 HOB SDE 38 SDE HG HG H 0 1 N N N 3.030 1.603 14.829 -6.163 -2.507 1.231 HG SDE 39 SDE HOG HOG H 0 1 N N N 5.272 1.596 14.200 -5.499 -4.003 -0.507 HOG SDE 40 SDE HD1 HD1 H 0 1 N N N 2.114 -0.471 14.049 -4.057 -1.551 -0.784 HD1 SDE 41 SDE HD2 HD2 H 0 1 N N N 3.534 -1.417 14.609 -3.804 -2.148 0.885 HD2 SDE 42 SDE H2 H2 H 0 1 N N N -1.791 -1.135 17.600 -3.655 3.400 -1.657 H2 SDE 43 SDE "H3'" "H3'" H 0 1 N N N 0.088 -9.220 16.706 2.838 1.641 1.861 "H3'" SDE 44 SDE "H2'2" "H2'2" H 0 0 N N N -1.428 -7.193 15.575 1.541 3.586 -0.056 "H2'2" SDE 45 SDE "H2'1" "H2'1" H 0 0 N N N 0.368 -7.225 15.539 0.799 2.655 1.282 "H2'1" SDE 46 SDE H4 H4 H 0 1 N N N -1.731 -9.614 18.085 3.544 3.918 1.709 H4 SDE 47 SDE O3P O3P O 0 1 N Y N ? ? ? 4.785 -2.903 0.082 O3P SDE 48 SDE H5 H5 H 0 1 N N N ? ? ? 6.502 -2.715 -1.380 H5 SDE 49 SDE H6 H6 H 0 1 N N N ? ? ? 5.136 -3.744 0.405 H6 SDE 50 # 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 SDE OG CG SING N N 1 SDE CD CG SING N N 2 SDE CD N6 SING N N 3 SDE CG CB SING N N 4 SDE O2P P SING N N 5 SDE N7 C8 DOUB Y N 6 SDE N7 C5 SING Y N 7 SDE C8 N9 SING Y N 8 SDE N6 C6 SING N N 9 SDE N6 CA SING N N 10 SDE "C2'" "C1'" SING N N 11 SDE "C2'" "C3'" SING N N 12 SDE C5 C6 DOUB Y N 13 SDE C5 C4 SING Y N 14 SDE CB OB SING N N 15 SDE CB CA SING N N 16 SDE C6 N1 SING Y N 17 SDE N9 C4 SING Y N 18 SDE N9 "C1'" SING N N 19 SDE C4 N3 DOUB Y N 20 SDE N1 C2 DOUB Y N 21 SDE "C1'" "O4'" SING N N 22 SDE "C3'" "O3'" SING N N 23 SDE "C3'" "C4'" SING N N 24 SDE P "O5'" SING N N 25 SDE P O1P SING N N 26 SDE N3 C2 SING Y N 27 SDE "O5'" "C5'" SING N N 28 SDE "C4'" "O4'" SING N N 29 SDE "C4'" "C5'" SING N N 30 SDE O1P H1 SING N N 31 SDE O2P H3 SING N N 32 SDE "C5'" "H5'2" SING N N 33 SDE "C5'" "H5'1" SING N N 34 SDE "C4'" "H4'" SING N N 35 SDE "C1'" "H1'" SING N N 36 SDE C8 H8 SING N N 37 SDE CA HA2 SING N N 38 SDE CA HA1 SING N N 39 SDE CB HB SING N N 40 SDE OB HOB SING N N 41 SDE CG HG SING N N 42 SDE OG HOG SING N N 43 SDE CD HD1 SING N N 44 SDE CD HD2 SING N N 45 SDE C2 H2 SING N N 46 SDE "C3'" "H3'" SING N N 47 SDE "C2'" "H2'2" SING N N 48 SDE "C2'" "H2'1" SING N N 49 SDE "O3'" H4 SING N N 50 SDE P O3P SING N N 51 SDE P H5 SING N N 52 SDE O3P H6 SING N N 53 # 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 SDE SMILES ACDLabs 12.01 "n3c1c(ncnc1N2CC(O)C(O)C2)n(c3)C4OC(C(O)C4)COP(O)(O)O" SDE InChI InChI 1.03 "InChI=1S/C14H22N5O8P/c20-7-1-11(27-10(7)4-26-28(23,24)25)19-6-17-12-13(15-5-16-14(12)19)18-2-8(21)9(22)3-18/h5-11,20-25,28H,1-4H2/t7-,8-,9-,10+,11+/m0/s1" SDE InChIKey InChI 1.03 AFIPVZHEZSDVQA-LADJIXMOSA-N SDE SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[C@H](O)[C@@H](O)C4" SDE SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[CH](O)[CH](O)C4" SDE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3C[C@@H]([C@H](C3)O)O)ncn2[C@H]4C[C@@H]([C@H](O4)COP(O)(O)O)O" SDE SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3CC(C(C3)O)O)ncn2C4CC(C(O4)COP(O)(O)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 SDE "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,4S)-1-{9-[(2R,4S,5R)-4-hydroxy-5-{[(trihydroxy-lambda~5~-phosphanyl)oxy]methyl}tetrahydrofuran-2-yl]-9H-purin-6-yl}pyrrolidine-3,4-diol (non-preferred name)" SDE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(3S,4S)-1-[9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]purin-6-yl]pyrrolidine-3,4-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SDE "Create component" 2014-01-07 RCSB SDE "Initial release" 2014-05-28 RCSB #