data_E1X # _chem_comp.id E1X _chem_comp.name "PHOSPHORIC ACID MONO-[5-(1-ETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-PURIN-9-YL)-3-HYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]ESTER" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H17 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms "N1-ETHYL-2'-DEOXYXANTHOSINE 5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-05-06 _chem_comp.pdbx_modified_date 2020-06-17 _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 376.259 _chem_comp.one_letter_code A _chem_comp.three_letter_code E1X _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1T39 _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 E1X P P P 0 1 N N N 101.289 -4.690 -24.207 1.592 -1.245 -4.964 P E1X 1 E1X OP1 O1P O 0 1 N N N 100.303 -3.579 -24.103 2.575 -0.951 -6.059 OP1 E1X 2 E1X OP2 O2P O 0 1 N N N 101.657 -5.225 -25.540 0.339 -0.227 -4.868 OP2 E1X 3 E1X "O5'" O5* O 0 1 N N N 100.792 -5.890 -23.290 2.211 -1.232 -3.468 "O5'" E1X 4 E1X N9 N9 N 0 1 Y N N 99.984 -9.543 -23.259 1.818 1.923 -0.049 N9 E1X 5 E1X C4 C4 C 0 1 Y N N 99.607 -10.851 -23.391 1.881 2.960 0.826 C4 E1X 6 E1X N3 N3 N 0 1 N N N 99.472 -11.839 -22.502 2.220 2.917 2.144 N3 E1X 7 E1X C2 C2 C 0 1 N N N 99.102 -13.065 -22.884 2.222 4.112 2.871 C2 E1X 8 E1X O2 O2 O 0 1 N N N 98.965 -14.048 -21.950 2.523 4.125 4.068 O2 E1X 9 E1X N1 N1 N 0 1 N N N 98.852 -13.346 -24.228 1.854 5.295 2.134 N1 E1X 10 E1X C10 C10 C 0 1 N N N 98.450 -14.727 -24.589 1.849 6.551 2.874 C10 E1X 11 E1X C11 C11 C 0 1 N N N 98.249 -14.922 -26.080 0.514 6.810 3.485 C11 E1X 12 E1X O6 O6 O 0 1 N N N 98.759 -12.624 -26.368 1.182 6.375 0.141 O6 E1X 13 E1X C6 C6 C 0 1 N N N 98.983 -12.326 -25.196 1.495 5.363 0.758 C6 E1X 14 E1X C5 C5 C 0 1 Y N N 99.375 -11.039 -24.734 1.532 4.074 0.124 C5 E1X 15 E1X N7 N7 N 0 1 Y N N 99.576 -9.856 -25.434 1.250 3.768 -1.179 N7 E1X 16 E1X C8 C8 C 0 1 Y N N 99.931 -8.995 -24.517 1.431 2.463 -1.252 C8 E1X 17 E1X "C2'" C2* C 0 1 N N N 101.741 -8.228 -21.996 0.878 -0.312 0.578 "C2'" E1X 18 E1X "C5'" C5* C 0 1 N N N 99.990 -5.623 -22.146 1.348 -1.500 -2.377 "C5'" E1X 19 E1X "C4'" C4* C 0 1 N N R 100.093 -6.753 -21.150 2.156 -1.432 -1.088 "C4'" E1X 20 E1X "O4'" O4* O 0 1 N N N 99.427 -7.923 -21.678 2.678 -0.093 -0.958 "O4'" E1X 21 E1X "C1'" C1* C 0 1 N N R 100.384 -8.908 -22.011 2.101 0.516 0.211 "C1'" E1X 22 E1X "C3'" C3* C 0 1 N N S 101.538 -7.179 -20.921 1.309 -1.697 0.152 "C3'" E1X 23 E1X "O3'" O3* O 0 1 N N N 101.662 -7.750 -19.619 2.127 -2.250 1.180 "O3'" E1X 24 E1X OP3 O3P O 0 1 N Y N ? ? ? 0.886 -2.697 -5.051 OP3 E1X 25 E1X HOP2 2HOP H 0 0 N N N 102.286 -5.933 -25.606 -0.163 -0.014 -5.684 HOP2 E1X 26 E1X HN3 HN3 H 0 1 N N N 98.827 -11.525 -21.776 2.465 2.035 2.582 HN3 E1X 27 E1X H101 1H10 H 0 0 N N N 99.178 -15.469 -24.186 2.618 6.485 3.649 H101 E1X 28 E1X H102 2H10 H 0 0 N N N 97.540 -15.035 -24.022 2.118 7.349 2.177 H102 E1X 29 E1X H111 1H11 H 0 0 N N N 97.946 -15.960 -26.351 -0.259 6.894 2.713 H111 E1X 30 E1X H112 2H11 H 0 0 N N N 97.521 -14.179 -26.482 0.242 6.010 4.182 H112 E1X 31 E1X H113 3H11 H 0 0 N N N 99.158 -14.613 -26.646 0.537 7.753 4.044 H113 E1X 32 E1X H8 H8 H 0 1 N N N 100.156 -7.945 -24.771 1.302 1.857 -2.139 H8 E1X 33 E1X "H2'" 1H2* H 0 1 N N N 102.612 -8.906 -21.841 0.008 0.008 -0.009 "H2'" E1X 34 E1X "H2''" 2H2* H 0 0 N N N 102.090 -7.839 -22.981 0.635 -0.225 1.641 "H2''" E1X 35 E1X "H5'" 1H5* H 0 1 N N N 100.241 -4.639 -21.684 0.551 -0.756 -2.359 "H5'" E1X 36 E1X "H5''" 2H5* H 0 0 N N N 98.931 -5.410 -22.423 0.917 -2.495 -2.497 "H5''" E1X 37 E1X "H4'" H4* H 0 1 N N N 99.637 -6.384 -20.201 3.008 -2.117 -1.157 "H4'" E1X 38 E1X "H1'" H1* H 0 1 N N N 100.452 -9.750 -21.284 2.853 0.503 1.007 "H1'" E1X 39 E1X H1 H1 H 0 1 N N N 102.280 -6.349 -20.974 0.475 -2.383 -0.018 H1 E1X 40 E1X "HO3'" H3T H 0 0 N Y N 101.534 -7.092 -18.945 2.740 -2.862 0.745 "HO3'" E1X 41 E1X HOP3 3HOP H 0 0 N N N 0.629 -0.708 -0.066 0.508 -2.990 -5.907 HOP3 E1X 42 # # 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 E1X P OP1 DOUB N N 1 E1X P OP2 SING N N 2 E1X P "O5'" SING N N 3 E1X P OP3 SING N N 4 E1X OP2 HOP2 SING N N 5 E1X "O5'" "C5'" SING N N 6 E1X N9 C4 SING Y N 7 E1X N9 C8 SING Y N 8 E1X N9 "C1'" SING N N 9 E1X C4 N3 SING N N 10 E1X C4 C5 DOUB Y N 11 E1X N3 C2 SING N N 12 E1X N3 HN3 SING N N 13 E1X C2 O2 DOUB N N 14 E1X C2 N1 SING N N 15 E1X N1 C10 SING N N 16 E1X N1 C6 SING N N 17 E1X C10 C11 SING N N 18 E1X C10 H101 SING N N 19 E1X C10 H102 SING N N 20 E1X C11 H111 SING N N 21 E1X C11 H112 SING N N 22 E1X C11 H113 SING N N 23 E1X O6 C6 DOUB N N 24 E1X C6 C5 SING N N 25 E1X C5 N7 SING Y N 26 E1X N7 C8 DOUB Y N 27 E1X C8 H8 SING N N 28 E1X "C2'" "C1'" SING N N 29 E1X "C2'" "C3'" SING N N 30 E1X "C2'" "H2'" SING N N 31 E1X "C2'" "H2''" SING N N 32 E1X "C5'" "C4'" SING N N 33 E1X "C5'" "H5'" SING N N 34 E1X "C5'" "H5''" SING N N 35 E1X "C4'" "O4'" SING N N 36 E1X "C4'" "C3'" SING N N 37 E1X "C4'" "H4'" SING N N 38 E1X "O4'" "C1'" SING N N 39 E1X "C1'" "H1'" SING N N 40 E1X "C3'" "O3'" SING N N 41 E1X "C3'" H1 SING N N 42 E1X "O3'" "HO3'" SING N N 43 E1X OP3 HOP3 SING N N 44 # # 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 E1X SMILES ACDLabs 10.04 "O=C3Nc1c(ncn1C2OC(C(O)C2)COP(=O)(O)O)C(=O)N3CC" E1X SMILES_CANONICAL CACTVS 3.341 "CCN1C(=O)Nc2n(cnc2C1=O)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" E1X SMILES CACTVS 3.341 "CCN1C(=O)Nc2n(cnc2C1=O)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" E1X SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCN1C(=O)c2c(n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)NC1=O" E1X SMILES "OpenEye OEToolkits" 1.5.0 "CCN1C(=O)c2c(n(cn2)C3CC(C(O3)COP(=O)(O)O)O)NC1=O" E1X InChI InChI 1.03 "InChI=1S/C12H17N4O8P/c1-2-15-11(18)9-10(14-12(15)19)16(5-13-9)8-3-6(17)7(24-8)4-23-25(20,21)22/h5-8,17H,2-4H2,1H3,(H,14,19)(H2,20,21,22)/t6-,7+,8+/m0/s1" E1X InChIKey InChI 1.03 VFHMPVNUUSNVNO-XLPZGREQSA-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 E1X "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-1-ethylxanthosine 5'-(dihydrogen phosphate)" E1X "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(1-ethyl-2,6-dioxo-3H-purin-9-yl)-3-hydroxy-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 E1X "Create component" 2004-05-06 RCSB E1X "Modify descriptor" 2011-06-04 RCSB E1X "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id E1X _pdbx_chem_comp_synonyms.name "N1-ETHYL-2'-DEOXYXANTHOSINE 5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##