data_A1EFN # _chem_comp.id A1EFN _chem_comp.name "[(2R,3S,5R)-5-[6-azanylidene-1-(phenylmethyl)purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C17 H20 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-11-12 _chem_comp.pdbx_modified_date 2025-09-12 _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 421.344 _chem_comp.one_letter_code A _chem_comp.three_letter_code A1EFN _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 9KFV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1EFN C7 C1 C 0 1 Y N N N N N 5.689 -22.057 -6.786 -6.004 1.404 -0.431 C7 A1EFN 1 A1EFN C9 C2 C 0 1 Y N N N N N 4.970 -22.368 -7.957 -6.315 2.395 0.481 C9 A1EFN 2 A1EFN N1 N1 N 0 1 N N N N N N 7.935 -19.991 -5.318 -4.101 -1.145 -1.092 N1 A1EFN 3 A1EFN C2 C3 C 0 1 N N N N N N 8.473 -20.058 -6.563 -3.376 -0.414 -1.986 C2 A1EFN 4 A1EFN C10 C4 C 0 1 Y N N N N N 4.354 -21.327 -8.694 -6.509 2.074 1.812 C10 A1EFN 5 A1EFN C4 C5 C 0 1 Y N N N N N 10.464 -19.213 -5.668 -1.441 -0.668 -0.787 C4 A1EFN 6 A1EFN N3 N2 N 0 1 N N N N N N 9.758 -19.657 -6.724 -2.104 -0.146 -1.835 N3 A1EFN 7 A1EFN C6 C6 C 0 1 N N N N N N 8.612 -19.558 -4.274 -3.432 -2.042 -0.254 C6 A1EFN 8 A1EFN C1 C7 C 0 1 N N N N N N 6.551 -20.400 -5.058 -5.555 -0.990 -1.008 C1 A1EFN 9 A1EFN "C1'" C8 C 0 1 N N R N N N 12.467 -18.753 -6.653 0.827 0.422 -0.821 "C1'" A1EFN 10 A1EFN C11 C9 C 0 1 Y N N N N N 4.451 -19.982 -8.260 -6.393 0.761 2.230 C11 A1EFN 11 A1EFN C12 C10 C 0 1 Y N N N N N 5.155 -19.673 -7.084 -6.083 -0.230 1.318 C12 A1EFN 12 A1EFN "C2'" C11 C 0 1 N N N N N N 13.202 -17.434 -6.740 0.675 1.829 -0.203 "C2'" A1EFN 13 A1EFN C3 C12 C 0 1 Y N N N N N 5.783 -20.721 -6.356 -5.888 0.091 -0.013 C3 A1EFN 14 A1EFN "C3'" C13 C 0 1 N N S N N N 14.582 -17.809 -7.103 2.129 2.319 -0.021 "C3'" A1EFN 15 A1EFN "C4'" C14 C 0 1 N N R N N N 14.787 -19.132 -6.543 2.988 1.148 -0.550 "C4'" A1EFN 16 A1EFN C5 C15 C 0 1 Y N N N N N 9.902 -19.156 -4.422 -2.051 -1.622 0.043 C5 A1EFN 17 A1EFN "C5'" C16 C 0 1 N N N N N N 15.096 -18.887 -5.108 4.251 0.988 0.299 "C5'" A1EFN 18 A1EFN C8 C17 C 0 1 Y N N N N N 12.001 -18.458 -4.386 -0.062 -1.297 0.798 C8 A1EFN 19 A1EFN N6 N3 N 0 1 N N N N N N 7.934 -19.534 -2.973 -3.976 -3.138 0.219 N6 A1EFN 20 A1EFN N7 N4 N 0 1 Y N N N N N 10.932 -18.650 -3.542 -1.171 -1.965 0.985 N7 A1EFN 21 A1EFN N9 N5 N 0 1 Y N N N N N 11.605 -18.806 -5.497 -0.195 -0.482 -0.287 N9 A1EFN 22 A1EFN "O3'" O1 O 0 1 N N N N N N 14.673 -17.940 -8.533 2.361 3.499 -0.792 "O3'" A1EFN 23 A1EFN "O4'" O2 O 0 1 N N N N N N 13.490 -19.847 -6.651 2.144 -0.016 -0.421 "O4'" A1EFN 24 A1EFN "O5'" O3 O 0 1 N N N N N N 15.587 -20.073 -4.579 5.085 -0.020 -0.275 "O5'" A1EFN 25 A1EFN OP3 O4 O 0 1 N Y N N N N 17.984 -19.484 -3.667 7.223 -1.513 -0.614 OP1 A1EFN 26 A1EFN OP1 O5 O 0 1 N N N N N N 17.793 -20.055 -6.231 7.359 0.744 0.510 OP2 A1EFN 27 A1EFN P P1 P 0 1 N N N N N N 17.218 -20.230 -4.692 6.501 -0.452 0.359 P A1EFN 28 A1EFN OP2 O6 O 0 1 N N N N N N 17.454 -21.781 -4.359 6.259 -1.125 1.801 O1 A1EFN 29 A1EFN H1 H1 H 0 1 N N N N N N 6.167 -22.843 -6.220 -5.856 1.654 -1.471 H1 A1EFN 30 A1EFN H3 H2 H 0 1 N N N N N N 4.889 -23.392 -8.290 -6.405 3.420 0.155 H2 A1EFN 31 A1EFN H2 H3 H 0 1 N N N N N N 7.894 -20.420 -7.400 -3.878 -0.037 -2.865 H3 A1EFN 32 A1EFN H4 H4 H 0 1 N N N N N N 3.806 -21.561 -9.595 -6.751 2.848 2.524 H4 A1EFN 33 A1EFN H5 H5 H 0 1 N N N N N N 6.033 -19.584 -4.533 -5.949 -0.716 -1.987 H5 A1EFN 34 A1EFN H6 H6 H 0 1 N N N N N N 6.561 -21.297 -4.421 -6.003 -1.930 -0.686 H6 A1EFN 35 A1EFN "H1'" H7 H 0 1 N N N N N N 11.853 -18.860 -7.560 0.757 0.473 -1.907 H7 A1EFN 36 A1EFN H7 H8 H 0 1 N N N N N N 3.984 -19.194 -8.833 -6.544 0.510 3.270 H8 A1EFN 37 A1EFN H9 H9 H 0 1 N N N N N N 5.218 -18.652 -6.737 -5.992 -1.255 1.645 H9 A1EFN 38 A1EFN "H2'" H10 H 0 1 N N N N N N 13.182 -16.912 -5.772 0.133 2.488 -0.881 H10 A1EFN 39 A1EFN "H2''" H11 H 0 1 N N N N N N 12.757 -16.790 -7.513 0.166 1.771 0.760 H11 A1EFN 40 A1EFN "H3'" H12 H 0 1 N N N N N N 15.310 -17.084 -6.710 2.342 2.502 1.033 H12 A1EFN 41 A1EFN "H4'" H13 H 0 1 N N N N N N 15.598 -19.678 -7.047 3.252 1.314 -1.594 H13 A1EFN 42 A1EFN "H5'" H14 H 0 1 N N N N N N 15.852 -18.093 -5.017 4.791 1.934 0.328 H14 A1EFN 43 A1EFN "H5''" H15 H 0 1 N N N N N N 14.183 -18.587 -4.573 3.973 0.696 1.312 H15 A1EFN 44 A1EFN H8 H16 H 0 1 N N N N N N 12.980 -18.082 -4.128 0.823 -1.377 1.412 H16 A1EFN 45 A1EFN H61 H17 H 0 1 N N N N N N 8.531 -19.195 -2.246 -3.463 -3.724 0.798 H17 A1EFN 46 A1EFN "HO3'" H19 H 0 1 N N N N N N 15.560 -18.182 -8.774 1.804 4.248 -0.541 H19 A1EFN 47 A1EFN HOP3 H20 H 0 1 N Y N N N N 18.699 -19.017 -4.083 8.083 -1.817 -0.294 H20 A1EFN 48 A1EFN HOP2 H21 H 0 1 N N N N N N 17.855 -22.208 -5.107 5.704 -1.916 1.778 H21 A1EFN 49 # 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 A1EFN C10 C11 DOUB Y N 1 A1EFN C10 C9 SING Y N 2 A1EFN "O3'" "C3'" SING N N 3 A1EFN C11 C12 SING Y N 4 A1EFN C9 C7 DOUB Y N 5 A1EFN "C3'" "C2'" SING N N 6 A1EFN "C3'" "C4'" SING N N 7 A1EFN C12 C3 DOUB Y N 8 A1EFN C7 C3 SING Y N 9 A1EFN "C2'" "C1'" SING N N 10 A1EFN N3 C2 DOUB N N 11 A1EFN N3 C4 SING N N 12 A1EFN "C1'" "O4'" SING N N 13 A1EFN "C1'" N9 SING N N 14 A1EFN "O4'" "C4'" SING N N 15 A1EFN C2 N1 SING N N 16 A1EFN "C4'" "C5'" SING N N 17 A1EFN C3 C1 SING N N 18 A1EFN OP1 P DOUB N N 19 A1EFN C4 N9 SING Y N 20 A1EFN C4 C5 DOUB Y N 21 A1EFN N9 C8 SING Y N 22 A1EFN N1 C1 SING N N 23 A1EFN N1 C6 SING N N 24 A1EFN "C5'" "O5'" SING N N 25 A1EFN P "O5'" SING N N 26 A1EFN P OP3 SING N N 27 A1EFN C5 C6 SING N N 28 A1EFN C5 N7 SING Y N 29 A1EFN C8 N7 DOUB Y N 30 A1EFN C6 N6 DOUB N N 31 A1EFN P OP2 SING N N 32 A1EFN C7 H1 SING N N 33 A1EFN C9 H3 SING N N 34 A1EFN C2 H2 SING N N 35 A1EFN C10 H4 SING N N 36 A1EFN C1 H5 SING N N 37 A1EFN C1 H6 SING N N 38 A1EFN "C1'" "H1'" SING N N 39 A1EFN C11 H7 SING N N 40 A1EFN C12 H9 SING N N 41 A1EFN "C2'" "H2'" SING N N 42 A1EFN "C2'" "H2''" SING N N 43 A1EFN "C3'" "H3'" SING N N 44 A1EFN "C4'" "H4'" SING N N 45 A1EFN "C5'" "H5'" SING N N 46 A1EFN "C5'" "H5''" SING N N 47 A1EFN C8 H8 SING N N 48 A1EFN N6 H61 SING N N 49 A1EFN "O3'" "HO3'" SING N N 50 A1EFN OP3 HOP3 SING N N 51 A1EFN OP2 HOP2 SING N N 52 # 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 A1EFN InChI InChI 1.06 "InChI=1S/C17H20N5O6P/c18-16-15-17(20-9-21(16)7-11-4-2-1-3-5-11)22(10-19-15)14-6-12(23)13(28-14)8-27-29(24,25)26/h1-5,9-10,12-14,18,23H,6-8H2,(H2,24,25,26)/b18-16-/t12-,13+,14+/m0/s1" A1EFN InChIKey InChI 1.06 VOTNTSLRIQPLTA-IFMMWNIESA-N A1EFN SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=N)N(Cc4ccccc4)C=Nc23" A1EFN SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=N)N(Cc4ccccc4)C=Nc23" A1EFN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C\1/c2c(n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=CN1Cc4ccccc4" A1EFN SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CN2C=Nc3c(ncn3C4CC(C(O4)COP(=O)(O)O)O)C2=N" # _pdbx_chem_comp_identifier.comp_id A1EFN _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-[6-azanylidene-1-(phenylmethyl)purin-9-yl]-3-oxidanyl-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 A1EFN "Create component" 2024-11-12 PDBC A1EFN "Other modification" 2024-11-29 PDBC A1EFN "Initial release" 2025-09-17 RCSB #