data_08T # _chem_comp.id 08T _chem_comp.name "[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 Be F3 N5 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge -4 _chem_comp.pdbx_initial_date 2011-10-18 _chem_comp.pdbx_modified_date 2026-07-31 _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 492.201 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 08T _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3U5Z _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_comp_type "metal-containing ligand" _chem_comp.pdbx_pcm Y # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 08T PA PA P 0 1 N N N N N N 20.482 -45.143 41.309 3.910 1.042 2.111 PA 08T 1 08T PB PB P 0 1 N N N N N N 18.739 -45.192 43.437 6.427 0.846 0.582 PB 08T 2 08T BE BE BE 2 0 N N N N N N 16.182 -44.835 44.070 7.487 2.807 1.996 BE 08T 3 08T "C5'" "C5'" C 0 1 N N N N N N 20.843 -43.910 39.212 2.517 0.367 -0.008 "C5'" 08T 4 08T "O5'" "O5'" O 0 1 N N N N N N 21.142 -44.029 40.580 3.144 -0.059 1.236 "O5'" 08T 5 08T "C4'" "C4'" C 0 1 N N R N N N 21.491 -42.802 38.509 1.466 -0.642 -0.409 "C4'" 08T 6 08T "O4'" "O4'" O 0 1 N N N N N N 21.751 -41.720 39.322 0.475 -0.736 0.634 "O4'" 08T 7 08T "C3'" "C3'" C 0 1 N N S N N N 22.757 -43.294 38.062 0.658 -0.308 -1.668 "C3'" 08T 8 08T "O3'" "O3'" O 0 1 N N N N N N 22.820 -43.023 36.679 1.384 -0.732 -2.816 "O3'" 08T 9 08T "C2'" "C2'" C 0 1 N N R N N N 23.737 -42.594 38.767 -0.656 -1.076 -1.449 "C2'" 08T 10 08T "O2'" "O2'" O 0 1 N N N N N N 24.604 -41.959 37.820 -0.619 -2.384 -1.987 "O2'" 08T 11 08T "C1'" "C1'" C 0 1 N N R N N N 23.116 -41.579 39.631 -0.785 -1.109 0.081 "C1'" 08T 12 08T N1 N1 N 0 1 Y N N N N N 27.462 -41.899 41.537 -5.788 -0.623 1.121 N1 08T 13 08T O1A O1A O -1 1 N N N N N N 21.471 -46.025 42.096 4.558 0.360 3.260 O1A 08T 14 08T O1B O1B O 0 1 N N N N N N 18.182 -46.442 42.888 6.156 -0.645 0.577 O1B 08T 15 08T F1 F1 F -1 1 N N N N N N 16.174 -46.189 43.878 8.869 3.190 2.585 F1 08T 16 08T C2 C2 C 0 1 Y N N N N N 27.068 -41.681 40.282 -5.062 -1.629 0.621 C2 08T 17 08T O2A O2A O 0 1 N N N N N N 19.810 -45.998 40.264 3.011 2.182 2.425 O2A 08T 18 08T O2B O2B O -1 1 N N N N N N 19.772 -45.451 44.598 6.650 1.403 -0.811 O2B 08T 19 08T F2 F2 F -1 1 N N N N N N 15.415 -44.180 43.098 6.411 3.013 3.092 F2 08T 20 08T N3 N3 N 0 1 Y N N N N N 25.754 -41.634 39.970 -3.757 -1.683 0.377 N3 08T 21 08T O3A O3A O 0 1 N N N N N N 19.482 -44.428 42.331 5.072 1.545 1.130 O3A 08T 22 08T O3B O3B O -1 1 N N N N N N 17.521 -44.321 43.988 7.531 1.235 1.548 O3B 08T 23 08T F3 F3 F -1 1 N N N N N N 15.626 -44.519 45.314 7.189 3.742 0.794 F3 08T 24 08T C4 C4 C 0 1 Y N N N N N 24.688 -41.792 40.849 -3.156 -0.527 0.706 C4 08T 25 08T C5 C5 C 0 1 Y N N N N N 25.199 -42.021 42.160 -3.769 0.595 1.230 C5 08T 26 08T C6 C6 C 0 1 Y N N N N N 26.548 -42.068 42.479 -5.159 0.533 1.445 C6 08T 27 08T N6 N6 N 0 1 N N N N N N 26.942 -42.304 43.826 -5.877 1.540 1.944 N6 08T 28 08T N7 N7 N 0 1 Y N N N N N 24.211 -42.180 43.017 -2.840 1.603 1.446 N7 08T 29 08T C8 C8 C 0 1 Y N N N N N 23.069 -42.061 42.374 -1.705 1.077 1.053 C8 08T 30 08T N9 N9 N 0 1 Y N N N N N 23.277 -41.878 41.069 -1.822 -0.212 0.595 N9 08T 31 08T H1 H1 H 0 1 N N N N N N 19.756 -43.763 39.125 2.097 1.257 0.110 H1 08T 32 08T H2 H2 H 0 1 N N N N N N 21.164 -44.842 38.723 3.202 0.435 -0.722 H2 08T 33 08T H3 H3 H 0 1 N N N N N N 20.820 -42.466 37.704 1.911 -1.523 -0.519 H3 08T 34 08T H4 H4 H 0 1 N N N N N N 22.901 -44.371 38.231 0.472 0.666 -1.726 H4 08T 35 08T H5 H5 H 0 1 N N N N N N 23.648 -43.333 36.332 1.011 -0.460 -3.520 H5 08T 36 08T H6 H6 H 0 1 N N N N N N 24.307 -43.288 39.402 -1.412 -0.566 -1.837 H6 08T 37 08T H7 H7 H 0 1 N N N N N N 25.279 -41.476 38.282 -1.389 -2.726 -1.990 H7 08T 38 08T H8 H8 H 0 1 N N N N N N 23.556 -40.585 39.465 -0.996 -2.059 0.374 H8 08T 39 08T H9 H9 H 0 1 N N N N N N 21.445 -46.912 41.756 -2.724 1.017 2.924 H9 08T 40 08T H10 H10 H 0 1 N N N N N N 27.807 -41.541 39.507 -5.548 -2.414 0.411 H10 08T 41 08T H11 H11 H 0 1 N N N N N N 19.857 -46.386 44.744 -7.157 2.709 -0.006 H11 08T 42 08T H12 H12 H 0 1 N N N N N N 27.940 -42.311 43.885 -6.746 1.452 2.059 H12 08T 43 08T H13 H13 H 0 1 N N N N N N 26.579 -41.579 44.411 -5.482 2.297 2.160 H13 08T 44 08T H14 H14 H 0 1 N N N N N N 22.096 -42.105 42.840 -0.884 1.537 1.084 H14 08T 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 _chem_comp_bond.pdbx_metal_coordination_flag _chem_comp_bond.pdbx_metal_pi_flag 08T "O3'" "C3'" SING N N 1 N N 08T "O2'" "C2'" SING N N 2 N N 08T "C3'" "C4'" SING N N 3 N N 08T "C3'" "C2'" SING N N 4 N N 08T "C4'" "C5'" SING N N 5 N N 08T "C4'" "O4'" SING N N 6 N N 08T "C2'" "C1'" SING N N 7 N N 08T "C5'" "O5'" SING N N 8 N N 08T "O4'" "C1'" SING N N 9 N N 08T "C1'" N9 SING N N 10 N N 08T N3 C2 DOUB Y N 11 N N 08T N3 C4 SING Y N 12 N N 08T O2A PA DOUB N N 13 N N 08T C2 N1 SING Y N 14 N N 08T "O5'" PA SING N N 15 N N 08T C4 N9 SING Y N 16 N N 08T C4 C5 DOUB Y N 17 N N 08T N9 C8 SING Y N 18 N N 08T PA O1A SING N N 19 N N 08T PA O3A SING N N 20 N N 08T N1 C6 DOUB Y N 21 N N 08T C5 C6 SING Y N 22 N N 08T C5 N7 SING Y N 23 N N 08T O3A PB SING N N 24 N N 08T C8 N7 DOUB Y N 25 N N 08T C6 N6 SING N N 26 N N 08T O1B PB DOUB N N 27 N N 08T PB O3B SING N N 28 N N 08T PB O2B SING N N 29 N N 08T F1 BE SING N N 30 Y N 08T BE F3 SING N N 31 Y N 08T O3B BE SING N N 32 Y N 08T BE F2 SING N N 33 Y N 08T "C5'" H1 SING N N 34 N N 08T "C5'" H2 SING N N 35 N N 08T "C4'" H3 SING N N 36 N N 08T "C3'" H4 SING N N 37 N N 08T "O3'" H5 SING N N 38 N N 08T "C2'" H6 SING N N 39 N N 08T "O2'" H7 SING N N 40 N N 08T "C1'" H8 SING N N 41 N N 08T O1A H9 SING N N 42 N N 08T C2 H10 SING N N 43 N N 08T O2B H11 SING N N 44 N N 08T N6 H12 SING N N 45 N N 08T N6 H13 SING N N 46 N N 08T C8 H14 SING N N 47 N N # 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 08T InChI InChI 1.03 "InChI=1S/C10H15N5O10P2.Be.3FH/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20;;;;/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20);;3*1H/q;+4;;;/p-4/t4-,6-,7-,10-;;;;/m1..../s1" 08T InChIKey InChI 1.03 WOGYHYSOODLXII-KWIZKVQNSA-J 08T SMILES_CANONICAL CACTVS 3.370 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[Be](F)(F)F)[C@@H](O)[C@H]3O" 08T SMILES CACTVS 3.370 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[Be](F)(F)F)[CH](O)[CH]3O" 08T SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "[Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)(F)(F)F" 08T SMILES "OpenEye OEToolkits" 1.7.2 "[Be](OP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)(F)(F)F" # _pdbx_chem_comp_identifier.comp_id 08T _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.7.2 _pdbx_chem_comp_identifier.identifier "[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium" # loop_ _pdbx_chem_comp_atom_coordination.geometry_id _pdbx_chem_comp_atom_coordination.comp_id _pdbx_chem_comp_atom_coordination.atom_id _pdbx_chem_comp_atom_coordination.number _pdbx_chem_comp_atom_coordination.geometry_calculated _pdbx_chem_comp_atom_coordination.geometry_generic _pdbx_chem_comp_atom_coordination.geometry_abbr _pdbx_chem_comp_atom_coordination.provenance _pdbx_chem_comp_atom_coordination.representative_entry_id 1 08T BE 4 tetrahedron tetrahedral TET FindGeo 8EAL 1 08T BE 4 tetrahedral tetrahedral TET MetalCoord 8EAL # _pdbx_chem_comp_atom_coordination_sphere.id 1 _pdbx_chem_comp_atom_coordination_sphere.geometry_id 1 _pdbx_chem_comp_atom_coordination_sphere.comp_id 08T _pdbx_chem_comp_atom_coordination_sphere.atom_id BE _pdbx_chem_comp_atom_coordination_sphere.descriptor "@TET{Be,F,F,F,O}" _pdbx_chem_comp_atom_coordination_sphere.provenance MetalCoord _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 8EAL # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession _pdbx_chem_comp_pcm.position 1 08T ARG None "Metal coordination" "Any position" BE NH1 ? ? "Amino-acid side chain" 2 08T ARG None "Metal coordination" "Any position" BE NH2 ? ? "Amino-acid side chain" 3 08T GLU None "Metal coordination" "Any position" BE OE2 ? ? "Amino-acid side chain" 4 08T SER None "Metal coordination" "Any position" BE OG ? ? "Amino-acid side chain" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 08T "Create component" 2011-10-18 RCSB 08T "Other modification" 2026-07-17 RCSB 08T "Other modification" 2026-07-31 RCSB #