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 0
_chem_comp.pdbx_initial_date 2011-10-18
_chem_comp.pdbx_modified_date 2011-12-30
_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 Corina
_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
#
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 2.264 -0.984 -0.942 PA 08T 1
08T PB PB P 0 1 N N N N N N 18.739 -45.192 43.437 4.823 0.346 -0.257 PB 08T 2
08T BE BE BE 0 0 N N N N N N 16.182 -44.835 44.070 6.712 1.379 1.127 BE 08T 3
08T "C5'" "C5'" C 0 1 N N N N N N 20.843 -43.910 39.212 -0.157 -2.027 -0.508 "C5'" 08T 4
08T "O5'" "O5'" O 0 1 N N N N N N 21.142 -44.029 40.580 0.883 -1.125 -0.127 "O5'" 08T 5
08T "C4'" "C4'" C 0 1 N N R N N N 21.491 -42.802 38.509 -1.322 -1.908 0.477 "C4'" 08T 6
08T "O4'" "O4'" O 0 1 N N N N N N 21.751 -41.720 39.322 -1.930 -0.610 0.361 "O4'" 08T 7
08T "C3'" "C3'" C 0 1 N N S N N N 22.757 -43.294 38.062 -2.404 -2.952 0.139 "C3'" 08T 8
08T "O3'" "O3'" O 0 1 N N N N N N 22.820 -43.023 36.679 -2.608 -3.837 1.242 "O3'" 08T 9
08T "C2'" "C2'" C 0 1 N N R N N N 23.737 -42.594 38.767 -3.676 -2.109 -0.123 "C2'" 08T 10
08T "O2'" "O2'" O 0 1 N N N N N N 24.604 -41.959 37.820 -4.827 -2.732 0.452 "O2'" 08T 11
08T "C1'" "C1'" C 0 1 N N R N N N 23.116 -41.579 39.631 -3.342 -0.783 0.606 "C1'" 08T 12
08T N1 N1 N 0 1 Y N N N N N 27.462 -41.899 41.537 -7.721 2.008 0.733 N1 08T 13
08T O1A O1A O 0 1 N N N N N N 21.471 -46.025 42.096 1.962 -0.403 -2.413 O1A 08T 14
08T O1B O1B O 0 1 N N N N N N 18.182 -46.442 42.888 5.574 -0.913 -0.463 O1B 08T 15
08T F1 F1 F 0 1 N N N N N N 16.174 -46.189 43.878 7.031 1.975 2.342 F1 08T 16
08T C2 C2 C 0 1 Y N N N N N 27.068 -41.681 40.282 -7.372 0.984 1.490 C2 08T 17
08T O2A O2A O 0 1 N N N N N N 19.810 -45.998 40.264 2.906 -2.312 -1.058 O2A 08T 18
08T O2B O2B O 0 1 N N N N N N 19.772 -45.451 44.598 5.091 1.339 -1.495 O2B 08T 19
08T F2 F2 F 0 1 N N N N N N 15.415 -44.180 43.098 7.466 0.222 0.966 F2 08T 20
08T N3 N3 N 0 1 Y N N N N N 25.754 -41.634 39.970 -6.221 0.361 1.350 N3 08T 21
08T O3A O3A O 0 1 N N N N N N 19.482 -44.428 42.331 3.249 0.022 -0.160 O3A 08T 22
08T O3B O3B O 0 1 N N N N N N 17.521 -44.321 43.988 5.312 1.046 1.108 O3B 08T 23
08T F3 F3 F 0 1 N N N N N N 15.626 -44.519 45.314 6.992 2.262 0.090 F3 08T 24
08T C4 C4 C 0 1 Y N N N N N 24.688 -41.792 40.849 -5.350 0.748 0.424 C4 08T 25
08T C5 C5 C 0 1 Y N N N N N 25.199 -42.021 42.160 -5.674 1.833 -0.407 C5 08T 26
08T C6 C6 C 0 1 Y N N N N N 26.548 -42.068 42.479 -6.915 2.466 -0.219 C6 08T 27
08T N6 N6 N 0 1 N N N N N N 26.942 -42.304 43.826 -7.288 3.540 -1.008 N6 08T 28
08T N7 N7 N 0 1 Y N N N N N 24.211 -42.180 43.017 -4.629 2.016 -1.249 N7 08T 29
08T C8 C8 C 0 1 Y N N N N N 23.069 -42.061 42.374 -3.707 1.134 -0.994 C8 08T 30
08T N9 N9 N 0 1 Y N N N N N 23.277 -41.878 41.069 -4.105 0.328 0.030 N9 08T 31
08T H1 H1 H 0 1 N N N N N N 19.756 -43.763 39.125 -0.503 -1.780 -1.511 H1 08T 32
08T H2 H2 H 0 1 N N N N N N 21.164 -44.842 38.723 0.225 -3.048 -0.497 H2 08T 33
08T H3 H3 H 0 1 N N N N N N 20.820 -42.466 37.704 -0.963 -2.060 1.495 H3 08T 34
08T H4 H4 H 0 1 N N N N N N 22.901 -44.371 38.231 -2.127 -3.512 -0.755 H4 08T 35
08T H5 H5 H 0 1 N N N N N N 23.648 -43.333 36.332 -3.279 -4.515 1.084 H5 08T 36
08T H6 H6 H 0 1 N N N N N N 24.307 -43.288 39.402 -3.819 -1.942 -1.191 H6 08T 37
08T H7 H7 H 0 1 N N N N N N 25.279 -41.476 38.282 -5.023 -3.607 0.090 H7 08T 38
08T H8 H8 H 0 1 N N N N N N 23.556 -40.585 39.465 -3.539 -0.872 1.674 H8 08T 39
08T H9 H9 H 0 1 N N N N N N 21.445 -46.912 41.756 1.540 0.467 -2.414 H9 08T 40
08T H10 H10 H 0 1 N N N N N N 27.807 -41.541 39.507 -8.058 0.644 2.252 H10 08T 41
08T H11 H11 H 0 1 N N N N N N 19.857 -46.386 44.744 4.629 2.186 -1.427 H11 08T 42
08T H12 H12 H 0 1 N N N N N N 27.940 -42.311 43.885 -8.148 3.968 -0.869 H12 08T 43
08T H13 H13 H 0 1 N N N N N N 26.579 -41.579 44.411 -6.691 3.865 -1.700 H13 08T 44
08T H14 H14 H 0 1 N N N N N N 22.096 -42.105 42.840 -2.766 1.052 -1.518 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
08T "O3'" "C3'" SING N N 1
08T "O2'" "C2'" SING N N 2
08T "C3'" "C4'" SING N N 3
08T "C3'" "C2'" SING N N 4
08T "C4'" "C5'" SING N N 5
08T "C4'" "O4'" SING N N 6
08T "C2'" "C1'" SING N N 7
08T "C5'" "O5'" SING N N 8
08T "O4'" "C1'" SING N N 9
08T "C1'" N9 SING N N 10
08T N3 C2 DOUB Y N 11
08T N3 C4 SING Y N 12
08T O2A PA DOUB N N 13
08T C2 N1 SING Y N 14
08T "O5'" PA SING N N 15
08T C4 N9 SING Y N 16
08T C4 C5 DOUB Y N 17
08T N9 C8 SING Y N 18
08T PA O1A SING N N 19
08T PA O3A SING N N 20
08T N1 C6 DOUB Y N 21
08T C5 C6 SING Y N 22
08T C5 N7 SING Y N 23
08T O3A PB SING N N 24
08T C8 N7 DOUB Y N 25
08T C6 N6 SING N N 26
08T O1B PB DOUB N N 27
08T PB O3B SING N N 28
08T PB O2B SING N N 29
08T F1 BE SING N N 30
08T BE F3 SING N N 31
08T O3B BE SING N N 32
08T BE F2 SING N N 33
08T "C5'" H1 SING N N 34
08T "C5'" H2 SING N N 35
08T "C4'" H3 SING N N 36
08T "C3'" H4 SING N N 37
08T "O3'" H5 SING N N 38
08T "C2'" H6 SING N N 39
08T "O2'" H7 SING N N 40
08T "C1'" H8 SING N N 41
08T O1A H9 SING N N 42
08T C2 H10 SING N N 43
08T O2B H11 SING N N 44
08T N6 H12 SING N N 45
08T N6 H13 SING N N 46
08T C8 H14 SING N N 47
#
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"
#
_pdbx_chem_comp_audit.comp_id 08T
_pdbx_chem_comp_audit.action_type 'Create component'
_pdbx_chem_comp_audit.date 2011-10-18
_pdbx_chem_comp_audit.processing_site RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
08T PA P -1.961 2.826 1
08T PB P -4.274 4.441 2
08T BE Be -5.621 6.592 3
08T "C5'" C -1.029 0.296 4
08T "O5'" O -0.862 1.746 5
08T "C4'" C 0.256 -0.580 6
08T "O4'" O 0.260 -2.083 7
08T "C3'" C 1.682 -0.118 8
08T "O3'" O 2.142 1.312 9
08T "C2'" C 2.570 -1.327 10
08T "O2'" O 4.068 -1.324 11
08T "C1'" C 1.688 -2.540 12
08T N1 N 6.180 -5.928 13
08T O1A O -3.140 1.865 14
08T O1B O -3.817 5.857 15
08T F1 F -7.114 6.671 16
08T C2 C 6.175 -4.428 17
08T O2A O -0.813 3.758 18
08T O2B O -4.761 3.009 19
08T F2 F -4.283 7.290 20
08T N3 N 4.876 -3.679 21
08T O3A O -2.784 4.122 22
08T O3B O -5.640 5.045 23
08T F3 F -6.292 7.941 24
08T C4 C 3.576 -4.432 25
08T C5 C 3.581 -5.932 26
08T C6 C 4.879 -6.678 27
08T N6 N 4.882 -8.179 28
08T N7 N 2.153 -6.394 29
08T C8 C 1.268 -5.185 30
08T N9 N 2.152 -3.967 31
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
08T "O3'" "C3'" SINGLE NONE 1
08T "O2'" "C2'" SINGLE NONE 2
08T "C3'" "C4'" SINGLE NONE 3
08T "C3'" "C2'" SINGLE NONE 4
08T "C4'" "C5'" SINGLE NONE 5
08T "C4'" "O4'" SINGLE NONE 6
08T "C2'" "C1'" SINGLE NONE 7
08T "C5'" "O5'" SINGLE NONE 8
08T "O4'" "C1'" SINGLE NONE 9
08T "C1'" N9 SINGLE NONE 10
08T N3 C2 DOUBLE NONE 11
08T N3 C4 SINGLE NONE 12
08T O2A PA DOUBLE NONE 13
08T C2 N1 SINGLE NONE 14
08T "O5'" PA SINGLE NONE 15
08T C4 N9 SINGLE NONE 16
08T C4 C5 DOUBLE NONE 17
08T N9 C8 SINGLE NONE 18
08T PA O1A SINGLE NONE 19
08T PA O3A SINGLE NONE 20
08T N1 C6 DOUBLE NONE 21
08T C5 C6 SINGLE NONE 22
08T C5 N7 SINGLE NONE 23
08T O3A PB SINGLE NONE 24
08T C8 N7 DOUBLE NONE 25
08T C6 N6 SINGLE NONE 26
08T O1B PB DOUBLE NONE 27
08T PB O3B SINGLE NONE 28
08T PB O2B SINGLE NONE 29
08T F1 BE SINGLE NONE 30
08T BE F3 SINGLE NONE 31
08T O3B BE SINGLE NONE 32
08T BE F2 SINGLE NONE 33
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
08T phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
08T ribose F2 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
08T "O5'" F1 1
08T PA F1 1
08T O2A F1 1
08T O1A F1 1
08T O3A F1 1
08T O2B F1 2
08T PB F1 2
08T O1B F1 2
08T O3A F1 2
08T O3B F1 2
08T "C2'" F2 1
08T "C3'" F2 1
08T "C4'" F2 1
08T "O4'" F2 1
08T "C1'" F2 1
08T "C5'" F2 1
08T "O5'" F2 1
08T "O3'" F2 1
08T "O2'" F2 1
#
#