data_OI6 # _chem_comp.id OI6 _chem_comp.name ;8-bromoadenosine 5'-diphosphoribose ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H22 Br N5 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate; [[(2R,3S,4R,5R)-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate; 8Br-ADPR" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-09-07 _chem_comp.pdbx_modified_date 2024-03-15 _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 638.212 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OI6 _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 8AZM _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 OI6 "C4'" C1 C 0 1 N N R N N N -20.251 -6.660 8.142 2.276 -1.668 -1.417 "C4'" OI6 1 OI6 "C1'" C2 C 0 1 N N R N N N -21.796 -4.825 8.059 3.872 -0.026 -1.251 "C1'" OI6 2 OI6 C2 C3 C 0 1 Y N N N N N -21.095 -0.538 7.930 6.199 3.783 -1.719 C2 OI6 3 OI6 C3D C4 C 0 1 N N S N N N -18.676 -10.793 -0.577 -8.029 1.576 0.828 C3D OI6 4 OI6 C4D C5 C 0 1 N N R N N N -19.276 -10.985 0.542 -6.562 1.357 0.407 C4D OI6 5 OI6 C5D C6 C 0 1 N N N N N N -18.402 -10.701 1.768 -6.205 -0.126 0.521 C5D OI6 6 OI6 "C5'" C7 C 0 1 N N N N N N -19.708 -7.384 6.970 1.303 -2.534 -0.614 "C5'" OI6 7 OI6 C4 C8 C 0 1 Y N N N N N -22.005 -2.541 7.199 5.263 1.994 -0.623 C4 OI6 8 OI6 C6 C9 C 0 1 Y N N N N N -22.457 -0.496 6.067 6.532 3.667 0.562 C6 OI6 9 OI6 C5 C10 C 0 1 Y N N N N N -22.632 -1.879 6.178 5.785 2.477 0.589 C5 OI6 10 OI6 C8 C11 C 0 1 Y N N N N N -23.127 -3.984 6.053 4.706 0.648 1.034 C8 OI6 11 OI6 "C2'" C12 C 0 1 N N R N N N -22.527 -6.292 8.109 4.683 -1.312 -1.523 "C2'" OI6 12 OI6 "C3'" C13 C 0 1 N N S N N N -21.421 -7.202 8.615 3.609 -2.417 -1.634 "C3'" OI6 13 OI6 C1D C14 C 0 1 N N R N N N -20.571 -9.273 -0.497 -7.464 2.780 -1.181 C1D OI6 14 OI6 C2D C15 C 0 1 N N R N N N -19.124 -9.357 -1.049 -8.689 2.214 -0.419 C2D OI6 15 OI6 N9 N1 N 0 1 Y N N N N N -22.330 -3.857 7.111 4.588 0.840 -0.311 N9 OI6 16 OI6 N3 N2 N 0 1 Y N N N N N -21.230 -1.854 8.067 5.493 2.673 -1.742 N3 OI6 17 OI6 N1 N3 N 0 1 Y N N N N N -21.680 0.128 6.961 6.710 4.277 -0.605 N1 OI6 18 OI6 N6 N4 N 0 1 N N N N N N -23.105 0.222 5.003 7.071 4.191 1.724 N6 OI6 19 OI6 N7 N5 N 0 1 Y N N N N N -23.308 -2.789 5.478 5.409 1.610 1.560 N7 OI6 20 OI6 O3D O1 O 0 1 N N N N N N -19.154 -11.804 -1.552 -8.102 2.465 1.944 O3D OI6 21 OI6 O5D O2 O 0 1 N N N N N N -19.157 -11.060 2.884 -4.814 -0.303 0.242 O5D OI6 22 OI6 O1B O3 O 0 1 N N N N N N -19.505 -11.082 5.530 -4.323 -2.385 1.582 O1B OI6 23 OI6 O2B O4 O 0 1 N N N N N N -17.186 -10.541 4.606 -4.695 -2.669 -0.898 O2B OI6 24 OI6 O3A O5 O 0 1 N N N N N N -19.046 -8.807 4.394 -2.509 -1.550 0.039 O3A OI6 25 OI6 O1A O6 O 0 1 N N N N N N -21.602 -9.068 4.033 -1.514 -3.848 -0.283 O1A OI6 26 OI6 O2A O7 O 0 1 N N N N N N -20.580 -6.815 3.806 -0.891 -2.605 1.823 O2A OI6 27 OI6 "O5'" O8 O 0 1 N N N N N N -20.790 -7.870 6.184 0.039 -1.873 -0.525 "O5'" OI6 28 OI6 "O4'" O9 O 0 1 N N N N N N -20.572 -5.066 7.730 2.634 -0.487 -0.667 "O4'" OI6 29 OI6 "O2'" O10 O 0 1 N N N N N N -23.554 -6.293 8.942 5.411 -1.196 -2.747 "O2'" OI6 30 OI6 "O3'" O11 O 0 1 N N N N N N -21.457 -7.133 10.068 3.641 -3.017 -2.931 "O3'" OI6 31 OI6 O4D O12 O 0 1 N N N N N N -20.575 -9.945 0.605 -6.441 1.786 -0.959 O4D OI6 32 OI6 O1D O13 O 0 1 N N N N N N -20.890 -7.916 -0.205 -7.753 2.902 -2.576 O1D OI6 33 OI6 O2D O14 O 0 1 N N N N N N -19.134 -9.231 -2.372 -9.584 3.263 -0.041 O2D OI6 34 OI6 PB P1 P 0 1 N N N N N N -18.720 -10.400 4.426 -4.090 -1.741 0.270 PB OI6 35 OI6 PA P2 P 0 1 N N N N N N -20.561 -8.135 4.541 -1.225 -2.499 0.252 PA OI6 36 OI6 BR28 BR1 BR 0 0 N N N N N N -23.966 -5.552 5.334 3.958 -0.800 1.993 BR28 OI6 37 OI6 "H'4" H1 H 0 1 N N N N N N -19.488 -6.635 8.934 1.835 -1.392 -2.375 "H'4" OI6 38 OI6 "H'1" H3 H 0 1 N N N N N N -21.863 -4.404 9.073 3.679 0.505 -2.183 "H'1" OI6 39 OI6 H2 H4 H 0 1 N N N N N N -20.484 0.001 8.639 6.372 4.309 -2.647 H2 OI6 40 OI6 "HR'3" H5 H 0 0 N N N N N N -17.579 -10.822 -0.502 -8.504 0.624 1.066 "HR'3" OI6 41 OI6 "HR'4" H6 H 0 0 N N N N N N -19.678 -12.005 0.629 -5.903 1.947 1.044 "HR'4" OI6 42 OI6 H5R1 H8 H 0 0 N N N N N N -17.480 -11.299 1.724 -6.420 -0.476 1.530 H5R1 OI6 43 OI6 H5R2 H9 H 0 0 N N N N N N -18.144 -9.633 1.811 -6.794 -0.698 -0.196 H5R2 OI6 44 OI6 "H5'1" H10 H 0 0 N N N N N N -19.092 -6.701 6.367 1.175 -3.495 -1.113 "H5'1" OI6 45 OI6 "H5'2" H11 H 0 0 N N N N N N -19.092 -8.229 7.311 1.701 -2.695 0.387 "H5'2" OI6 46 OI6 "H'2" H12 H 0 1 N N N N N N -22.805 -6.576 7.083 5.359 -1.519 -0.693 "H'2" OI6 47 OI6 "H'3" H13 H 0 1 N N N N N N -21.582 -8.231 8.261 3.754 -3.171 -0.860 "H'3" OI6 48 OI6 "HR'2" H14 H 0 0 N N N N N N -18.497 -8.602 -0.552 -9.205 1.461 -1.015 "HR'2" OI6 49 OI6 H61 H15 H 0 1 N N N N N N -22.874 1.193 5.067 6.934 3.737 2.570 H61 OI6 50 OI6 H62 H16 H 0 1 N N N N N N -22.796 -0.137 4.122 7.585 5.013 1.692 H62 OI6 51 OI6 HOR3 H17 H 0 0 N N N N N N -18.717 -11.672 -2.385 -9.003 2.639 2.250 HOR3 OI6 52 OI6 HOB2 H18 H 0 0 N N N N N N -17.004 -11.041 5.393 -4.578 -2.308 -1.787 HOB2 OI6 53 OI6 HOA2 H19 H 0 0 N N N N N N -21.264 -6.829 3.147 -0.691 -1.756 2.241 HOA2 OI6 54 OI6 "HO'2" H21 H 0 0 N N N N N N -23.956 -7.154 8.949 5.939 -1.976 -2.966 "HO'2" OI6 55 OI6 "HO'3" H22 H 0 0 N N N N N N -22.270 -7.510 10.383 4.456 -3.501 -3.120 "HO'3" OI6 56 OI6 HOR1 H24 H 0 0 N N N N N N -21.776 -7.864 0.133 -7.019 3.252 -3.100 HOR1 OI6 57 OI6 HOR2 H25 H 0 0 N N N N N N -19.409 -8.352 -2.605 -10.022 3.693 -0.787 HOR2 OI6 58 OI6 "HR'1" H2 H 0 0 N N N N N N -21.263 -9.681 -1.249 -7.163 3.741 -0.765 "HR'1" OI6 59 # 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 OI6 "C4'" "C5'" SING N N 1 OI6 "C4'" "C3'" SING N N 2 OI6 "C1'" "C2'" SING N N 3 OI6 "C1'" N9 SING N N 4 OI6 "C1'" "O4'" SING N N 5 OI6 C2 N3 DOUB Y N 6 OI6 C2 N1 SING Y N 7 OI6 C3D C4D SING N N 8 OI6 C3D C2D SING N N 9 OI6 C3D O3D SING N N 10 OI6 C4D C5D SING N N 11 OI6 C5D O5D SING N N 12 OI6 "C5'" "O5'" SING N N 13 OI6 C4 C5 DOUB Y N 14 OI6 C4 N9 SING Y N 15 OI6 C4 N3 SING Y N 16 OI6 C6 C5 SING Y N 17 OI6 C6 N1 DOUB Y N 18 OI6 C6 N6 SING N N 19 OI6 C5 N7 SING Y N 20 OI6 C8 N9 SING Y N 21 OI6 C8 N7 DOUB Y N 22 OI6 C8 BR28 SING N N 23 OI6 "C2'" "C3'" SING N N 24 OI6 "C2'" "O2'" SING N N 25 OI6 "C3'" "O3'" SING N N 26 OI6 C1D C2D SING N N 27 OI6 C1D O4D SING N N 28 OI6 C1D O1D SING N N 29 OI6 C2D O2D SING N N 30 OI6 O5D PB SING N N 31 OI6 O1B PB DOUB N N 32 OI6 O2B PB SING N N 33 OI6 O3A PB SING N N 34 OI6 O3A PA SING N N 35 OI6 O1A PA DOUB N N 36 OI6 O2A PA SING N N 37 OI6 "O5'" PA SING N N 38 OI6 "C4'" "H'4" SING N N 39 OI6 "C1'" "H'1" SING N N 40 OI6 C2 H2 SING N N 41 OI6 C3D "HR'3" SING N N 42 OI6 C4D "HR'4" SING N N 43 OI6 C5D H5R1 SING N N 44 OI6 C5D H5R2 SING N N 45 OI6 "C5'" "H5'1" SING N N 46 OI6 "C5'" "H5'2" SING N N 47 OI6 "C2'" "H'2" SING N N 48 OI6 "C3'" "H'3" SING N N 49 OI6 C2D "HR'2" SING N N 50 OI6 N6 H61 SING N N 51 OI6 N6 H62 SING N N 52 OI6 O3D HOR3 SING N N 53 OI6 O2B HOB2 SING N N 54 OI6 O2A HOA2 SING N N 55 OI6 "O2'" "HO'2" SING N N 56 OI6 "O3'" "HO'3" SING N N 57 OI6 O1D HOR1 SING N N 58 OI6 O2D HOR2 SING N N 59 OI6 "C4'" "O4'" SING N N 60 OI6 C4D O4D SING N N 61 OI6 C1D "HR'1" SING N N 62 # 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 OI6 InChI InChI 1.06 "InChI=1S/C15H22BrN5O14P2/c16-15-20-6-11(17)18-3-19-12(6)21(15)13-9(24)7(22)4(33-13)1-31-36(27,28)35-37(29,30)32-2-5-8(23)10(25)14(26)34-5/h3-5,7-10,13-14,22-26H,1-2H2,(H,27,28)(H,29,30)(H2,17,18,19)/t4-,5-,7-,8-,9-,10-,13-,14-/m1/s1" OI6 InChIKey InChI 1.06 DPZGAPGUTMHLAW-AIKIOGRUSA-N OI6 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O)c(Br)nc12" OI6 SMILES CACTVS 3.385 "Nc1ncnc2n([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O)c(Br)nc12" OI6 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(c(n2)Br)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N" OI6 SMILES "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(c(n2)Br)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N" # _pdbx_chem_comp_identifier.comp_id OI6 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 OI6 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" PDB ? 2 OI6 "[[(2R,3S,4R,5R)-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" PDB ? 3 OI6 8Br-ADPR AUTHOR ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site OI6 "Create component" 2022-09-08 PDBE OI6 "Initial release" 2024-03-20 RCSB #