data_OI3
# 
_chem_comp.id                                    OI3 
_chem_comp.name                                  
;2'-deoxyadenosine 5'-fluoro-diphosphoribose
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H22 F N5 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-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,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate; 2'-deoxy-2'-fluoro-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                        561.307 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OI3 
_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        8AZL 
_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 
OI3 "C4'"  C1  C 0 1 N N R N N N 19.869 -6.555  -8.155  2.726   1.873  0.777  "C4'"  OI3 1  
OI3 "C1'"  C2  C 0 1 N N R N N N 21.695 -5.094  -8.153  4.435   0.340  0.823  "C1'"  OI3 2  
OI3 C5     C3  C 0 1 Y N N N N N 22.524 -2.271  -6.083  6.635   -2.153 -0.678 C5     OI3 3  
OI3 C6     C4  C 0 1 Y N N N N N 22.400 -0.880  -5.904  7.707   -3.048 -0.523 C6     OI3 4  
OI3 "C2'"  C5  C 0 1 N N R N N N 22.256 -6.270  -8.111  5.156   1.707  0.844  "C2'"  OI3 5  
OI3 C3D    C6  C 0 1 N N S N N N 18.585 -10.718 0.409   -7.596  -2.022 -0.164 C3D    OI3 6  
OI3 C4D    C7  C 0 1 N N R N N N 19.184 -10.886 -0.734  -6.241  -1.442 0.286  C4D    OI3 7  
OI3 C5D    C8  C 0 1 N N N N N N 18.251 -10.684 -1.884  -5.596  -0.672 -0.868 C5D    OI3 8  
OI3 "C5'"  C9  C 0 1 N N N N N N 19.342 -7.349  -6.916  1.669   2.522  -0.118 "C5'"  OI3 9  
OI3 C8     C10 C 0 1 Y N N N N N 22.900 -4.417  -6.084  4.975   -0.906 -1.304 C8     OI3 10 
OI3 C2     C11 C 0 1 Y N N N N N 21.145 -0.748  -7.805  7.881   -2.403 1.687  C2     OI3 11 
OI3 C4     C12 C 0 1 Y N N N N N 21.916 -2.834  -7.181  6.236   -1.396 0.437  C4     OI3 12 
OI3 "C3'"  C13 C 0 1 N N R N N N 21.189 -7.178  -8.680  4.005   2.738  0.813  "C3'"  OI3 13 
OI3 C1D    C14 C 0 1 N N R N N N 20.517 -9.295  0.367   -7.715  -1.006 2.017  C1D    OI3 14 
OI3 C2D    C15 C 0 1 N N R N N N 19.031 -9.294  0.861   -8.618  -1.407 0.823  C2D    OI3 15 
OI3 F1     F1  F 0 1 N N N N N N 23.398 -6.367  -9.022  5.908   1.846  2.014  F1     OI3 16 
OI3 N9     N1  N 0 1 Y N N N N N 22.176 -4.155  -7.161  5.188   -0.620 0.012  N9     OI3 17 
OI3 N7     N2  N 0 1 Y N N N N N 23.114 -3.283  -5.425  5.828   -1.802 -1.708 N7     OI3 18 
OI3 N6     N3  N 0 1 N N N N N N 23.002 -0.208  -4.774  8.145   -3.819 -1.585 N6     OI3 19 
OI3 N1     N4  N 0 1 Y N N N N N 21.709 -0.157  -6.758  8.291   -3.136 0.668  N1     OI3 20 
OI3 N3     N5  N 0 1 Y N N N N N 21.227 -2.051  -8.017  6.881   -1.553 1.588  N3     OI3 21 
OI3 O3D    O1  O 0 1 N N N N N N 19.119 -11.755 1.331   -7.591  -3.447 -0.056 O3D    OI3 22 
OI3 O5D    O2  O 0 1 N N N N N N 18.922 -11.132 -3.027  -4.291  -0.238 -0.481 O5D    OI3 23 
OI3 O1B    O3  O 0 1 N N N N N N 17.138 -10.433 -4.737  -4.027  1.818  -1.921 O1B    OI3 24 
OI3 O2B    O4  O 0 1 N N N N N N 19.417 -11.096 -5.518  -2.913  -0.301 -2.719 O2B    OI3 25 
OI3 O3A    O5  O 0 1 N N N N N N 19.044 -8.812  -4.313  -1.994  1.032  -0.648 O3A    OI3 26 
OI3 O1A    O6  O 0 1 N N N N N N 20.587 -6.783  -4.182  -0.551  2.274  -2.304 O1A    OI3 27 
OI3 O2A    O7  O 0 1 N N N N N N 21.638 -9.066  -4.368  -1.428  3.580  -0.331 O2A    OI3 28 
OI3 "O5'"  O8  O 0 1 N N N N N N 20.424 -8.058  -6.394  0.456   1.769  -0.046 "O5'"  OI3 29 
OI3 "O4'"  O9  O 0 1 N N N N N N 20.139 -5.345  -7.819  3.151   0.610  0.220  "O4'"  OI3 30 
OI3 "O3'"  O10 O 0 1 N N N N N N 21.201 -7.103  -10.049 4.029   3.549  1.990  "O3'"  OI3 31 
OI3 O4D    O11 O 0 1 N N N N N N 20.414 -9.767  -0.826  -6.500  -0.551 1.383  O4D    OI3 32 
OI3 O1D    O12 O 0 1 N N N N N N 21.001 -7.968  0.309   -8.315  0.050  2.770  O1D    OI3 33 
OI3 O2D    O13 O 0 1 N N N N N N 18.981 -9.116  2.178   -9.589  -2.376 1.221  O2D    OI3 34 
OI3 PB     P1  P 0 1 N N N N N N 18.615 -10.387 -4.466  -3.322  0.604  -1.452 PB     OI3 35 
OI3 PA     P2  P 0 1 N N N N N N 20.486 -8.174  -4.775  -0.872  2.166  -0.864 PA     OI3 36 
OI3 "H'4"  H1  H 0 1 N N N N N N 19.113 -6.614  -8.952  2.335   1.732  1.785  "H'4"  OI3 37 
OI3 "H'1"  H2  H 0 1 N N N N N N 21.754 -4.642  -9.154  4.309   -0.037 1.837  "H'1"  OI3 38 
OI3 "H'2"  H3  H 0 1 N N N N N N 22.532 -6.594  -7.096  5.791   1.817  -0.035 "H'2"  OI3 39 
OI3 "HR'3" H4  H 0 0 N N N N N N 17.488 -10.768 0.353   -7.821  -1.717 -1.186 "HR'3" OI3 40 
OI3 "HR'4" H5  H 0 0 N N N N N N 19.646 -11.881 -0.816  -5.581  -2.248 0.608  "HR'4" OI3 41 
OI3 H5R1   H7  H 0 0 N N N N N N 17.330 -11.266 -1.732  -5.518  -1.321 -1.740 H5R1   OI3 42 
OI3 H5R2   H8  H 0 0 N N N N N N 17.999 -9.618  -1.985  -6.209  0.195  -1.114 H5R2   OI3 43 
OI3 "H5'1" H9  H 0 0 N N N N N N 18.947 -6.653  -6.161  1.484   3.542  0.219  "H5'1" OI3 44 
OI3 "H5'2" H10 H 0 0 N N N N N N 18.548 -8.045  -7.224  2.026   2.538  -1.148 "H5'2" OI3 45 
OI3 H8     H11 H 0 1 N N N N N N 23.258 -5.392  -5.789  4.213   -0.454 -1.921 H8     OI3 46 
OI3 H2     H12 H 0 1 N N N N N N 20.598 -0.141  -8.511  8.384   -2.506 2.637  H2     OI3 47 
OI3 "H'3"  H13 H 0 1 N N N N N N 21.305 -8.204  -8.302  4.072   3.358  -0.081 "H'3"  OI3 48 
OI3 "HR'2" H14 H 0 0 N N N N N N 18.461 -8.537  0.303   -9.099  -0.531 0.388  "HR'2" OI3 49 
OI3 H61    H15 H 0 1 N N N N N N 22.789 0.768   -4.814  7.711   -3.745 -2.449 H61    OI3 50 
OI3 H62    H16 H 0 1 N N N N N N 22.640 -0.594  -3.925  8.886   -4.433 -1.465 H62    OI3 51 
OI3 HOR3   H17 H 0 0 N N N N N N 18.705 -11.667 2.182   -8.420  -3.864 -0.326 HOR3   OI3 52 
OI3 HOB2   H18 H 0 0 N N N N N N 18.832 -11.452 -6.177  -2.446  -1.115 -2.487 HOB2   OI3 53 
OI3 HOA2   H19 H 0 0 N N N N N N 22.229 -8.583  -3.802  -1.660  3.583  0.608  HOA2   OI3 54 
OI3 "HO'3" H20 H 0 0 N N N N N N 22.006 -7.482  -10.380 4.811   4.113  2.063  "HO'3" OI3 55 
OI3 HOR1   H22 H 0 0 N N N N N N 21.902 -7.972  0.009   -7.791  0.340  3.529  HOR1   OI3 56 
OI3 HOR2   H23 H 0 0 N N N N N N 19.263 -8.234  2.390   -10.252 -2.038 1.839  HOR2   OI3 57 
OI3 "HR'1" H6  H 0 0 N N N N N N 21.125 -9.918  1.040   -7.516  -1.867 2.655  "HR'1" OI3 58 
# 
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 
OI3 "C4'" "C5'"  SING N N 1  
OI3 "C4'" "C3'"  SING N N 2  
OI3 "C4'" "O4'"  SING N N 3  
OI3 "C1'" "C2'"  SING N N 4  
OI3 "C1'" N9     SING N N 5  
OI3 "C1'" "O4'"  SING N N 6  
OI3 C5    C6     DOUB Y N 7  
OI3 C5    C4     SING Y N 8  
OI3 C5    N7     SING Y N 9  
OI3 C6    N6     SING N N 10 
OI3 C6    N1     SING Y N 11 
OI3 "C2'" "C3'"  SING N N 12 
OI3 "C2'" F1     SING N N 13 
OI3 C3D   C4D    SING N N 14 
OI3 C3D   C2D    SING N N 15 
OI3 C3D   O3D    SING N N 16 
OI3 C4D   C5D    SING N N 17 
OI3 C5D   O5D    SING N N 18 
OI3 "C5'" "O5'"  SING N N 19 
OI3 C8    N9     SING Y N 20 
OI3 C8    N7     DOUB Y N 21 
OI3 C2    N1     DOUB Y N 22 
OI3 C2    N3     SING Y N 23 
OI3 C4    N9     SING Y N 24 
OI3 C4    N3     DOUB Y N 25 
OI3 "C3'" "O3'"  SING N N 26 
OI3 C1D   C2D    SING N N 27 
OI3 C1D   O4D    SING N N 28 
OI3 C1D   O1D    SING N N 29 
OI3 C2D   O2D    SING N N 30 
OI3 O5D   PB     SING N N 31 
OI3 O1B   PB     DOUB N N 32 
OI3 O2B   PB     SING N N 33 
OI3 O3A   PB     SING N N 34 
OI3 O3A   PA     SING N N 35 
OI3 O1A   PA     DOUB N N 36 
OI3 O2A   PA     SING N N 37 
OI3 "O5'" PA     SING N N 38 
OI3 "C4'" "H'4"  SING N N 39 
OI3 "C1'" "H'1"  SING N N 40 
OI3 "C2'" "H'2"  SING N N 41 
OI3 C3D   "HR'3" SING N N 42 
OI3 C4D   "HR'4" SING N N 43 
OI3 C5D   H5R1   SING N N 44 
OI3 C5D   H5R2   SING N N 45 
OI3 "C5'" "H5'1" SING N N 46 
OI3 "C5'" "H5'2" SING N N 47 
OI3 C8    H8     SING N N 48 
OI3 C2    H2     SING N N 49 
OI3 "C3'" "H'3"  SING N N 50 
OI3 C2D   "HR'2" SING N N 51 
OI3 N6    H61    SING N N 52 
OI3 N6    H62    SING N N 53 
OI3 O3D   HOR3   SING N N 54 
OI3 O2B   HOB2   SING N N 55 
OI3 O2A   HOA2   SING N N 56 
OI3 "O3'" "HO'3" SING N N 57 
OI3 O1D   HOR1   SING N N 58 
OI3 O2D   HOR2   SING N N 59 
OI3 C4D   O4D    SING N N 60 
OI3 C1D   "HR'1" SING N N 61 
# 
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 
OI3 InChI            InChI                1.06    "InChI=1S/C15H22FN5O13P2/c16-7-9(22)5(32-14(7)21-4-20-8-12(17)18-3-19-13(8)21)1-30-35(26,27)34-36(28,29)31-2-6-10(23)11(24)15(25)33-6/h3-7,9-11,14-15,22-25H,1-2H2,(H,26,27)(H,28,29)(H2,17,18,19)/t5-,6-,7-,9-,10-,11-,14-,15-/m1/s1" 
OI3 InChIKey         InChI                1.06    DGMUNKKEZYJBEL-IUNVFAKASA-N                                                                                                                                                                                                            
OI3 SMILES_CANONICAL CACTVS               3.385   "Nc1ncnc2n(cnc12)[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]3F"                                                                                                                             
OI3 SMILES           CACTVS               3.385   "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3F"                                                                                                                                         
OI3 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)[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)F)N"                                                                                                                         
OI3 SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)F)N"                                                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           OI3 
_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~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-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 OI3 "[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-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 OI3 "[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"                         PDB    ? 
3 OI3 "2'-deoxy-2'-fluoro-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 
OI3 "Create component" 2022-09-08 PDBE 
OI3 "Initial release"  2024-03-20 RCSB 
# 
