data_AVU # _chem_comp.id AVU _chem_comp.name ;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H22 F N5 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;arabinosyl-2-fluoro-deoxy-adenosine diphosphate ribose, ara-2'F-ADPR ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-07-14 _chem_comp.pdbx_modified_date 2024-09-27 _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 545.307 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AVU _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 3I9M _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 AVU N1 N1 N 0 1 Y N N N N N 1.677 -4.374 5.236 -7.380 -3.716 -0.370 N1 AVU 1 AVU C2 C2 C 0 1 Y N N N N N 2.989 -4.535 5.471 -7.171 -2.907 -1.393 C2 AVU 2 AVU N3 N3 N 0 1 Y N N N N N 3.911 -3.792 4.829 -6.312 -1.911 -1.342 N3 AVU 3 AVU C4 C4 C 0 1 Y N N N N N 3.483 -2.806 3.981 -5.611 -1.677 -0.237 C4 AVU 4 AVU C5 C5 C 0 1 Y N N N N N 2.135 -2.595 3.725 -5.798 -2.509 0.879 C5 AVU 5 AVU C6 C6 C 0 1 Y N N N N N 1.213 -3.388 4.404 -6.726 -3.560 0.775 C6 AVU 6 AVU N6 N6 N 0 1 N N N N N N -0.121 -3.205 4.192 -6.952 -4.412 1.842 N6 AVU 7 AVU N7 N7 N 0 1 Y N N N N N 2.020 -1.552 2.848 -4.973 -2.059 1.855 N7 AVU 8 AVU C8 C8 C 0 1 Y N N N N N 3.276 -1.179 2.563 -4.308 -1.029 1.419 C8 AVU 9 AVU N9 N9 N 0 1 Y N N N N N 4.164 -1.971 3.230 -4.666 -0.754 0.133 N9 AVU 10 AVU PA PA P 0 1 N N N N N N 7.186 3.590 4.762 1.066 2.748 0.483 PA AVU 11 AVU PB PB P 0 1 N N N N N N 4.547 4.767 4.255 3.741 1.491 0.704 PB AVU 12 AVU "C1'" "C1'" C 0 1 N N R N N N 5.644 -1.939 3.287 -4.139 0.329 -0.701 "C1'" AVU 13 AVU O1A O1A O 0 1 N N N N N N 8.287 4.363 4.128 0.907 2.753 1.954 O1A AVU 14 AVU O1B O1B O 0 1 N N N N N N 4.979 6.207 4.217 3.627 1.345 2.172 O1B AVU 15 AVU C1R C1R C 0 1 N N N N N N 2.718 2.918 -0.682 6.893 -2.533 -2.193 C1R AVU 16 AVU "C2'" "C2'" C 0 1 N N R N N N 6.294 -1.348 2.050 -5.018 1.592 -0.563 "C2'" AVU 17 AVU "O2'" "O2'" O 0 1 N N N N N N 7.456 -2.158 1.818 -5.935 1.685 -1.656 "O2'" AVU 18 AVU O2A O2A O 0 1 N N N N N N 6.938 3.826 6.222 1.378 4.243 -0.028 O2A AVU 19 AVU O2B O2B O 0 1 N N N N N N 3.743 4.202 5.378 4.724 2.719 0.362 O2B AVU 20 AVU C2R C2R C 0 1 N N R N N N 2.141 1.600 -0.136 7.561 -3.252 -1.006 C2R AVU 21 AVU F2R F2R F 0 1 N N N N N N 3.257 0.778 -0.002 8.953 -3.215 -1.131 F2R AVU 22 AVU "C3'" "C3'" C 0 1 N N S N N N 6.697 0.025 2.476 -4.008 2.760 -0.603 "C3'" AVU 23 AVU "O3'" "O3'" O 0 1 N N N N N N 7.888 0.344 1.752 -4.269 3.610 -1.721 "O3'" AVU 24 AVU O3A O3A O 0 1 N N N N N N 5.821 3.851 3.904 2.286 1.778 0.079 O3A AVU 25 AVU C3R C3R C 0 1 N N R N N N 1.578 2.019 1.206 7.107 -2.442 0.233 C3R AVU 26 AVU O3R O3R O 0 1 N N N N N N 0.147 2.103 1.178 6.782 -3.311 1.320 O3R AVU 27 AVU "C4'" "C4'" C 0 1 N N R N N N 6.899 -0.122 3.994 -2.637 2.065 -0.760 "C4'" AVU 28 AVU "O4'" "O4'" O 0 1 N N N N N N 6.017 -1.149 4.424 -2.835 0.735 -0.231 "O4'" AVU 29 AVU C4R C4R C 0 1 N N R N N N 2.147 3.383 1.534 5.840 -1.722 -0.297 C4R AVU 30 AVU O4R O4R O 0 1 N N N N N N 3.004 3.729 0.458 6.181 -1.402 -1.663 O4R AVU 31 AVU "C5'" "C5'" C 0 1 N N N N N N 6.545 1.066 4.861 -1.569 2.806 0.047 "C5'" AVU 32 AVU "O5'" "O5'" O 0 1 N N N N N N 7.461 2.085 4.492 -0.291 2.219 -0.203 "O5'" AVU 33 AVU C5R C5R C 0 1 N N N N N N 3.097 3.246 2.730 5.571 -0.447 0.504 C5R AVU 34 AVU O5R O5R O 0 1 N N N N N N 3.665 4.527 2.942 4.338 0.134 0.075 O5R AVU 35 AVU H2 H2 H 0 1 N N N N N N 3.311 -5.275 6.189 -7.724 -3.069 -2.306 H2 AVU 36 AVU HN6 HN6 H 0 1 N N N N N N -0.638 -3.878 4.721 -6.468 -4.288 2.673 HN6 AVU 37 AVU HN6A HN6A H 0 0 N N N N N N -0.381 -2.283 4.480 -7.595 -5.134 1.758 HN6A AVU 38 AVU H8 H8 H 0 1 N N N N N N 3.545 -0.369 1.901 -3.580 -0.474 1.992 H8 AVU 39 AVU "H1'" "H1'" H 0 1 N N N N N N 5.995 -2.979 3.356 -4.085 0.013 -1.742 "H1'" AVU 40 AVU H1R H1R H 0 1 N N N N N N 3.634 2.729 -1.262 7.653 -2.195 -2.897 H1R AVU 41 AVU H1RA H1RA H 0 0 N N N N N N 1.990 3.417 -1.339 6.197 -3.208 -2.692 H1RA AVU 42 AVU "H2'" "H2'" H 0 1 N N N N N N 5.667 -1.315 1.146 -5.554 1.582 0.386 "H2'" AVU 43 AVU "HO2'" "HO2'" H 0 0 N N N N N N 7.916 -1.840 1.050 -6.512 2.459 -1.620 "HO2'" AVU 44 AVU HO2A HO2A H 0 0 N N N N N N 7.555 4.471 6.548 1.495 4.315 -0.985 HO2A AVU 45 AVU HO2B HO2B H 0 0 N N N N N N 3.570 4.882 6.018 4.846 2.874 -0.585 HO2B AVU 46 AVU H2R H2R H 0 1 N N N N N N 1.375 1.083 -0.733 7.212 -4.283 -0.939 H2R AVU 47 AVU "H3'" "H3'" H 0 1 N N N N N N 5.984 0.838 2.276 -4.044 3.328 0.327 "H3'" AVU 48 AVU "HO3'" "HO3'" H 0 0 N N N N N N 8.182 1.215 1.993 -5.143 4.025 -1.704 "HO3'" AVU 49 AVU H3R H3R H 0 1 N N N N N N 1.853 1.269 1.962 7.869 -1.721 0.527 H3R AVU 50 AVU HO3R HO3R H 0 0 N N N N N N -0.172 2.367 2.033 7.524 -3.850 1.627 HO3R AVU 51 AVU "H4'" "H4'" H 0 1 N N N N N N 7.979 -0.295 4.115 -2.354 2.017 -1.811 "H4'" AVU 52 AVU H4R H4R H 0 1 N N N N N N 1.333 4.099 1.721 4.977 -2.387 -0.259 H4R AVU 53 AVU "H5'" "H5'" H 0 1 N N N N N N 5.508 1.387 4.682 -1.552 3.855 -0.249 "H5'" AVU 54 AVU "H5'A" "H5'A" H 0 0 N N N N N N 6.645 0.817 5.928 -1.801 2.733 1.110 "H5'A" AVU 55 AVU H5R H5R H 0 1 N N N N N N 2.546 2.917 3.623 5.508 -0.690 1.565 H5R AVU 56 AVU H5RA H5RA H 0 0 N N N N N N 3.883 2.508 2.514 6.383 0.263 0.342 H5RA AVU 57 # 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 AVU C6 N1 DOUB Y N 1 AVU N1 C2 SING Y N 2 AVU N3 C2 DOUB Y N 3 AVU C2 H2 SING N N 4 AVU C4 N3 SING Y N 5 AVU N9 C4 SING Y N 6 AVU C5 C4 DOUB Y N 7 AVU N7 C5 SING Y N 8 AVU C5 C6 SING Y N 9 AVU N6 C6 SING N N 10 AVU N6 HN6 SING N N 11 AVU N6 HN6A SING N N 12 AVU C8 N7 DOUB Y N 13 AVU C8 N9 SING Y N 14 AVU C8 H8 SING N N 15 AVU N9 "C1'" SING N N 16 AVU O3A PA SING N N 17 AVU O1A PA DOUB N N 18 AVU "O5'" PA SING N N 19 AVU PA O2A SING N N 20 AVU O5R PB SING N N 21 AVU O3A PB SING N N 22 AVU O1B PB DOUB N N 23 AVU PB O2B SING N N 24 AVU "C2'" "C1'" SING N N 25 AVU "C1'" "O4'" SING N N 26 AVU "C1'" "H1'" SING N N 27 AVU C1R C2R SING N N 28 AVU C1R O4R SING N N 29 AVU C1R H1R SING N N 30 AVU C1R H1RA SING N N 31 AVU "O2'" "C2'" SING N N 32 AVU "C2'" "C3'" SING N N 33 AVU "C2'" "H2'" SING N N 34 AVU "O2'" "HO2'" SING N N 35 AVU O2A HO2A SING N N 36 AVU O2B HO2B SING N N 37 AVU C2R F2R SING N N 38 AVU C2R C3R SING N N 39 AVU C2R H2R SING N N 40 AVU "O3'" "C3'" SING N N 41 AVU "C3'" "C4'" SING N N 42 AVU "C3'" "H3'" SING N N 43 AVU "O3'" "HO3'" SING N N 44 AVU O3R C3R SING N N 45 AVU C3R C4R SING N N 46 AVU C3R H3R SING N N 47 AVU O3R HO3R SING N N 48 AVU "C4'" "O4'" SING N N 49 AVU "C4'" "C5'" SING N N 50 AVU "C4'" "H4'" SING N N 51 AVU O4R C4R SING N N 52 AVU C4R C5R SING N N 53 AVU C4R H4R SING N N 54 AVU "O5'" "C5'" SING N N 55 AVU "C5'" "H5'" SING N N 56 AVU "C5'" "H5'A" SING N N 57 AVU C5R O5R SING N N 58 AVU C5R H5R SING N N 59 AVU C5R H5RA SING N N 60 # 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 AVU SMILES ACDLabs 11.02 "FC1C(O)C(OC1)COP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O" AVU SMILES_CANONICAL CACTVS 3.352 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4OC[C@@H](F)[C@@H]4O)[C@@H](O)[C@H]3O" AVU SMILES CACTVS 3.352 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4OC[CH](F)[CH]4O)[CH](O)[CH]3O" AVU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@@H](CO4)F)O)O)O)N" AVU SMILES "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(CO4)F)O)O)O)N" AVU InChI InChI 1.03 "InChI=1S/C15H22FN5O12P2/c16-6-1-29-7(10(6)22)2-30-34(25,26)33-35(27,28)31-3-8-11(23)12(24)15(32-8)21-5-20-9-13(17)18-4-19-14(9)21/h4-8,10-12,15,22-24H,1-3H2,(H,25,26)(H,27,28)(H2,17,18,19)/t6-,7-,8-,10+,11-,12-,15-/m1/s1" AVU InChIKey InChI 1.03 GOCJJDZHXMDJEZ-WFCIOUKESA-N # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier AVU "SYSTEMATIC NAME" ACDLabs 11.02 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" AVU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4R)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl hydrogen 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 AVU "Create component" 2009-07-14 PDBJ AVU "Modify aromatic_flag" 2011-06-04 RCSB AVU "Modify descriptor" 2011-06-04 RCSB AVU "Modify synonyms" 2020-06-05 PDBE AVU "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id AVU _pdbx_chem_comp_synonyms.name ;arabinosyl-2-fluoro-deoxy-adenosine diphosphate ribose, ara-2'F-ADPR ; _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id AVU _pdbx_chem_comp_pcm.modified_residue_id GLU _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C1R _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #