data_5AJ # _chem_comp.id 5AJ _chem_comp.name "5'-azido-8-[(2-{[2-(1H-benzimidazol-2-yl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H23 N11 O4 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-08-31 _chem_comp.pdbx_modified_date 2016-09-09 _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 525.544 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5AJ _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 5DHR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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.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 5AJ C2 C1 C 0 1 Y N N -13.280 12.682 5.461 -6.572 -3.092 -0.500 C2 5AJ 1 5AJ C4 C2 C 0 1 Y N N -12.641 12.240 3.352 -4.752 -1.714 -0.234 C4 5AJ 2 5AJ C5 C3 C 0 1 Y N N -13.852 11.694 3.102 -3.903 -2.815 -0.433 C5 5AJ 3 5AJ C6 C4 C 0 1 Y N N -14.778 11.661 4.104 -4.489 -4.071 -0.664 C6 5AJ 4 5AJ N9 N1 N 0 1 Y N N -11.920 12.150 2.284 -3.931 -0.629 -0.028 N9 5AJ 5 5AJ NBH N2 N -1 1 N N N -8.737 17.102 -2.623 -1.957 6.208 -2.079 NBH 5AJ 6 5AJ NBG N3 N 1 1 N N N -8.994 16.310 -1.610 -2.048 5.133 -1.765 NBG 5AJ 7 5AJ NBF N4 N 0 1 N N N -9.241 15.521 -0.600 -2.139 4.058 -1.451 NBF 5AJ 8 5AJ CBE C5 C 0 1 N N N -9.090 14.064 -0.695 -2.358 3.723 -0.041 CBE 5AJ 9 5AJ CBC C6 C 0 1 N N R -9.237 13.465 0.691 -3.674 2.956 0.102 CBC 5AJ 10 5AJ OBD O1 O 0 1 N N N -10.582 13.411 1.055 -3.568 1.678 -0.545 OBD 5AJ 11 5AJ CBB C7 C 0 1 N N S -8.902 11.994 0.655 -3.967 2.693 1.592 CBB 5AJ 12 5AJ OBI O2 O 0 1 N N N -7.514 11.827 0.790 -5.204 3.298 1.973 OBI 5AJ 13 5AJ CBA C8 C 0 1 N N R -9.612 11.520 1.911 -4.065 1.151 1.692 CBA 5AJ 14 5AJ OBJ O3 O 0 1 N N N -8.682 11.465 2.943 -5.137 0.763 2.554 OBJ 5AJ 15 5AJ CAZ C9 C 0 1 N N R -10.593 12.637 2.195 -4.360 0.748 0.225 CAZ 5AJ 16 5AJ N3 N5 N 0 1 Y N N -12.378 12.721 4.537 -6.067 -1.897 -0.275 N3 5AJ 17 5AJ N1 N6 N 0 1 Y N N -14.452 12.164 5.251 -5.815 -4.157 -0.687 N1 5AJ 18 5AJ N6 N7 N 0 1 N N N -15.961 11.149 3.958 -3.702 -5.193 -0.867 N6 5AJ 19 5AJ N7 N8 N 0 1 Y N N -13.827 11.275 1.869 -2.628 -2.363 -0.342 N7 5AJ 20 5AJ C8 C10 C 0 1 Y N N -12.655 11.575 1.379 -2.639 -1.074 -0.104 C8 5AJ 21 5AJ SAP S1 S 0 1 N N N -12.183 11.232 -0.198 -1.206 -0.067 0.091 SAP 5AJ 22 5AJ CAO C11 C 0 1 N N N -13.353 9.894 -0.572 0.087 -1.313 -0.132 CAO 5AJ 23 5AJ CAM C12 C 0 1 N N N -14.587 10.297 -1.360 1.440 -0.661 -0.004 CAM 5AJ 24 5AJ OAN O4 O 0 1 N N N -14.589 10.351 -2.577 1.521 0.529 0.216 OAN 5AJ 25 5AJ NAL N9 N 0 1 N N N -15.648 10.503 -0.632 2.559 -1.400 -0.135 NAL 5AJ 26 5AJ CAK C13 C 0 1 N N N -16.900 10.925 -1.212 3.874 -0.767 -0.010 CAK 5AJ 27 5AJ CAJ C14 C 0 1 N N N -16.781 12.384 -1.601 4.968 -1.820 -0.199 CAJ 5AJ 28 5AJ CAH C15 C 0 1 Y N N -15.996 13.185 -0.586 6.321 -1.168 -0.071 CAH 5AJ 29 5AJ NAI N10 N 0 1 Y N N -16.431 13.496 0.607 7.297 -1.562 0.791 NAI 5AJ 30 5AJ CAD C16 C 0 1 Y N N -15.513 14.192 1.217 8.374 -0.719 0.604 CAD 5AJ 31 5AJ CAC C17 C 0 1 Y N N -15.464 14.757 2.465 9.635 -0.620 1.176 CAC 5AJ 32 5AJ CAB C18 C 0 1 Y N N -14.348 15.448 2.845 10.501 0.366 0.752 CAB 5AJ 33 5AJ CAA C19 C 0 1 Y N N -13.297 15.579 1.968 10.121 1.258 -0.240 CAA 5AJ 34 5AJ CAF C20 C 0 1 Y N N -13.357 15.007 0.723 8.884 1.176 -0.814 CAF 5AJ 35 5AJ CAE C21 C 0 1 Y N N -14.475 14.315 0.349 7.990 0.185 -0.401 CAE 5AJ 36 5AJ NAG N11 N 0 1 Y N N -14.801 13.700 -0.752 6.727 -0.150 -0.772 NAG 5AJ 37 5AJ H1 H1 H 0 1 N N N -13.053 13.091 6.434 -7.646 -3.206 -0.527 H1 5AJ 38 5AJ H3 H3 H 0 1 N N N -9.866 13.655 -1.359 -1.536 3.103 0.317 H3 5AJ 39 5AJ H4 H4 H 0 1 N N N -8.096 13.821 -1.099 -2.405 4.639 0.547 H4 5AJ 40 5AJ H5 H5 H 0 1 N N N -8.613 13.999 1.423 -4.487 3.530 -0.342 H5 5AJ 41 5AJ H6 H6 H 0 1 N N N -9.311 11.509 -0.244 -3.153 3.067 2.213 H6 5AJ 42 5AJ H7 H7 H 0 1 N N N -7.302 10.901 0.767 -5.219 4.260 1.874 H7 5AJ 43 5AJ H8 H8 H 0 1 N N N -10.131 10.565 1.740 -3.121 0.723 2.031 H8 5AJ 44 5AJ H9 H9 H 0 1 N N N -9.109 11.170 3.739 -5.041 1.071 3.465 H9 5AJ 45 5AJ H10 H10 H 0 1 N N N -10.295 13.197 3.094 -5.420 0.868 0.000 H10 5AJ 46 5AJ H11 H11 H 0 1 N N N -16.468 11.230 4.816 -2.735 -5.117 -0.851 H11 5AJ 47 5AJ H12 H12 H 0 1 N N N -16.449 11.638 3.235 -4.118 -6.055 -1.025 H12 5AJ 48 5AJ H13 H13 H 0 1 N N N -13.688 9.462 0.382 -0.017 -2.085 0.629 H13 5AJ 49 5AJ H14 H14 H 0 1 N N N -12.817 9.129 -1.153 -0.007 -1.762 -1.121 H14 5AJ 50 5AJ H15 H15 H 0 1 N N N -15.593 10.365 0.357 2.494 -2.352 -0.311 H15 5AJ 51 5AJ H16 H16 H 0 1 N N N -17.710 10.801 -0.478 3.979 0.006 -0.772 H16 5AJ 52 5AJ H17 H17 H 0 1 N N N -17.119 10.320 -2.104 3.969 -0.317 0.978 H17 5AJ 53 5AJ H18 H18 H 0 1 N N N -16.273 12.451 -2.574 4.863 -2.593 0.563 H18 5AJ 54 5AJ H19 H19 H 0 1 N N N -17.791 12.812 -1.685 4.873 -2.269 -1.188 H19 5AJ 55 5AJ H20 H20 H 0 1 N N N -17.320 13.242 0.988 7.246 -2.299 1.420 H20 5AJ 56 5AJ H21 H21 H 0 1 N N N -16.300 14.657 3.142 9.936 -1.311 1.949 H21 5AJ 57 5AJ H22 H22 H 0 1 N N N -14.292 15.889 3.829 11.483 0.444 1.197 H22 5AJ 58 5AJ H23 H23 H 0 1 N N N -12.419 16.136 2.261 10.810 2.025 -0.561 H23 5AJ 59 5AJ H24 H24 H 0 1 N N N -12.525 15.103 0.041 8.598 1.875 -1.585 H24 5AJ 60 # 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 5AJ NBH NBG DOUB N N 1 5AJ OAN CAM DOUB N N 2 5AJ NBG NBF DOUB N N 3 5AJ CAJ CAK SING N N 4 5AJ CAJ CAH SING N N 5 5AJ CAM NAL SING N N 6 5AJ CAM CAO SING N N 7 5AJ CAK NAL SING N N 8 5AJ NAG CAH DOUB Y N 9 5AJ NAG CAE SING Y N 10 5AJ CBE NBF SING N N 11 5AJ CBE CBC SING N N 12 5AJ CAH NAI SING Y N 13 5AJ CAO SAP SING N N 14 5AJ SAP C8 SING N N 15 5AJ CAE CAF DOUB Y N 16 5AJ CAE CAD SING Y N 17 5AJ NAI CAD SING Y N 18 5AJ CBB CBC SING N N 19 5AJ CBB OBI SING N N 20 5AJ CBB CBA SING N N 21 5AJ CBC OBD SING N N 22 5AJ CAF CAA SING Y N 23 5AJ OBD CAZ SING N N 24 5AJ CAD CAC DOUB Y N 25 5AJ C8 N7 DOUB Y N 26 5AJ C8 N9 SING Y N 27 5AJ N7 C5 SING Y N 28 5AJ CBA CAZ SING N N 29 5AJ CBA OBJ SING N N 30 5AJ CAA CAB DOUB Y N 31 5AJ CAZ N9 SING N N 32 5AJ N9 C4 SING Y N 33 5AJ CAC CAB SING Y N 34 5AJ C5 C4 DOUB Y N 35 5AJ C5 C6 SING Y N 36 5AJ C4 N3 SING Y N 37 5AJ N6 C6 SING N N 38 5AJ C6 N1 DOUB Y N 39 5AJ N3 C2 DOUB Y N 40 5AJ N1 C2 SING Y N 41 5AJ C2 H1 SING N N 42 5AJ CBE H3 SING N N 43 5AJ CBE H4 SING N N 44 5AJ CBC H5 SING N N 45 5AJ CBB H6 SING N N 46 5AJ OBI H7 SING N N 47 5AJ CBA H8 SING N N 48 5AJ OBJ H9 SING N N 49 5AJ CAZ H10 SING N N 50 5AJ N6 H11 SING N N 51 5AJ N6 H12 SING N N 52 5AJ CAO H13 SING N N 53 5AJ CAO H14 SING N N 54 5AJ NAL H15 SING N N 55 5AJ CAK H16 SING N N 56 5AJ CAK H17 SING N N 57 5AJ CAJ H18 SING N N 58 5AJ CAJ H19 SING N N 59 5AJ NAI H20 SING N N 60 5AJ CAC H21 SING N N 61 5AJ CAB H22 SING N N 62 5AJ CAA H23 SING N N 63 5AJ CAF H24 SING N N 64 # 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 5AJ SMILES ACDLabs 12.01 "c1nc2c(c(n1)N)nc(n2C3OC(C/N=[N+]=[N-])C(O)C3O)SCC(NCCc5nc4ccccc4n5)=O" 5AJ InChI InChI 1.03 "InChI=1S/C21H23N11O4S/c22-18-15-19(26-9-25-18)32(20-17(35)16(34)12(36-20)7-27-31-23)21(30-15)37-8-14(33)24-6-5-13-28-10-3-1-2-4-11(10)29-13/h1-4,9,12,16-17,20,34-35H,5-8H2,(H,24,33)(H,28,29)(H2,22,25,26)/t12-,16-,17-,20-/m1/s1" 5AJ InChIKey InChI 1.03 QNDDYPVSXWRDOZ-QQRWZLOUSA-N 5AJ SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4[nH]c5ccccc5n4)nc12" 5AJ SMILES CACTVS 3.385 "Nc1ncnc2n([CH]3O[CH](CN=[N+]=[N-])[CH](O)[CH]3O)c(SCC(=O)NCCc4[nH]c5ccccc5n4)nc12" 5AJ SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1ccc2c(c1)[nH]c(n2)CCNC(=O)CSc3nc4c(ncnc4n3[C@H]5[C@@H]([C@@H]([C@H](O5)CN=[N+]=[N-])O)O)N" 5AJ SMILES "OpenEye OEToolkits" 1.9.2 "c1ccc2c(c1)[nH]c(n2)CCNC(=O)CSc3nc4c(ncnc4n3C5C(C(C(O5)CN=[N+]=[N-])O)O)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 5AJ "SYSTEMATIC NAME" ACDLabs 12.01 "5'-azido-8-[(2-{[2-(1H-benzimidazol-2-yl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine" 5AJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "2-[6-azanyl-9-[(2R,3R,4S,5R)-5-(azidomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanyl-N-[2-(1H-benzimidazol-2-yl)ethyl]ethanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5AJ "Create component" 2015-08-31 EBI 5AJ "Initial release" 2016-09-14 RCSB #