data_5A9 # _chem_comp.id 5A9 _chem_comp.name "5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H22 Br N9 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 564.416 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5A9 _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 5DHT _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 5A9 C4 C1 C 0 1 Y N N 11.007 -4.450 -58.755 5.256 -1.758 0.508 C4 5A9 1 5A9 C5 C2 C 0 1 Y N N 10.792 -5.008 -57.573 4.393 -2.858 0.645 C5 5A9 2 5A9 C6 C3 C 0 1 Y N N 11.545 -4.674 -56.538 4.951 -4.101 0.986 C6 5A9 3 5A9 C8 C4 C 0 1 Y N N 9.386 -5.804 -58.946 3.170 -1.136 0.118 C8 5A9 4 5A9 N1 N1 N 0 1 Y N N 12.530 -3.794 -56.629 6.266 -4.178 1.162 N1 5A9 5 5A9 N3 N2 N 0 1 Y N N 11.975 -3.554 -58.919 6.559 -1.931 0.704 N3 5A9 6 5A9 CBC C5 C 0 1 Y N N 7.482 -3.863 -55.935 -6.483 -0.746 0.093 CBC 5A9 7 5A9 CBD C6 C 0 1 Y N N 7.799 -3.019 -56.978 -7.704 -0.159 -0.185 CBD 5A9 8 5A9 BR BR1 BR 0 0 N N N 9.132 -1.834 -56.762 -8.736 0.586 1.213 BR 5A9 9 5A9 CBE C7 C 0 1 Y N N 7.097 -3.096 -58.164 -8.171 -0.118 -1.487 CBE 5A9 10 5A9 CAX C8 C 0 1 Y N N 6.076 -4.025 -58.294 -7.417 -0.662 -2.509 CAX 5A9 11 5A9 CAW C9 C 0 1 Y N N 5.761 -4.873 -57.245 -6.196 -1.249 -2.231 CAW 5A9 12 5A9 CAV C10 C 0 1 Y N N 6.470 -4.793 -56.066 -5.727 -1.286 -0.931 CAV 5A9 13 5A9 CAM C11 C 0 1 N N N 6.169 -5.614 -54.995 -4.396 -1.925 -0.629 CAM 5A9 14 5A9 CAL C12 C 0 1 N N N 6.213 -7.089 -55.373 -3.291 -0.872 -0.726 CAL 5A9 15 5A9 NAK N3 N 0 1 N N N 7.232 -7.307 -56.387 -1.997 -1.493 -0.432 NAK 5A9 16 5A9 CAJ C13 C 0 1 N N N 6.920 -7.952 -57.491 -0.872 -0.751 -0.458 CAJ 5A9 17 5A9 OAB O1 O 0 1 N N N 5.803 -8.400 -57.696 -0.930 0.430 -0.726 OAB 5A9 18 5A9 CAI C14 C 0 1 N N N 8.048 -8.116 -58.495 0.459 -1.390 -0.156 CAI 5A9 19 5A9 SAH S1 S 0 1 N N N 8.106 -6.701 -59.644 1.767 -0.144 -0.271 SAH 5A9 20 5A9 N7 N4 N 0 1 Y N N 9.779 -5.855 -57.690 3.135 -2.416 0.395 N7 5A9 21 5A9 N6 N5 N 0 1 N N N 11.275 -5.266 -55.396 4.149 -5.220 1.135 N6 5A9 22 5A9 C2 C15 C 0 1 Y N N 12.771 -3.197 -57.849 7.038 -3.116 1.023 C2 5A9 23 5A9 N9 N6 N 0 1 Y N N 10.131 -4.946 -59.608 4.460 -0.685 0.181 N9 5A9 24 5A9 CAR C16 C 0 1 N N R 10.006 -4.616 -61.025 4.912 0.687 -0.065 CAR 5A9 25 5A9 OAS O2 O 0 1 N N N 8.688 -4.160 -61.221 4.009 1.632 0.549 OAS 5A9 26 5A9 CAZ C17 C 0 1 N N R 10.096 -5.865 -61.873 4.859 1.009 -1.574 CAZ 5A9 27 5A9 OAY O3 O 0 1 N N N 11.305 -5.839 -62.604 6.151 0.860 -2.165 OAY 5A9 28 5A9 CBA C18 C 0 1 N N S 8.963 -5.739 -62.840 4.403 2.485 -1.627 CBA 5A9 29 5A9 OBF O4 O 0 1 N N N 9.503 -5.854 -64.145 5.401 3.295 -2.252 OBF 5A9 30 5A9 CAT C19 C 0 1 N N R 8.491 -4.327 -62.598 4.236 2.880 -0.141 CAT 5A9 31 5A9 CAU C20 C 0 1 N N N 6.991 -4.200 -62.829 3.035 3.811 0.032 CAU 5A9 32 5A9 NBB N7 N 0 1 N N N 6.651 -2.773 -62.876 2.966 4.267 1.422 NBB 5A9 33 5A9 NBG N8 N 1 1 N N N 5.849 -2.447 -62.243 3.028 5.365 1.657 NBG 5A9 34 5A9 NBI N9 N -1 1 N N N 5.035 -2.108 -61.604 3.089 6.462 1.892 NBI 5A9 35 5A9 H1 H1 H 0 1 N N N 8.030 -3.796 -55.007 -6.118 -0.779 1.109 H1 5A9 36 5A9 H2 H2 H 0 1 N N N 7.341 -2.438 -58.985 -9.125 0.340 -1.705 H2 5A9 37 5A9 H3 H3 H 0 1 N N N 5.523 -4.088 -59.219 -7.781 -0.630 -3.525 H3 5A9 38 5A9 H4 H4 H 0 1 N N N 4.963 -5.594 -57.351 -5.607 -1.674 -3.030 H4 5A9 39 5A9 H5 H5 H 0 1 N N N 6.899 -5.432 -54.192 -4.413 -2.341 0.379 H5 5A9 40 5A9 H6 H6 H 0 1 N N N 5.159 -5.370 -54.634 -4.203 -2.721 -1.347 H6 5A9 41 5A9 H7 H7 H 0 1 N N N 5.233 -7.394 -55.769 -3.273 -0.455 -1.733 H7 5A9 42 5A9 H8 H8 H 0 1 N N N 6.451 -7.688 -54.481 -3.483 -0.075 -0.007 H8 5A9 43 5A9 H9 H9 H 0 1 N N N 8.163 -6.969 -56.247 -1.950 -2.438 -0.218 H9 5A9 44 5A9 H10 H10 H 0 1 N N N 7.887 -9.040 -59.069 0.442 -1.806 0.851 H10 5A9 45 5A9 H11 H11 H 0 1 N N N 9.004 -8.181 -57.955 0.652 -2.186 -0.875 H11 5A9 46 5A9 H12 H12 H 0 1 N N N 11.907 -4.940 -54.693 3.190 -5.151 1.004 H12 5A9 47 5A9 H13 H13 H 0 1 N N N 10.336 -5.053 -55.124 4.546 -6.074 1.371 H13 5A9 48 5A9 H14 H14 H 0 1 N N N 13.561 -2.470 -57.964 8.102 -3.223 1.175 H14 5A9 49 5A9 H15 H15 H 0 1 N N N 10.758 -3.876 -61.337 5.924 0.826 0.317 H15 5A9 50 5A9 H16 H16 H 0 1 N N N 9.995 -6.770 -61.255 4.134 0.368 -2.076 H16 5A9 51 5A9 H17 H17 H 0 1 N N N 12.039 -5.918 -62.006 6.175 1.050 -3.113 H17 5A9 52 5A9 H18 H18 H 0 1 N N N 8.169 -6.472 -62.636 3.453 2.573 -2.155 H18 5A9 53 5A9 H19 H19 H 0 1 N N N 9.798 -6.746 -64.289 5.193 4.240 -2.258 H19 5A9 54 5A9 H20 H20 H 0 1 N N N 9.052 -3.604 -63.208 5.144 3.357 0.229 H20 5A9 55 5A9 H21 H21 H 0 1 N N N 6.446 -4.685 -62.006 3.145 4.672 -0.628 H21 5A9 56 5A9 H22 H22 H 0 1 N N N 6.720 -4.679 -63.782 2.120 3.275 -0.220 H22 5A9 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 5A9 OBF CBA SING N N 1 5A9 NBB CAU SING N N 2 5A9 NBB NBG DOUB N N 3 5A9 CBA CAT SING N N 4 5A9 CBA CAZ SING N N 5 5A9 CAU CAT SING N N 6 5A9 OAY CAZ SING N N 7 5A9 CAT OAS SING N N 8 5A9 NBG NBI DOUB N N 9 5A9 CAZ CAR SING N N 10 5A9 OAS CAR SING N N 11 5A9 CAR N9 SING N N 12 5A9 SAH C8 SING N N 13 5A9 SAH CAI SING N N 14 5A9 N9 C8 SING Y N 15 5A9 N9 C4 SING Y N 16 5A9 C8 N7 DOUB Y N 17 5A9 N3 C4 DOUB Y N 18 5A9 N3 C2 SING Y N 19 5A9 C4 C5 SING Y N 20 5A9 CAI CAJ SING N N 21 5A9 CAX CBE DOUB Y N 22 5A9 CAX CAW SING Y N 23 5A9 CBE CBD SING Y N 24 5A9 C2 N1 DOUB Y N 25 5A9 OAB CAJ DOUB N N 26 5A9 N7 C5 SING Y N 27 5A9 C5 C6 DOUB Y N 28 5A9 CAJ NAK SING N N 29 5A9 CAW CAV DOUB Y N 30 5A9 CBD BR SING N N 31 5A9 CBD CBC DOUB Y N 32 5A9 N1 C6 SING Y N 33 5A9 C6 N6 SING N N 34 5A9 NAK CAL SING N N 35 5A9 CAV CBC SING Y N 36 5A9 CAV CAM SING N N 37 5A9 CAL CAM SING N N 38 5A9 CBC H1 SING N N 39 5A9 CBE H2 SING N N 40 5A9 CAX H3 SING N N 41 5A9 CAW H4 SING N N 42 5A9 CAM H5 SING N N 43 5A9 CAM H6 SING N N 44 5A9 CAL H7 SING N N 45 5A9 CAL H8 SING N N 46 5A9 NAK H9 SING N N 47 5A9 CAI H10 SING N N 48 5A9 CAI H11 SING N N 49 5A9 N6 H12 SING N N 50 5A9 N6 H13 SING N N 51 5A9 C2 H14 SING N N 52 5A9 CAR H15 SING N N 53 5A9 CAZ H16 SING N N 54 5A9 OAY H17 SING N N 55 5A9 CBA H18 SING N N 56 5A9 OBF H19 SING N N 57 5A9 CAT H20 SING N N 58 5A9 CAU H21 SING N N 59 5A9 CAU H22 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 5A9 SMILES ACDLabs 12.01 "c13c(c(N)ncn1)nc(SCC(NCCc2cc(Br)ccc2)=O)n3C4OC(C(C4O)O)CN=[N+]=[N-]" 5A9 InChI InChI 1.03 "InChI=1S/C20H22BrN9O4S/c21-11-3-1-2-10(6-11)4-5-24-13(31)8-35-20-28-14-17(22)25-9-26-18(14)30(20)19-16(33)15(32)12(34-19)7-27-29-23/h1-3,6,9,12,15-16,19,32-33H,4-5,7-8H2,(H,24,31)(H2,22,25,26)/t12-,15-,16-,19-/m1/s1" 5A9 InChIKey InChI 1.03 JYGMOYIMZQWVHO-BGIGGGFGSA-N 5A9 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4cccc(Br)c4)nc12" 5A9 SMILES CACTVS 3.385 "Nc1ncnc2n([CH]3O[CH](CN=[N+]=[N-])[CH](O)[CH]3O)c(SCC(=O)NCCc4cccc(Br)c4)nc12" 5A9 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1cc(cc(c1)Br)CCNC(=O)CSc2nc3c(ncnc3n2[C@H]4[C@@H]([C@@H]([C@H](O4)CN=[N+]=[N-])O)O)N" 5A9 SMILES "OpenEye OEToolkits" 1.9.2 "c1cc(cc(c1)Br)CCNC(=O)CSc2nc3c(ncnc3n2C4C(C(C(O4)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 5A9 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine" 5A9 "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-(3-bromophenyl)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 5A9 "Create component" 2015-08-31 EBI 5A9 "Initial release" 2016-09-14 RCSB #