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 
# 
