data_KD9
# 
_chem_comp.id                                    KD9 
_chem_comp.name                                  
;3'-O-(4-benzoylbenzoyl)adenosine 5'-(tetrahydrogen triphosphate)
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H24 N5 O15 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-08-10 
_chem_comp.pdbx_modified_date                    2024-08-09 
_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                        715.393 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     KD9 
_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        8TRJ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
KD9 C10  C1  C 0 1 Y N N N N N 169.053 208.867 244.731 5.629  2.015  0.155  C10  KD9 1  
KD9 C13  C2  C 0 1 Y N N N N N 169.934 206.397 243.860 5.463  0.974  -2.421 C13  KD9 2  
KD9 C15  C3  C 0 1 N N N N N N 172.269 207.267 243.469 3.259  -0.058 -1.890 C15  KD9 3  
KD9 C21  C4  C 0 1 N N R N N N 174.058 203.947 241.542 0.588  -2.766 0.168  C21  KD9 4  
KD9 C22  C5  C 0 1 N N R N N N 174.431 204.961 242.755 1.378  -2.575 -1.152 C22  KD9 5  
KD9 C28  C6  C 0 1 Y N N N N N 174.941 199.295 240.657 0.714  -7.525 1.325  C28  KD9 6  
KD9 C01  C7  C 0 1 Y N N N N N 164.742 211.723 244.333 7.900  5.042  3.372  C01  KD9 7  
KD9 C02  C8  C 0 1 Y N N N N N 164.811 210.756 243.344 6.709  4.913  2.680  C02  KD9 8  
KD9 C03  C9  C 0 1 Y N N N N N 165.449 209.552 243.595 6.681  4.265  1.463  C03  KD9 9  
KD9 C04  C10 C 0 1 Y N N N N N 166.016 209.313 244.837 7.859  3.737  0.930  C04  KD9 10 
KD9 C05  C11 C 0 1 Y N N N N N 165.949 210.280 245.825 9.058  3.870  1.634  C05  KD9 11 
KD9 C06  C12 C 0 1 Y N N N N N 165.310 211.484 245.574 9.071  4.521  2.850  C06  KD9 12 
KD9 C07  C13 C 0 1 N N N N N N 166.722 207.983 245.115 7.837  3.041  -0.373 C07  KD9 13 
KD9 C09  C14 C 0 1 Y N N N N N 168.175 207.798 244.685 6.655  2.243  -0.765 C09  KD9 14 
KD9 C11  C15 C 0 1 Y N N N N N 170.371 208.699 244.340 4.531  1.266  -0.208 C11  KD9 15 
KD9 C12  C16 C 0 1 Y N N N N N 170.813 207.461 243.904 4.440  0.741  -1.499 C12  KD9 16 
KD9 C14  C17 C 0 1 Y N N N N N 168.615 206.563 244.251 6.564  1.717  -2.056 C14  KD9 17 
KD9 C18  C18 C 0 1 N N S N N N 173.987 206.102 242.379 1.143  -1.075 -1.455 C18  KD9 18 
KD9 C19  C19 C 0 1 N N R N N N 174.208 206.094 240.840 -0.122 -0.720 -0.650 C19  KD9 19 
KD9 C25  C20 C 0 1 Y N N N N N 176.084 202.607 241.067 -1.004 -4.715 -0.023 C25  KD9 20 
KD9 C27  C21 C 0 1 Y N N N N N 175.261 200.644 240.841 0.168  -6.330 0.826  C27  KD9 21 
KD9 C30  C22 C 0 1 Y N N N N N 172.738 199.772 241.016 2.652  -6.383 1.843  C30  KD9 22 
KD9 C32  C23 C 0 1 Y N N N N N 174.236 201.514 241.114 0.958  -5.168 0.876  C32  KD9 23 
KD9 C34  C24 C 0 1 N N N N N N 175.534 206.774 240.528 -1.207 -0.193 -1.592 C34  KD9 24 
KD9 N24  N1  N 0 1 Y N N N N N 174.786 202.728 241.248 0.192  -4.167 0.334  N24  KD9 25 
KD9 N26  N2  N 0 1 Y N N N N N 176.395 201.354 240.817 -1.016 -5.984 0.267  N26  KD9 26 
KD9 N29  N3  N 0 1 Y N N N N N 173.687 198.895 240.750 1.948  -7.501 1.817  N29  KD9 27 
KD9 N31  N4  N 0 1 Y N N N N N 172.983 201.052 241.196 2.182  -5.241 1.388  N31  KD9 28 
KD9 N33  N5  N 0 1 N N N N N N 175.997 198.355 240.373 -0.018 -8.699 1.307  N33  KD9 29 
KD9 O08  O1  O 0 1 N N N N N N 166.142 207.100 245.650 8.790  3.123  -1.122 O08  KD9 30 
KD9 O16  O2  O 0 1 N N N N N N 173.104 208.020 243.830 3.178  -0.511 -3.014 O16  KD9 31 
KD9 O17  O3  O 0 1 N N N N N N 172.616 206.198 242.637 2.273  -0.282 -1.001 O17  KD9 32 
KD9 O20  O4  O 0 1 N N N N N N 174.256 204.618 240.440 -0.572 -1.925 -0.008 O20  KD9 33 
KD9 O23  O5  O 0 1 N N N N N N 173.806 204.539 243.925 2.767  -2.845 -0.959 O23  KD9 34 
KD9 O35  O6  O 0 1 N N N N N N 176.534 205.807 240.428 -2.332 0.242  -0.827 O35  KD9 35 
KD9 O37  O7  O 0 1 N N N N N N 178.322 207.624 240.738 -4.389 -0.275 -2.381 O37  KD9 36 
KD9 O38  O8  O 0 1 N N N N N N 179.045 205.314 240.312 -3.297 2.000  -2.359 O38  KD9 37 
KD9 O39  O9  O 0 1 N N N N N N 178.082 205.890 242.623 -4.663 1.356  -0.337 O39  KD9 38 
KD9 O41  O10 O 0 1 N N N N N N 177.083 208.134 243.414 -6.855 1.944  -1.440 O41  KD9 39 
KD9 O42  O11 O 0 1 N N N N N N 179.436 207.649 243.932 -5.509 3.842  -0.461 O42  KD9 40 
KD9 O43  O12 O 0 1 N N N N N N 177.611 206.391 245.215 -6.749 2.106  1.077  O43  KD9 41 
KD9 O45  O13 O 0 1 N N N N N N 178.347 203.983 244.636 -9.208 1.937  0.534  O45  KD9 42 
KD9 O46  O14 O 0 1 N N N N N N 175.981 204.395 245.158 -8.534 1.631  2.947  O46  KD9 43 
KD9 O47  O15 O 0 1 N N N N N N 177.669 204.498 246.932 -8.441 3.989  1.788  O47  KD9 44 
KD9 P36  P1  P 0 1 N N N N N N 178.025 206.175 241.008 -3.662 0.856  -1.495 P36  KD9 45 
KD9 P40  P2  P 0 1 N N N N N N 178.063 207.055 243.782 -5.964 2.304  -0.315 P40  KD9 46 
KD9 P44  P3  P 0 1 N N N N N N 177.397 204.784 245.482 -8.254 2.405  1.564  P44  KD9 47 
KD9 H101 H1  H 0 0 N N N N N N 168.710 209.833 245.072 5.699  2.421  1.153  H101 KD9 48 
KD9 H131 H2  H 0 0 N N N N N N 170.276 205.431 243.519 5.390  0.571  -3.420 H131 KD9 49 
KD9 H1   H3  H 0 1 N N N N N N 172.993 203.698 241.659 1.179  -2.432 1.021  H1   KD9 50 
KD9 H2   H4  H 0 1 N N N N N N 175.525 204.951 242.873 0.968  -3.201 -1.944 H2   KD9 51 
KD9 H011 H5  H 0 0 N N N N N N 164.246 212.662 244.137 7.917  5.554  4.323  H011 KD9 52 
KD9 H021 H6  H 0 0 N N N N N N 164.367 210.940 242.377 5.799  5.321  3.094  H021 KD9 53 
KD9 H031 H7  H 0 0 N N N N N N 165.505 208.799 242.822 5.750  4.165  0.925  H031 KD9 54 
KD9 H051 H8  H 0 0 N N N N N N 166.395 210.096 246.791 9.973  3.464  1.227  H051 KD9 55 
KD9 H061 H9  H 0 0 N N N N N N 165.255 212.237 246.347 9.998  4.629  3.393  H061 KD9 56 
KD9 H111 H10 H 0 0 N N N N N N 171.055 209.534 244.375 3.740  1.086  0.505  H111 KD9 57 
KD9 H141 H11 H 0 0 N N N N N N 167.932 205.727 244.216 7.355  1.896  -2.769 H141 KD9 58 
KD9 H3   H12 H 0 1 N N N N N N 174.536 206.949 242.816 0.976  -0.923 -2.521 H3   KD9 59 
KD9 H4   H13 H 0 1 N N N N N N 173.378 206.607 240.332 0.115  0.034  0.100  H4   KD9 60 
KD9 H251 H14 H 0 0 N N N N N N 176.793 203.421 241.117 -1.821 -4.176 -0.479 H251 KD9 61 
KD9 H301 H15 H 0 0 N N N N N N 171.718 199.425 241.089 3.651  -6.408 2.252  H301 KD9 62 
KD9 H341 H16 H 0 0 N N N N N N 175.784 207.480 241.334 -0.813 0.645  -2.168 H341 KD9 63 
KD9 H342 H17 H 0 0 N N N N N N 175.453 207.319 239.576 -1.515 -0.988 -2.272 H342 KD9 64 
KD9 H332 H18 H 0 0 N N N N N N 175.610 197.438 240.274 0.369  -9.517 1.656  H332 KD9 65 
KD9 H331 H19 H 0 0 N N N N N N 176.456 198.616 239.524 -0.918 -8.704 0.945  H331 KD9 66 
KD9 H231 H20 H 0 0 N N N N N N 174.025 205.133 244.633 2.956  -3.751 -0.679 H231 KD9 67 
KD9 H5   H21 H 0 1 N N N N N N 179.091 207.692 240.185 -4.657 -1.056 -1.878 H5   KD9 68 
KD9 H6   H22 H 0 1 N N N N N N 179.398 208.583 243.763 -4.922 4.147  0.244  H6   KD9 69 
KD9 H7   H23 H 0 1 N N N N N N 175.982 203.724 244.486 -9.424 1.766  3.300  H7   KD9 70 
KD9 H8   H24 H 0 1 N N N N N N 178.381 203.874 247.004 -7.846 4.365  2.451  H8   KD9 71 
# 
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 
KD9 O38 P36  DOUB N N 1  
KD9 N33 C28  SING N N 2  
KD9 O35 C34  SING N N 3  
KD9 O35 P36  SING N N 4  
KD9 O20 C19  SING N N 5  
KD9 O20 C21  SING N N 6  
KD9 C34 C19  SING N N 7  
KD9 C28 N29  DOUB Y N 8  
KD9 C28 C27  SING Y N 9  
KD9 O37 P36  SING N N 10 
KD9 N29 C30  SING Y N 11 
KD9 N26 C27  SING Y N 12 
KD9 N26 C25  DOUB Y N 13 
KD9 C19 C18  SING N N 14 
KD9 C27 C32  DOUB Y N 15 
KD9 P36 O39  SING N N 16 
KD9 C30 N31  DOUB Y N 17 
KD9 C25 N24  SING Y N 18 
KD9 C32 N31  SING Y N 19 
KD9 C32 N24  SING Y N 20 
KD9 N24 C21  SING N N 21 
KD9 C21 C22  SING N N 22 
KD9 C18 O17  SING N N 23 
KD9 C18 C22  SING N N 24 
KD9 O39 P40  SING N N 25 
KD9 O17 C15  SING N N 26 
KD9 C22 O23  SING N N 27 
KD9 C02 C03  DOUB Y N 28 
KD9 C02 C01  SING Y N 29 
KD9 O41 P40  DOUB N N 30 
KD9 C15 O16  DOUB N N 31 
KD9 C15 C12  SING N N 32 
KD9 C03 C04  SING Y N 33 
KD9 P40 O42  SING N N 34 
KD9 P40 O43  SING N N 35 
KD9 C13 C12  DOUB Y N 36 
KD9 C13 C14  SING Y N 37 
KD9 C12 C11  SING Y N 38 
KD9 C14 C09  DOUB Y N 39 
KD9 C01 C06  DOUB Y N 40 
KD9 C11 C10  DOUB Y N 41 
KD9 O45 P44  DOUB N N 42 
KD9 C09 C10  SING Y N 43 
KD9 C09 C07  SING N N 44 
KD9 C04 C07  SING N N 45 
KD9 C04 C05  DOUB Y N 46 
KD9 C07 O08  DOUB N N 47 
KD9 O46 P44  SING N N 48 
KD9 O43 P44  SING N N 49 
KD9 P44 O47  SING N N 50 
KD9 C06 C05  SING Y N 51 
KD9 C10 H101 SING N N 52 
KD9 C13 H131 SING N N 53 
KD9 C21 H1   SING N N 54 
KD9 C22 H2   SING N N 55 
KD9 C01 H011 SING N N 56 
KD9 C02 H021 SING N N 57 
KD9 C03 H031 SING N N 58 
KD9 C05 H051 SING N N 59 
KD9 C06 H061 SING N N 60 
KD9 C11 H111 SING N N 61 
KD9 C14 H141 SING N N 62 
KD9 C18 H3   SING N N 63 
KD9 C19 H4   SING N N 64 
KD9 C25 H251 SING N N 65 
KD9 C30 H301 SING N N 66 
KD9 C34 H341 SING N N 67 
KD9 C34 H342 SING N N 68 
KD9 N33 H332 SING N N 69 
KD9 N33 H331 SING N N 70 
KD9 O23 H231 SING N N 71 
KD9 O37 H5   SING N N 72 
KD9 O42 H6   SING N N 73 
KD9 O46 H7   SING N N 74 
KD9 O47 H8   SING N N 75 
# 
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 
KD9 SMILES           ACDLabs              12.01 "O=C(c1ccccc1)c1ccc(cc1)C(=O)OC1C(COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OC(n2cnc3c(N)ncnc32)C1O"                                                                                                                                                                                         
KD9 InChI            InChI                1.06  "InChI=1S/C24H24N5O15P3/c25-21-17-22(27-11-26-21)29(12-28-17)23-19(31)20(16(41-23)10-40-46(36,37)44-47(38,39)43-45(33,34)35)42-24(32)15-8-6-14(7-9-15)18(30)13-4-2-1-3-5-13/h1-9,11-12,16,19-20,23,31H,10H2,(H,36,37)(H,38,39)(H2,25,26,27)(H2,33,34,35)/t16-,19-,20-,23-/m1/s1" 
KD9 InChIKey         InChI                1.06  AWJJLYZBWRIBCZ-UGTJMOTHSA-N                                                                                                                                                                                                                                                      
KD9 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](OC(=O)c4ccc(cc4)C(=O)c5ccccc5)[C@H]3O"                                                                                                                                                                 
KD9 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](OC(=O)c4ccc(cc4)C(=O)c5ccccc5)[CH]3O"                                                                                                                                                                       
KD9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C(=O)c2ccc(cc2)C(=O)O[C@@H]3[C@H](O[C@H]([C@@H]3O)n4cnc5c4ncnc5N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O"                                                                                                                                                                       
KD9 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C(=O)c2ccc(cc2)C(=O)OC3C(OC(C3O)n4cnc5c4ncnc5N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O"                                                                                                                                                                                         
# 
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 
KD9 "SYSTEMATIC NAME" ACDLabs              12.01 
;3'-O-(4-benzoylbenzoyl)adenosine 5'-(tetrahydrogen triphosphate)
;
KD9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl] 4-(phenylcarbonyl)benzoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
KD9 "Create component" 2023-08-10 RCSB 
KD9 "Initial release"  2024-08-14 RCSB 
# 
