data_6KB
# 
_chem_comp.id                                    6KB 
_chem_comp.name                                  "4-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxybutanoic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H30 N5 O19 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-04-21 
_chem_comp.pdbx_modified_date                    2024-11-11 
_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                        725.385 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6KB 
_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        5JGY 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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 
6KB O18 O1  O 0 1 N N N N N N 17.502 32.243 40.533 -8.730 -5.285 2.711  O18 6KB 1  
6KB C18 C1  C 0 1 N N N N N N 17.388 31.805 41.717 -7.564 -5.486 2.467  C18 6KB 2  
6KB O19 O2  O 0 1 N N N N N N 16.476 32.141 42.498 -6.926 -6.518 3.042  O19 6KB 3  
6KB C17 C2  C 0 1 N N N N N N 18.394 30.820 42.251 -6.827 -4.583 1.511  C17 6KB 4  
6KB C16 C3  C 0 1 N N N N N N 19.765 31.447 42.038 -7.778 -3.501 0.996  C16 6KB 5  
6KB C15 C4  C 0 1 N N N N N N 19.569 32.929 41.848 -7.031 -2.585 0.026  C15 6KB 6  
6KB O17 O3  O 0 1 N N N N N N 20.579 33.745 41.239 -7.919 -1.574 -0.455 O17 6KB 7  
6KB C14 C5  C 0 1 N N R N N N 21.919 33.441 40.859 -7.317 -0.659 -1.373 C14 6KB 8  
6KB O14 O4  O 0 1 N N N N N N 22.821 34.204 41.679 -6.310 0.133  -0.706 O14 6KB 9  
6KB C13 C6  C 0 1 N N R N N N 22.138 33.984 39.444 -8.359 0.366  -1.873 C13 6KB 10 
6KB O16 O5  O 0 1 N N N N N N 23.210 33.361 38.720 -8.867 -0.020 -3.151 O16 6KB 11 
6KB C12 C7  C 0 1 N N S N N N 22.478 35.440 39.729 -7.564 1.686  -1.982 C12 6KB 12 
6KB O15 O6  O 0 1 N N N N N N 23.005 36.165 38.615 -7.557 2.156  -3.331 O15 6KB 13 
6KB C20 C8  C 0 1 N N R N N N 23.452 35.223 40.883 -6.136 1.303  -1.535 C20 6KB 14 
6KB C19 C9  C 0 1 N N N N N N 23.799 36.458 41.703 -5.507 2.440  -0.727 C19 6KB 15 
6KB O13 O7  O 0 1 N N N N N N 22.626 37.092 42.191 -4.149 2.114  -0.424 O13 6KB 16 
6KB PN  P1  P 0 0 N N N N N N 22.008 38.404 41.516 -3.181 3.087  0.418  NP  6KB 17 
6KB O12 O8  O 0 1 N N N N N N 20.586 38.465 41.997 -3.741 3.232  1.921  O12 6KB 18 
6KB O11 O9  O 0 1 N N N N N N 22.288 38.427 40.033 -3.142 4.420  -0.225 O11 6KB 19 
6KB O3  O10 O 0 1 N N N N N N 22.724 39.658 42.202 -1.697 2.466  0.456  O3  6KB 20 
6KB PA  P2  P 0 0 N N N N N N 24.150 40.031 42.879 -0.248 3.052  0.842  AP  6KB 21 
6KB O9  O11 O 0 1 N N N N N N 23.986 40.032 44.366 0.279  4.005  -0.344 O9  6KB 22 
6KB O10 O12 O 0 1 N N N N N N 25.273 39.258 42.256 -0.350 3.835  2.094  O10 6KB 23 
6KB O8  O13 O 0 1 N N N N N N 24.202 41.574 42.430 0.785  1.836  1.052  O8  6KB 24 
6KB C10 C10 C 0 1 N N N N N N 24.198 41.923 41.046 2.128  2.024  1.504  C10 6KB 25 
6KB C7  C11 C 0 1 N N R N N N 24.049 43.432 40.971 2.831  0.668  1.594  C7  6KB 26 
6KB C9  C12 C 0 1 N N R N N N 23.983 43.948 39.552 4.244  0.848  2.182  C9  6KB 27 
6KB O7  O14 O 0 1 N N N N N N 23.151 45.121 39.570 4.381  0.100  3.392  O7  6KB 28 
6KB O6  O15 O 0 1 N N N N N N 25.209 44.054 41.547 2.983  0.108  0.279  O6  6KB 29 
6KB C6  C13 C 0 1 N N R N N N 25.921 44.830 40.567 4.228  -0.622 0.273  C6  6KB 30 
6KB C8  C14 C 0 1 N N R N N N 25.423 44.304 39.237 5.184  0.286  1.088  C8  6KB 31 
6KB O4  O16 O 0 1 N N N N N N 25.490 45.297 38.227 6.243  -0.478 1.669  O4  6KB 32 
6KB PA2 P3  P 0 0 N N N N N N 26.280 45.056 36.851 7.799  -0.127 1.452  AP2 6KB 33 
6KB OP3 O17 O 0 1 N N N N N N 25.721 46.202 36.028 8.094  -0.067 0.003  OP3 6KB 34 
6KB OP2 O18 O 0 1 N N N N N N 27.744 45.205 37.162 8.126  1.298  2.125  OP2 6KB 35 
6KB OP1 O19 O 0 1 N N N N N N 25.876 43.705 36.301 8.707  -1.266 2.138  OP1 6KB 36 
6KB N5  N1  N 0 1 Y N N N N N 27.356 44.650 40.879 4.720  -0.793 -1.096 N5  6KB 37 
6KB C3  C15 C 0 1 Y N N N N N 28.072 45.480 41.644 5.576  -1.771 -1.535 C3  6KB 38 
6KB N3  N2  N 0 1 Y N N N N N 27.785 46.672 42.232 6.201  -2.796 -0.965 N3  6KB 39 
6KB C5  C16 C 0 1 Y N N N N N 28.731 47.300 42.925 6.983  -3.583 -1.674 C5  6KB 40 
6KB N2  N3  N 0 1 Y N N N N N 29.957 46.779 43.064 7.189  -3.401 -2.966 N2  6KB 41 
6KB C1  C17 C 0 1 Y N N N N N 30.283 45.597 42.511 6.607  -2.403 -3.622 C1  6KB 42 
6KB N1  N4  N 0 1 N N N N N N 31.535 45.115 42.682 6.828  -2.221 -4.976 N1  6KB 43 
6KB C2  C18 C 0 1 Y N N N N N 29.330 44.919 41.777 5.762  -1.536 -2.908 C2  6KB 44 
6KB N4  N5  N 0 1 Y N N N N N 29.335 43.741 41.106 5.023  -0.446 -3.230 N4  6KB 45 
6KB C4  C19 C 0 1 Y N N N N N 28.115 43.581 40.577 4.407  -0.012 -2.169 C4  6KB 46 
6KB H1  H1  H 0 1 N N N N N N 15.901 32.761 42.066 -7.441 -7.071 3.645  H1  6KB 47 
6KB H2  H2  H 0 1 N N N N N N 18.220 30.641 43.322 -5.989 -4.115 2.027  H2  6KB 48 
6KB H3  H3  H 0 1 N N N N N N 18.322 29.868 41.704 -6.455 -5.170 0.671  H3  6KB 49 
6KB H4  H4  H 0 1 N N N N N N 20.240 31.015 41.145 -8.617 -3.970 0.481  H4  6KB 50 
6KB H5  H5  H 0 1 N N N N N N 20.401 31.263 42.916 -8.150 -2.915 1.837  H5  6KB 51 
6KB H6  H6  H 0 1 N N N N N N 19.391 33.350 42.849 -6.192 -2.116 0.542  H6  6KB 52 
6KB H7  H7  H 0 1 N N N N N N 18.663 33.046 41.235 -6.659 -3.171 -0.814 H7  6KB 53 
6KB H8  H8  H 0 1 N N N N N N 22.132 32.363 40.900 -6.880 -1.199 -2.213 H8  6KB 54 
6KB H9  H9  H 0 1 N N N N N N 21.197 33.927 38.878 -9.171 0.467  -1.153 H9  6KB 55 
6KB H10 H10 H 0 1 N N N N N N 22.990 32.453 38.546 -9.375 -0.843 -3.141 H10 6KB 56 
6KB H11 H11 H 0 1 N N N N N N 21.580 35.944 40.115 -7.983 2.440  -1.316 H11 6KB 57 
6KB H12 H12 H 0 1 N N N N N N 22.915 37.098 38.773 -8.436 2.355  -3.683 H12 6KB 58 
6KB H13 H13 H 0 1 N N N N N N 24.387 34.822 40.464 -5.518 1.065  -2.402 H13 6KB 59 
6KB H14 H14 H 0 1 N N N N N N 24.427 36.159 42.555 -5.539 3.360  -1.310 H14 6KB 60 
6KB H15 H15 H 0 1 N N N N N N 24.353 37.166 41.070 -6.064 2.577  0.200  H15 6KB 61 
6KB H16 H16 H 0 1 N N N N N N 20.001 38.514 41.250 -3.794 2.396  2.403  H16 6KB 62 
6KB H17 H17 H 0 1 N N N N N N 24.668 39.501 44.761 0.370  3.557  -1.197 H17 6KB 63 
6KB H18 H18 H 0 1 N N N N N N 23.355 41.434 40.535 2.661  2.664  0.801  H18 6KB 64 
6KB H19 H19 H 0 1 N N N N N N 25.142 41.612 40.575 2.118  2.494  2.487  H19 6KB 65 
6KB H20 H20 H 0 1 N N N N N N 23.141 43.735 41.513 2.250  -0.009 2.220  H20 6KB 66 
6KB H21 H21 H 0 1 N N N N N N 23.605 43.177 38.865 4.451  1.903  2.361  H21 6KB 67 
6KB H22 H22 H 0 1 N N N N N N 22.256 44.872 39.769 3.774  0.372  4.093  H22 6KB 68 
6KB H23 H23 H 0 1 N N N N N N 25.654 45.893 40.657 4.108  -1.590 0.760  H23 6KB 69 
6KB H24 H24 H 0 1 N N N N N N 25.983 43.400 38.954 5.581  1.089  0.466  H24 6KB 70 
6KB H25 H25 H 0 1 N N N N N N 28.069 46.011 36.779 7.956  1.332  3.077  H25 6KB 71 
6KB H26 H26 H 0 1 N N N N N N 25.337 43.826 35.528 9.658  -1.119 2.046  H26 6KB 72 
6KB H27 H27 H 0 1 N N N N N N 28.506 48.251 43.386 7.476  -4.407 -1.180 H27 6KB 73 
6KB H28 H28 H 0 1 N N N N N N 32.067 45.757 43.234 7.413  -2.826 -5.457 H28 6KB 74 
6KB H29 H29 H 0 1 N N N N N N 31.491 44.232 43.148 6.397  -1.488 -5.443 H29 6KB 75 
6KB H30 H30 H 0 1 N N N N N N 27.791 42.728 39.999 3.747  0.842  -2.141 H30 6KB 76 
# 
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 
6KB OP3 PA2 DOUB N N 1  
6KB OP1 PA2 SING N N 2  
6KB PA2 OP2 SING N N 3  
6KB PA2 O4  SING N N 4  
6KB O4  C8  SING N N 5  
6KB O15 C12 SING N N 6  
6KB O16 C13 SING N N 7  
6KB C8  C9  SING N N 8  
6KB C8  C6  SING N N 9  
6KB C13 C12 SING N N 10 
6KB C13 C14 SING N N 11 
6KB C9  O7  SING N N 12 
6KB C9  C7  SING N N 13 
6KB C12 C20 SING N N 14 
6KB O11 PN  DOUB N N 15 
6KB O18 C18 DOUB N N 16 
6KB C6  N5  SING N N 17 
6KB C6  O6  SING N N 18 
6KB C4  N5  SING Y N 19 
6KB C4  N4  DOUB Y N 20 
6KB C14 O17 SING N N 21 
6KB C14 O14 SING N N 22 
6KB N5  C3  SING Y N 23 
6KB C20 O14 SING N N 24 
6KB C20 C19 SING N N 25 
6KB C7  C10 SING N N 26 
6KB C7  O6  SING N N 27 
6KB C10 O8  SING N N 28 
6KB N4  C2  SING Y N 29 
6KB O17 C15 SING N N 30 
6KB PN  O12 SING N N 31 
6KB PN  O13 SING N N 32 
6KB PN  O3  SING N N 33 
6KB C3  C2  DOUB Y N 34 
6KB C3  N3  SING Y N 35 
6KB C19 O13 SING N N 36 
6KB C18 C17 SING N N 37 
6KB C18 O19 SING N N 38 
6KB C2  C1  SING Y N 39 
6KB C15 C16 SING N N 40 
6KB C16 C17 SING N N 41 
6KB O3  PA  SING N N 42 
6KB N3  C5  DOUB Y N 43 
6KB O10 PA  DOUB N N 44 
6KB O8  PA  SING N N 45 
6KB C1  N1  SING N N 46 
6KB C1  N2  DOUB Y N 47 
6KB PA  O9  SING N N 48 
6KB C5  N2  SING Y N 49 
6KB O19 H1  SING N N 50 
6KB C17 H2  SING N N 51 
6KB C17 H3  SING N N 52 
6KB C16 H4  SING N N 53 
6KB C16 H5  SING N N 54 
6KB C15 H6  SING N N 55 
6KB C15 H7  SING N N 56 
6KB C14 H8  SING N N 57 
6KB C13 H9  SING N N 58 
6KB O16 H10 SING N N 59 
6KB C12 H11 SING N N 60 
6KB O15 H12 SING N N 61 
6KB C20 H13 SING N N 62 
6KB C19 H14 SING N N 63 
6KB C19 H15 SING N N 64 
6KB O12 H16 SING N N 65 
6KB O9  H17 SING N N 66 
6KB C10 H18 SING N N 67 
6KB C10 H19 SING N N 68 
6KB C7  H20 SING N N 69 
6KB C9  H21 SING N N 70 
6KB O7  H22 SING N N 71 
6KB C6  H23 SING N N 72 
6KB C8  H24 SING N N 73 
6KB OP2 H25 SING N N 74 
6KB OP1 H26 SING N N 75 
6KB C5  H27 SING N N 76 
6KB N1  H28 SING N N 77 
6KB N1  H29 SING N N 78 
6KB C4  H30 SING N N 79 
# 
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 
6KB SMILES           ACDLabs              12.01 "O=C(CCCOC1OC(C(C1O)O)COP(O)(OP(O)(=O)OCC4OC(n3c2c(c(ncn2)N)nc3)C(C4O)OP(O)(=O)O)=O)O"                                                                                                                                                                                                         
6KB InChI            InChI                1.03  "InChI=1S/C19H30N5O19P3/c20-16-11-17(22-6-21-16)24(7-23-11)18-15(42-44(30,31)32)13(28)9(40-18)5-39-46(35,36)43-45(33,34)38-4-8-12(27)14(29)19(41-8)37-3-1-2-10(25)26/h6-9,12-15,18-19,27-29H,1-5H2,(H,25,26)(H,33,34)(H,35,36)(H2,20,21,22)(H2,30,31,32)/t8-,9-,12-,13-,14-,15-,18-,19-/m1/s1" 
6KB InChIKey         InChI                1.03  NTVANGFJFQEJLS-LKAJGUBRSA-N                                                                                                                                                                                                                                                                    
6KB SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@@H](OCCCC(O)=O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O[P](O)(O)=O"                                                                                                                                                                 
6KB SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](OCCCC(O)=O)[CH](O)[CH]4O)[CH](O)[CH]3O[P](O)(O)=O"                                                                                                                                                                             
6KB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)OCCCC(=O)O)O)O)O)OP(=O)(O)O)N"                                                                                                                                                               
6KB SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)OCCCC(=O)O)O)O)O)OP(=O)(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 
6KB "SYSTEMATIC NAME" ACDLabs              12.01 "4-{[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]oxy}butanoic acid (non-preferred name)" 
6KB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxybutanoic acid"                              
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
6KB "Create component" 2016-04-21 RCSB 
6KB "Initial release"  2017-05-03 RCSB 
6KB "Modify atom id"   2019-02-11 RCSB 
6KB "Modify atom id"   2024-11-11 RCSB 
# 
