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 2019-02-11 _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 # 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 6KB O18 O1 O 0 1 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 17.388 31.805 41.717 -7.564 -5.486 2.467 C18 6KB 2 6KB O19 O2 O 0 1 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 18.394 30.820 42.251 -6.827 -4.583 1.511 C17 6KB 4 6KB C16 C3 C 0 1 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 19.569 32.929 41.848 -7.031 -2.585 0.026 C15 6KB 6 6KB O17 O3 O 0 1 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 21.919 33.441 40.859 -7.317 -0.659 -1.373 C14 6KB 8 6KB O14 O4 O 0 1 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 22.138 33.984 39.444 -8.359 0.366 -1.873 C13 6KB 10 6KB O16 O5 O 0 1 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 22.478 35.440 39.729 -7.564 1.686 -1.982 C12 6KB 12 6KB O15 O6 O 0 1 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 23.452 35.223 40.883 -6.136 1.303 -1.535 C20 6KB 14 6KB C19 C9 C 0 1 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 22.626 37.092 42.191 -4.149 2.114 -0.424 O13 6KB 16 6KB NP P1 P 0 0 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 20.586 38.465 41.997 -3.741 3.232 1.921 O12 6KB 18 6KB O11 O9 O 0 1 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 22.724 39.658 42.202 -1.697 2.466 0.456 O3 6KB 20 6KB AP P2 P 0 0 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 23.986 40.032 44.366 0.279 4.005 -0.344 O9 6KB 22 6KB O10 O12 O 0 1 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 24.202 41.574 42.430 0.785 1.836 1.052 O8 6KB 24 6KB C10 C10 C 0 1 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 24.049 43.432 40.971 2.831 0.668 1.594 C7 6KB 26 6KB C9 C12 C 0 1 N N R 23.983 43.948 39.552 4.244 0.848 2.182 C9 6KB 27 6KB O7 O14 O 0 1 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 25.209 44.054 41.547 2.983 0.108 0.279 O6 6KB 29 6KB C6 C13 C 0 1 N N R 25.921 44.830 40.567 4.228 -0.622 0.273 C6 6KB 30 6KB C8 C14 C 0 1 N N R 25.423 44.304 39.237 5.184 0.286 1.088 C8 6KB 31 6KB O4 O16 O 0 1 N N N 25.490 45.297 38.227 6.243 -0.478 1.669 O4 6KB 32 6KB AP2 P3 P 0 0 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 25.721 46.202 36.028 8.094 -0.067 0.003 OP3 6KB 34 6KB OP2 O18 O 0 1 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 25.876 43.705 36.301 8.707 -1.266 2.138 OP1 6KB 36 6KB N5 N1 N 0 1 Y 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 28.072 45.480 41.644 5.576 -1.771 -1.535 C3 6KB 38 6KB N3 N2 N 0 1 Y 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 28.731 47.300 42.925 6.983 -3.583 -1.674 C5 6KB 40 6KB N2 N3 N 0 1 Y 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 30.283 45.597 42.511 6.607 -2.403 -3.622 C1 6KB 42 6KB N1 N4 N 0 1 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 29.330 44.919 41.777 5.762 -1.536 -2.908 C2 6KB 44 6KB N4 N5 N 0 1 Y 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 28.115 43.581 40.577 4.407 -0.012 -2.169 C4 6KB 46 6KB H1 H1 H 0 1 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 18.220 30.641 43.322 -5.989 -4.115 2.027 H2 6KB 48 6KB H3 H3 H 0 1 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 20.240 31.015 41.145 -8.617 -3.970 0.481 H4 6KB 50 6KB H5 H5 H 0 1 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 19.391 33.350 42.849 -6.192 -2.116 0.542 H6 6KB 52 6KB H7 H7 H 0 1 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 22.132 32.363 40.900 -6.880 -1.199 -2.213 H8 6KB 54 6KB H9 H9 H 0 1 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 22.990 32.453 38.546 -9.375 -0.843 -3.141 H10 6KB 56 6KB H11 H11 H 0 1 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 22.915 37.098 38.773 -8.436 2.355 -3.683 H12 6KB 58 6KB H13 H13 H 0 1 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 24.427 36.159 42.555 -5.539 3.360 -1.310 H14 6KB 60 6KB H15 H15 H 0 1 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 20.001 38.514 41.250 -3.794 2.396 2.403 H16 6KB 62 6KB H17 H17 H 0 1 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 23.355 41.434 40.535 2.661 2.664 0.801 H18 6KB 64 6KB H19 H19 H 0 1 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 23.141 43.735 41.513 2.250 -0.009 2.220 H20 6KB 66 6KB H21 H21 H 0 1 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 22.256 44.872 39.769 3.774 0.372 4.093 H22 6KB 68 6KB H23 H23 H 0 1 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 25.983 43.400 38.954 5.581 1.089 0.466 H24 6KB 70 6KB H25 H25 H 0 1 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 25.337 43.826 35.528 9.658 -1.119 2.046 H26 6KB 72 6KB H27 H27 H 0 1 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 32.067 45.757 43.234 7.413 -2.826 -5.457 H28 6KB 74 6KB H29 H29 H 0 1 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 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 AP2 DOUB N N 1 6KB OP1 AP2 SING N N 2 6KB AP2 OP2 SING N N 3 6KB AP2 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 NP 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 NP O12 SING N N 31 6KB NP O13 SING N N 32 6KB NP 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 AP SING N N 42 6KB N3 C5 DOUB Y N 43 6KB O10 AP DOUB N N 44 6KB O8 AP SING N N 45 6KB C1 N1 SING N N 46 6KB C1 N2 DOUB Y N 47 6KB AP 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 #