data_5J8 # _chem_comp.id 5J8 _chem_comp.name "[[(2R,3S,4R,5R)-5-(5-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H32 N7 O17 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-09-30 _chem_comp.pdbx_modified_date 2016-09-30 _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 747.437 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5J8 _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 5DXY _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 5J8 C4 C1 C 0 1 Y N N 63.003 107.427 107.279 6.179 -2.238 -0.291 C4 5J8 1 5J8 C5 C2 C 0 1 Y N N 64.358 106.999 107.361 6.357 -2.768 -1.579 C5 5J8 2 5J8 C6 C3 C 0 1 Y N N 64.620 105.650 107.109 7.293 -3.803 -1.748 C6 5J8 3 5J8 C8 C4 C 0 1 Y N N 64.282 109.157 107.810 4.850 -1.215 -1.722 C8 5J8 4 5J8 N1 N1 N 0 1 Y N N 63.576 104.829 106.801 7.964 -4.229 -0.683 N1 5J8 5 5J8 N3 N2 N 0 1 Y N N 62.043 106.541 106.967 6.894 -2.731 0.715 N3 5J8 6 5J8 NBU N3 N 0 1 N N N 55.590 95.926 108.065 -9.858 -0.716 4.346 NBU 5J8 7 5J8 CBT C5 C 0 1 N N N 54.534 96.695 107.460 -9.103 -0.423 3.268 CBT 5J8 8 5J8 OBV O1 O 0 1 N N N 53.472 96.169 107.115 -8.884 0.739 2.977 OBV 5J8 9 5J8 CBR C6 C 0 1 N N N 54.861 98.199 107.199 -8.566 -1.464 2.476 CBR 5J8 10 5J8 CBQ C7 C 0 1 N N N 55.863 98.674 108.230 -7.819 -1.143 1.409 CBQ 5J8 11 5J8 CBS C8 C 0 1 N N N 53.647 99.041 107.154 -8.849 -2.888 2.865 CBS 5J8 12 5J8 CBN C9 C 0 1 N N N 53.936 100.492 107.307 -8.623 -3.816 1.669 CBN 5J8 13 5J8 CBO C10 C 0 1 N N N 55.358 100.958 107.495 -7.255 -3.495 1.051 CBO 5J8 14 5J8 NBP N4 N 0 1 N N N 56.407 99.961 107.808 -7.280 -2.099 0.595 NBP 5J8 15 5J8 CBM C11 C 0 1 N N R 57.373 100.424 108.728 -6.739 -1.737 -0.717 CBM 5J8 16 5J8 OBG O2 O 0 1 N N N 56.744 101.111 109.858 -5.765 -0.679 -0.586 OBG 5J8 17 5J8 CBF C12 C 0 1 N N R 58.322 101.412 108.142 -7.850 -1.143 -1.611 CBF 5J8 18 5J8 OBI O3 O 0 1 N N N 59.472 100.810 107.545 -8.364 -2.137 -2.500 OBI 5J8 19 5J8 CBE C13 C 0 1 N N S 58.712 102.242 109.276 -7.135 -0.025 -2.404 CBE 5J8 20 5J8 OBJ O4 O 0 1 N N N 59.837 101.671 109.979 -7.186 -0.295 -3.806 OBJ 5J8 21 5J8 CBH C14 C 0 1 N N R 57.508 102.264 110.166 -5.678 -0.077 -1.895 CBH 5J8 22 5J8 CBK C15 C 0 1 N N N 56.707 103.536 109.957 -5.098 1.335 -1.795 CBK 5J8 23 5J8 OBL O5 O 0 1 N N N 56.401 103.684 108.593 -3.737 1.262 -1.364 OBL 5J8 24 5J8 PAA P1 P 0 1 N N N 55.854 105.059 108.006 -2.815 2.564 -1.149 PAA 5J8 25 5J8 OAC O6 O 0 1 N N N 55.604 104.925 106.539 -2.801 3.369 -2.391 OAC 5J8 26 5J8 OAB O7 O 0 1 N N N 54.627 105.483 108.722 -3.407 3.449 0.058 OAB 5J8 27 5J8 OAD O8 O 0 1 N N N 56.944 106.200 108.312 -1.314 2.104 -0.791 OAD 5J8 28 5J8 PAE P2 P 0 1 N N N 58.521 106.172 107.989 0.110 2.856 -0.764 PAE 5J8 29 5J8 OAG O9 O 0 1 N N N 58.840 105.234 106.835 -0.040 4.171 -0.101 OAG 5J8 30 5J8 OAF O10 O 0 1 N N N 59.280 105.818 109.270 0.632 3.071 -2.272 OAF 5J8 31 5J8 "O5'" O11 O 0 1 N N N 58.899 107.653 107.555 1.173 1.963 0.050 "O5'" 5J8 32 5J8 "C5'" C16 C 0 1 N N N 58.638 108.727 108.490 2.501 2.405 0.340 "C5'" 5J8 33 5J8 "C4'" C17 C 0 1 N N R 59.709 109.754 108.325 3.240 1.318 1.123 "C4'" 5J8 34 5J8 "O4'" O12 O 0 1 N N N 60.994 109.151 108.656 3.434 0.162 0.291 "O4'" 5J8 35 5J8 "C3'" C18 C 0 1 N N R 59.834 110.226 106.907 4.636 1.826 1.534 "C3'" 5J8 36 5J8 "O3'" O13 O 0 1 N N N 60.151 111.619 106.911 4.771 1.821 2.957 "O3'" 5J8 37 5J8 "C2'" C19 C 0 1 N N R 61.007 109.483 106.390 5.613 0.811 0.893 "C2'" 5J8 38 5J8 "O2'" O14 O 0 1 N N N 61.639 110.138 105.295 6.682 0.497 1.789 "O2'" 5J8 39 5J8 "P2'" P3 P 0 1 N N N 61.238 109.781 103.752 8.231 0.738 1.423 "P2'" 5J8 40 5J8 OP1 O15 O 0 1 N N N 61.133 108.250 103.609 8.649 -0.218 0.197 OP1 5J8 41 5J8 OP3 O16 O 0 1 N N N 62.372 110.347 102.847 8.433 2.152 1.037 OP3 5J8 42 5J8 OP2 O17 O 0 1 N N N 59.908 110.410 103.427 9.144 0.397 2.705 OP2 5J8 43 5J8 "C1'" C20 C 0 1 N N R 61.871 109.575 107.601 4.700 -0.421 0.668 "C1'" 5J8 44 5J8 N9 N5 N 0 1 Y N N 63.014 108.778 107.561 5.224 -1.261 -0.412 N9 5J8 45 5J8 N7 N6 N 0 1 Y N N 65.121 108.091 107.691 5.516 -2.100 -2.405 N7 5J8 46 5J8 C2 C21 C 0 1 Y N N 62.335 105.259 106.734 7.763 -3.698 0.510 C2 5J8 47 5J8 N6 N7 N 0 1 N N N 65.973 105.148 107.176 7.511 -4.365 -2.994 N6 5J8 48 5J8 H1 H1 H 0 1 N N N 64.589 110.160 108.067 4.110 -0.544 -2.133 H1 5J8 49 5J8 H2 H2 H 0 1 N N N 55.472 94.944 108.214 -10.226 -0.002 4.889 H2 5J8 50 5J8 H3 H3 H 0 1 N N N 56.442 96.374 108.337 -10.032 -1.642 4.578 H3 5J8 51 5J8 H5 H5 H 0 1 N N N 56.132 98.145 109.133 -7.638 -0.101 1.188 H5 5J8 52 5J8 H7 H7 H 0 1 N N N 53.148 98.884 106.186 -8.184 -3.179 3.679 H7 5J8 53 5J8 H8 H8 H 0 1 N N N 52.975 98.730 107.968 -9.883 -2.972 3.198 H8 5J8 54 5J8 H9 H9 H 0 1 N N N 53.555 100.990 106.403 -8.640 -4.853 2.003 H9 5J8 55 5J8 H10 H10 H 0 1 N N N 55.658 101.459 106.563 -6.474 -3.620 1.801 H10 5J8 56 5J8 H11 H11 H 0 1 N N N 57.952 99.571 109.111 -6.291 -2.608 -1.196 H11 5J8 57 5J8 H12 H12 H 0 1 N N N 57.791 102.027 107.400 -8.650 -0.725 -1.000 H12 5J8 58 5J8 H13 H13 H 0 1 N N N 60.037 101.487 107.191 -9.064 -1.817 -3.085 H13 5J8 59 5J8 H14 H14 H 0 1 N N N 58.945 103.263 108.940 -7.584 0.944 -2.186 H14 5J8 60 5J8 H15 H15 H 0 1 N N N 60.070 102.230 110.711 -8.083 -0.334 -4.167 H15 5J8 61 5J8 H16 H16 H 0 1 N N N 57.840 102.226 111.214 -5.067 -0.693 -2.556 H16 5J8 62 5J8 H17 H17 H 0 1 N N N 57.298 104.400 110.295 -5.145 1.817 -2.771 H17 5J8 63 5J8 H18 H18 H 0 1 N N N 55.774 103.480 110.537 -5.676 1.915 -1.075 H18 5J8 64 5J8 H19 H19 H 0 1 N N N 53.917 105.587 108.100 -3.446 2.984 0.905 H19 5J8 65 5J8 H20 H20 H 0 1 N N N 59.828 105.058 109.114 0.753 2.250 -2.767 H20 5J8 66 5J8 H21 H21 H 0 1 N N N 57.656 109.175 108.279 3.029 2.604 -0.592 H21 5J8 67 5J8 H22 H22 H 0 1 N N N 58.650 108.337 109.519 2.458 3.316 0.936 H22 5J8 68 5J8 H23 H23 H 0 1 N N N 59.508 110.611 108.985 2.667 1.045 2.009 H23 5J8 69 5J8 H24 H24 H 0 1 N N N 58.925 110.003 106.329 4.809 2.827 1.139 H24 5J8 70 5J8 H25 H25 H 0 1 N N N 59.409 112.112 107.240 4.143 2.397 3.414 H25 5J8 71 5J8 H26 H26 H 0 1 N N N 60.751 108.438 106.161 5.999 1.187 -0.054 H26 5J8 72 5J8 H27 H27 H 0 1 N N N 61.786 107.944 102.991 8.542 -1.162 0.381 H27 5J8 73 5J8 H28 H28 H 0 1 N N N 60.018 111.039 102.724 10.092 0.520 2.557 H28 5J8 74 5J8 H29 H29 H 0 1 N N N 62.150 110.628 107.757 4.598 -0.997 1.588 H29 5J8 75 5J8 H30 H30 H 0 1 N N N 61.543 104.567 106.488 8.330 -4.075 1.348 H30 5J8 76 5J8 H31 H31 H 0 1 N N N 65.977 104.170 106.969 7.014 -4.045 -3.763 H31 5J8 77 5J8 H32 H32 H 0 1 N N N 66.541 105.632 106.510 8.160 -5.078 -3.097 H32 5J8 78 5J8 H4 H4 H 0 1 N N N 53.369 100.839 108.183 -9.406 -3.654 0.928 H4 5J8 79 5J8 H6 H6 H 0 1 N N N 55.351 101.688 108.318 -7.067 -4.158 0.207 H6 5J8 80 # 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 5J8 OP3 "P2'" DOUB N N 1 5J8 OP2 "P2'" SING N N 2 5J8 OP1 "P2'" SING N N 3 5J8 "P2'" "O2'" SING N N 4 5J8 "O2'" "C2'" SING N N 5 5J8 "C2'" "C3'" SING N N 6 5J8 "C2'" "C1'" SING N N 7 5J8 OAC PAA DOUB N N 8 5J8 C2 N1 SING Y N 9 5J8 C2 N3 DOUB Y N 10 5J8 N1 C6 DOUB Y N 11 5J8 OAG PAE DOUB N N 12 5J8 "C3'" "O3'" SING N N 13 5J8 "C3'" "C4'" SING N N 14 5J8 N3 C4 SING Y N 15 5J8 C6 N6 SING N N 16 5J8 C6 C5 SING Y N 17 5J8 OBV CBT DOUB N N 18 5J8 CBS CBR SING N N 19 5J8 CBS CBN SING N N 20 5J8 CBR CBT SING N N 21 5J8 CBR CBQ DOUB N N 22 5J8 C4 C5 DOUB Y N 23 5J8 C4 N9 SING Y N 24 5J8 CBN CBO SING N N 25 5J8 C5 N7 SING Y N 26 5J8 CBT NBU SING N N 27 5J8 CBO NBP SING N N 28 5J8 OBI CBF SING N N 29 5J8 "O5'" PAE SING N N 30 5J8 "O5'" "C5'" SING N N 31 5J8 N9 "C1'" SING N N 32 5J8 N9 C8 SING Y N 33 5J8 "C1'" "O4'" SING N N 34 5J8 N7 C8 DOUB Y N 35 5J8 NBP CBQ SING N N 36 5J8 NBP CBM SING N N 37 5J8 PAE OAD SING N N 38 5J8 PAE OAF SING N N 39 5J8 PAA OAD SING N N 40 5J8 PAA OBL SING N N 41 5J8 PAA OAB SING N N 42 5J8 CBF CBM SING N N 43 5J8 CBF CBE SING N N 44 5J8 "C4'" "C5'" SING N N 45 5J8 "C4'" "O4'" SING N N 46 5J8 OBL CBK SING N N 47 5J8 CBM OBG SING N N 48 5J8 CBE OBJ SING N N 49 5J8 CBE CBH SING N N 50 5J8 OBG CBH SING N N 51 5J8 CBK CBH SING N N 52 5J8 C8 H1 SING N N 53 5J8 NBU H2 SING N N 54 5J8 NBU H3 SING N N 55 5J8 CBQ H5 SING N N 56 5J8 CBS H7 SING N N 57 5J8 CBS H8 SING N N 58 5J8 CBN H9 SING N N 59 5J8 CBO H10 SING N N 60 5J8 CBM H11 SING N N 61 5J8 CBF H12 SING N N 62 5J8 OBI H13 SING N N 63 5J8 CBE H14 SING N N 64 5J8 OBJ H15 SING N N 65 5J8 CBH H16 SING N N 66 5J8 CBK H17 SING N N 67 5J8 CBK H18 SING N N 68 5J8 OAB H19 SING N N 69 5J8 OAF H20 SING N N 70 5J8 "C5'" H21 SING N N 71 5J8 "C5'" H22 SING N N 72 5J8 "C4'" H23 SING N N 73 5J8 "C3'" H24 SING N N 74 5J8 "O3'" H25 SING N N 75 5J8 "C2'" H26 SING N N 76 5J8 OP1 H27 SING N N 77 5J8 OP2 H28 SING N N 78 5J8 "C1'" H29 SING N N 79 5J8 C2 H30 SING N N 80 5J8 N6 H31 SING N N 81 5J8 N6 H32 SING N N 82 5J8 CBN H4 SING N N 83 5J8 CBO H6 SING N N 84 # 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 5J8 InChI InChI 1.03 ;InChI=1S/C21H32N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h4,7-8,10-11,13-16,20-21,29-31H,1-3,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 ; 5J8 InChIKey InChI 1.03 XBYZUJOLVDCGQT-NNYOXOHSSA-N 5J8 SMILES_CANONICAL CACTVS 3.385 "NC(=O)C1=CN(CCC1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O" 5J8 SMILES CACTVS 3.385 "NC(=O)C1=CN(CCC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O" 5J8 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "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)N5CCCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N" 5J8 SMILES "OpenEye OEToolkits" 1.9.2 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5CCCC(=C5)C(=O)N)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 5J8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[[(2R,3S,4R,5R)-5-(5-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5J8 "Create component" 2015-09-30 RCSB 5J8 "Initial release" 2016-10-05 RCSB #