data_SL3 # _chem_comp.id SL3 _chem_comp.name ;2'-DEOXY-3'-O-(2,2,5,5-TETRAMETHYL-1-OXYL-PYRROLIN-3-YL) ADENOSINE 5'-DIPHOSPHATE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H28 N6 O11 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-04-23 _chem_comp.pdbx_modified_date 2011-06-04 _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 578.407 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SL3 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 SL3 N6 N6 N 0 1 N N N -2.671 15.259 38.319 -3.826 4.091 2.985 N6 SL3 1 SL3 C6 C6 C 0 1 Y N N -2.382 14.872 39.215 -2.655 3.315 3.026 C6 SL3 2 SL3 N1 N1 N 0 1 Y N N -2.441 14.924 40.642 -2.313 2.657 4.159 N1 SL3 3 SL3 C2 C2 C 0 1 Y N N -1.859 14.322 41.692 -1.173 1.925 4.138 C2 SL3 4 SL3 N3 N3 N 0 1 Y N N -0.828 13.497 41.534 -0.299 1.747 3.123 N3 SL3 5 SL3 C4 C4 C 0 1 Y N N -0.398 13.250 40.272 -0.699 2.425 2.036 C4 SL3 6 SL3 C5 C5 C 0 1 Y N N -0.968 13.937 39.251 -1.833 3.210 1.908 C5 SL3 7 SL3 N7 N7 N 0 1 Y N N -0.583 13.542 38.104 -1.913 3.746 0.647 N7 SL3 8 SL3 C8 C8 C 0 1 Y N N 0.234 12.534 38.389 -0.847 3.294 0.021 C8 SL3 9 SL3 N9 N9 N 0 1 Y N N 0.345 12.330 39.679 -0.077 2.488 0.819 N9 SL3 10 SL3 "C1'" "C1'" C 0 1 N N R 1.299 11.479 40.346 1.171 1.827 0.433 "C1'" SL3 11 SL3 "C2'" "C2'" C 0 1 N N N 1.055 10.028 40.359 0.970 0.461 -0.212 "C2'" SL3 12 SL3 "O4'" "O4'" O 0 1 N N N 2.288 11.318 39.418 1.879 2.654 -0.508 "O4'" SL3 13 SL3 "C4'" "C4'" C 0 1 N N R 3.277 10.378 39.966 2.219 1.846 -1.646 "C4'" SL3 14 SL3 "C5'" "C5'" C 0 1 N N N 3.963 9.649 38.799 2.240 2.706 -2.896 "C5'" SL3 15 SL3 "O5'" "O5'" O 0 1 N N N 3.157 9.932 37.613 0.966 3.305 -3.056 "O5'" SL3 16 SL3 PA PA P 0 1 N N R 2.682 8.766 36.643 0.684 4.285 -4.313 PA SL3 17 SL3 O2A O2A O 0 1 N N N 3.466 7.571 37.038 -0.704 4.855 -4.367 O2A SL3 18 SL3 O1A O1A O 0 1 N N N 0.840 8.980 36.347 1.858 5.395 -4.230 O1A SL3 19 SL3 O3A O3A O 0 1 N N N 2.974 9.257 35.146 1.092 3.410 -5.610 O3A SL3 20 SL3 PB PB P 0 1 N N N 3.887 8.718 33.946 0.436 2.073 -6.236 PB SL3 21 SL3 O2B O2B O 0 1 N N N 3.862 9.896 33.056 0.423 0.890 -5.313 O2B SL3 22 SL3 O1B O1B O 0 1 N N N 5.172 8.277 34.526 1.263 1.867 -7.609 O1B SL3 23 SL3 O3B O3B O 0 1 N N N 3.119 7.540 33.426 -1.016 2.571 -6.741 O3B SL3 24 SL3 "C3'" "C3'" C 0 1 N N S 2.414 9.382 40.661 1.177 0.741 -1.684 "C3'" SL3 25 SL3 "O3'" "O3'" O 0 1 N N N 2.581 9.034 42.033 1.636 -0.408 -2.366 "O3'" SL3 26 SL3 C1 C1 C 0 1 N N N 2.081 7.794 42.300 0.794 -1.477 -2.361 C1 SL3 27 SL3 OC OC O 0 1 N N N 2.417 6.821 41.628 -0.310 -1.540 -1.829 OC SL3 28 SL3 CA CA C 0 1 N N N 1.255 7.637 43.547 1.407 -2.570 -3.097 CA SL3 29 SL3 CB CB C 0 1 N N N 0.473 6.411 43.926 2.730 -2.730 -3.155 CB SL3 30 SL3 CC CC C 0 1 N N N -0.482 6.671 45.047 3.076 -3.963 -3.944 CC SL3 31 SL3 CC1 CC1 C 0 1 N N N -0.125 5.801 46.249 3.563 -5.072 -2.992 CC1 SL3 32 SL3 CC2 CC2 C 0 1 N N N -1.931 6.554 44.585 4.214 -3.684 -4.944 CC2 SL3 33 SL3 ND ND N 0 1 N N N -0.198 8.105 45.215 1.771 -4.406 -4.561 ND SL3 34 SL3 OR OR O 0 1 N N N -0.769 8.740 46.193 1.769 -3.934 -5.941 OR SL3 35 SL3 CE CE C 0 1 N N N 0.810 8.790 44.389 0.676 -3.658 -3.830 CE SL3 36 SL3 CE2 CE2 C 0 1 N N N 1.897 9.546 45.146 0.027 -4.634 -2.828 CE2 SL3 37 SL3 CE1 CE1 C 0 1 N N N 0.120 9.907 43.609 -0.448 -3.121 -4.741 CE1 SL3 38 SL3 H61 H61 H 0 1 N N N -2.094 15.038 37.524 -4.719 3.638 3.033 H61 SL3 39 SL3 H62 H62 H 0 1 N N N -3.521 15.782 38.311 -3.758 5.076 2.815 H62 SL3 40 SL3 H2 H2 H 0 1 N N N -2.190 14.470 42.708 -0.929 1.412 5.062 H2 SL3 41 SL3 H8 H8 H 0 1 N N N 0.911 12.096 37.656 -0.579 3.514 -1.004 H8 SL3 42 SL3 "H1'" "H1'" H 0 1 N N N 1.262 11.849 41.371 1.753 1.756 1.357 "H1'" SL3 43 SL3 "H21'" "H21'" H 0 0 N N N 0.758 9.815 39.351 -0.002 0.004 0.001 "H21'" SL3 44 SL3 "H22'" "H22'" H 0 0 N N N 0.231 9.486 41.011 1.736 -0.240 0.147 "H22'" SL3 45 SL3 "H4'" "H4'" H 0 1 N N N 4.066 10.365 40.548 3.224 1.436 -1.487 "H4'" SL3 46 SL3 "H51'" "H51'" H 0 0 N N N 4.528 8.618 39.144 2.459 2.091 -3.771 "H51'" SL3 47 SL3 "H52'" "H52'" H 0 0 N N N 4.566 10.205 38.277 2.994 3.488 -2.801 "H52'" SL3 48 SL3 "H3'" "H3'" H 0 1 N N N 2.741 8.721 40.008 0.241 1.086 -2.140 "H3'" SL3 49 SL3 HCB HCB H 0 1 N N N 0.411 5.487 43.368 3.459 -2.090 -2.676 HCB SL3 50 SL3 H1CC H1CC H 0 0 N N N -0.793 6.152 47.034 4.055 -4.639 -2.116 H1CC SL3 51 SL3 H2CC H2CC H 0 0 N N N 0.833 5.968 46.738 2.721 -5.681 -2.648 H2CC SL3 52 SL3 H3CC H3CC H 0 0 N N N -0.110 4.758 45.931 4.277 -5.728 -3.499 H3CC SL3 53 SL3 H4CC H4CC H 0 0 N N N -1.979 5.485 44.382 4.364 -2.607 -5.065 H4CC SL3 54 SL3 H5CC H5CC H 0 0 N N N -2.130 7.091 43.657 5.152 -4.125 -4.593 H5CC SL3 55 SL3 H6CC H6CC H 0 0 N N N -2.522 6.777 45.474 3.979 -4.111 -5.924 H6CC SL3 56 SL3 HOR HOR H 0 1 N N N -0.053 8.687 46.834 1.414 -3.036 -5.813 HOR SL3 57 SL3 H4CE H4CE H 0 0 N N N 1.451 10.159 45.931 -0.819 -5.152 -3.289 H4CE SL3 58 SL3 H5CE H5CE H 0 0 N N N 2.513 10.207 44.537 0.752 -5.385 -2.498 H5CE SL3 59 SL3 H6CE H6CE H 0 0 N N N 2.488 8.917 45.811 -0.337 -4.096 -1.948 H6CE SL3 60 SL3 H1CE H1CE H 0 0 N N N -0.291 10.666 44.274 -0.834 -3.917 -5.385 H1CE SL3 61 SL3 H2CE H2CE H 0 0 N N N -0.682 9.352 43.117 -1.275 -2.731 -4.142 H2CE SL3 62 SL3 H3CE H3CE H 0 0 N N N 0.846 10.763 42.670 -0.074 -2.315 -5.379 H3CE SL3 63 SL3 HO1 HO1 H 0 1 N N N 5.816 8.182 33.834 1.108 1.057 -8.140 HO1 SL3 64 SL3 HO2 HO2 H 0 1 N N N 2.957 7.652 32.497 -1.648 1.910 -7.097 HO2 SL3 65 SL3 HO3 HO3 H 0 1 N N N 0.387 9.016 37.181 1.763 6.140 -3.599 HO3 SL3 66 # 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 SL3 N6 C6 SING N N 1 SL3 N6 H61 SING N N 2 SL3 N6 H62 SING N N 3 SL3 C6 N1 DOUB Y N 4 SL3 C6 C5 SING Y N 5 SL3 N1 C2 SING Y N 6 SL3 C2 N3 DOUB Y N 7 SL3 C2 H2 SING N N 8 SL3 N3 C4 SING Y N 9 SL3 C4 C5 DOUB Y N 10 SL3 C4 N9 SING Y N 11 SL3 C5 N7 SING Y N 12 SL3 N7 C8 DOUB Y N 13 SL3 C8 N9 SING Y N 14 SL3 C8 H8 SING N N 15 SL3 N9 "C1'" SING N N 16 SL3 "C1'" "C2'" SING N N 17 SL3 "C1'" "O4'" SING N N 18 SL3 "C1'" "H1'" SING N N 19 SL3 "C2'" "C3'" SING N N 20 SL3 "C2'" "H21'" SING N N 21 SL3 "C2'" "H22'" SING N N 22 SL3 "O4'" "C4'" SING N N 23 SL3 "C4'" "C5'" SING N N 24 SL3 "C4'" "C3'" SING N N 25 SL3 "C4'" "H4'" SING N N 26 SL3 "C5'" "O5'" SING N N 27 SL3 "C5'" "H51'" SING N N 28 SL3 "C5'" "H52'" SING N N 29 SL3 "O5'" PA SING N N 30 SL3 PA O2A DOUB N N 31 SL3 PA O1A SING N N 32 SL3 PA O3A SING N N 33 SL3 O3A PB SING N N 34 SL3 PB O2B DOUB N N 35 SL3 PB O1B SING N N 36 SL3 PB O3B SING N N 37 SL3 "C3'" "O3'" SING N N 38 SL3 "C3'" "H3'" SING N N 39 SL3 "O3'" C1 SING N N 40 SL3 C1 OC DOUB N N 41 SL3 C1 CA SING N N 42 SL3 CA CB DOUB N N 43 SL3 CA CE SING N N 44 SL3 CB CC SING N N 45 SL3 CB HCB SING N N 46 SL3 CC CC1 SING N N 47 SL3 CC CC2 SING N N 48 SL3 CC ND SING N N 49 SL3 CC1 H1CC SING N N 50 SL3 CC1 H2CC SING N N 51 SL3 CC1 H3CC SING N N 52 SL3 CC2 H4CC SING N N 53 SL3 CC2 H5CC SING N N 54 SL3 CC2 H6CC SING N N 55 SL3 ND OR SING N N 56 SL3 ND CE SING N N 57 SL3 OR HOR SING N N 58 SL3 CE CE2 SING N N 59 SL3 CE CE1 SING N N 60 SL3 CE2 H4CE SING N N 61 SL3 CE2 H5CE SING N N 62 SL3 CE2 H6CE SING N N 63 SL3 CE1 H1CE SING N N 64 SL3 CE1 H2CE SING N N 65 SL3 CE1 H3CE SING N N 66 SL3 HO1 O1B SING N N 67 SL3 HO2 O3B SING N N 68 SL3 HO3 O1A SING N N 69 # 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 SL3 SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC4OC(n2cnc1c(ncnc12)N)CC4OC(=O)C3=CC(N(O)C3(C)C)(C)C" SL3 SMILES_CANONICAL CACTVS 3.341 "CC1(C)C=C(C(=O)O[C@H]2C[C@@H](O[C@@H]2CO[P@](O)(=O)O[P](O)(O)=O)n3cnc4c(N)ncnc34)C(C)(C)N1O" SL3 SMILES CACTVS 3.341 "CC1(C)C=C(C(=O)O[CH]2C[CH](O[CH]2CO[P](O)(=O)O[P](O)(O)=O)n3cnc4c(N)ncnc34)C(C)(C)N1O" SL3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1(C=C(C(N1O)(C)C)C(=O)O[C@H]2C[C@@H](O[C@@H]2CO[P@@](=O)(O)OP(=O)(O)O)n3cnc4c3ncnc4N)C" SL3 SMILES "OpenEye OEToolkits" 1.5.0 "CC1(C=C(C(N1O)(C)C)C(=O)OC2CC(OC2COP(=O)(O)OP(=O)(O)O)n3cnc4c3ncnc4N)C" SL3 InChI InChI 1.03 "InChI=1S/C19H28N6O11P2/c1-18(2)6-10(19(3,4)25(18)27)17(26)35-11-5-13(24-9-23-14-15(20)21-8-22-16(14)24)34-12(11)7-33-38(31,32)36-37(28,29)30/h6,8-9,11-13,27H,5,7H2,1-4H3,(H,31,32)(H2,20,21,22)(H2,28,29,30)/t11-,12+,13+/m0/s1" SL3 InChIKey InChI 1.03 FRRWKBVVFMOZOW-YNEHKIRRSA-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 SL3 "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-3'-O-[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)carbonyl]adenosine 5'-(trihydrogen diphosphate) ; SL3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-[(hydroxy-phosphonooxy-phosphoryl)oxymethyl]oxolan-3-yl] 1-hydroxy-2,2,5,5-tetramethyl-pyrrole-3-carboxylate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SL3 "Create component" 2003-04-23 RCSB SL3 "Modify descriptor" 2011-06-04 RCSB #