data_12A # _chem_comp.id 12A _chem_comp.name "2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C16 H23 N6 O11 P S" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-08-09 _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 538.426 _chem_comp.one_letter_code A _chem_comp.three_letter_code 12A _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1FIR _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 12A OP3 O3P O 0 1 N Y N 17.331 20.018 -1.562 -2.878 1.720 -7.838 OP3 12A 1 12A P P P 0 1 N N N 17.138 21.317 -0.657 -2.012 0.414 -7.469 P 12A 2 12A OP1 O1P O 0 1 N N N 17.941 22.427 -1.245 -2.916 -0.662 -7.007 OP1 12A 3 12A OP2 O2P O 0 1 N N N 15.687 21.501 -0.408 -1.208 -0.082 -8.773 OP2 12A 4 12A "O5'" O5* O 0 1 N N N 17.832 20.896 0.707 -0.967 0.776 -6.300 "O5'" 12A 5 12A "C5'" C5* C 0 1 N N N 18.260 21.879 1.610 -0.232 -0.416 -6.019 "C5'" 12A 6 12A "C4'" C4* C 0 1 N N R 18.565 21.264 2.941 0.783 -0.140 -4.909 "C4'" 12A 7 12A "O4'" O4* O 0 1 N N N 19.647 20.316 2.805 0.108 0.259 -3.697 "O4'" 12A 8 12A "C3'" C3* C 0 1 N N S 19.021 22.296 3.958 1.537 -1.435 -4.533 "C3'" 12A 9 12A "O3'" O3* O 0 1 N N N 17.874 22.660 4.714 2.805 -1.485 -5.189 "O3'" 12A 10 12A "C2'" C2* C 0 1 N N R 20.040 21.524 4.782 1.723 -1.330 -3.001 "C2'" 12A 11 12A "O2'" O2* O 0 1 N N N 19.452 20.704 5.771 3.112 -1.315 -2.665 "O2'" 12A 12 12A "C1'" C1* C 0 1 N N R 20.674 20.651 3.703 1.056 0.014 -2.635 "C1'" 12A 13 12A N9 N9 N 0 1 Y N N 21.642 21.390 2.921 0.364 -0.093 -1.348 N9 12A 14 12A C8 C8 C 0 1 Y N N 21.521 21.717 1.604 -0.925 -0.494 -1.156 C8 12A 15 12A N7 N7 N 0 1 Y N N 22.538 22.383 1.132 -1.214 -0.471 0.111 N7 12A 16 12A C5 C5 C 0 1 Y N N 23.384 22.501 2.218 -0.131 -0.056 0.813 C5 12A 17 12A C6 C6 C 0 1 Y N N 24.620 23.092 2.364 0.138 0.155 2.175 C6 12A 18 12A N6 N6 N 0 1 N N N 25.272 23.674 1.383 -0.838 -0.072 3.135 N6 12A 19 12A N1 N1 N 0 1 Y N N 25.197 23.048 3.574 1.346 0.579 2.525 N1 12A 20 12A C2 C2 C 0 1 Y N N 24.562 22.419 4.563 2.286 0.801 1.615 C2 12A 21 12A N3 N3 N 0 1 Y N N 23.384 21.820 4.549 2.073 0.619 0.321 N3 12A 22 12A C4 C4 C 0 1 Y N N 22.842 21.897 3.328 0.894 0.191 -0.115 C4 12A 23 12A S2 S2 S 0 1 N N N 25.169 22.353 5.752 3.870 1.363 2.145 S2 12A 24 12A C2M C2M C 0 1 N N N 26.447 23.647 5.613 3.594 1.437 3.933 C2M 12A 25 12A CC CC C 0 1 N N N 26.582 23.549 1.361 -0.564 0.135 4.438 CC 12A 26 12A OO OO O 0 1 N N N 27.160 22.913 2.239 0.538 0.523 4.773 OO 12A 27 12A N N N 0 1 N N N 27.248 24.126 0.375 -1.512 -0.086 5.370 N 12A 28 12A CA CA C 0 1 N N S 28.700 24.021 0.300 -1.214 0.140 6.786 CA 12A 29 12A C C C 0 1 N N N 29.332 23.725 1.677 -0.676 -1.128 7.396 C 12A 30 12A O O O 0 1 N N N 29.722 22.549 1.886 0.107 -1.072 8.314 O 12A 31 12A OXT OXT O 0 1 N N N 29.398 24.640 2.534 -1.066 -2.320 6.918 OXT 12A 32 12A CB CB C 0 1 N N R 29.307 25.315 -0.332 -2.493 0.553 7.517 CB 12A 33 12A OG1 OG1 O 0 1 N N N 30.688 25.432 0.037 -3.468 -0.483 7.395 OG1 12A 34 12A CG2 CG2 C 0 1 N N N 28.515 26.563 0.099 -3.040 1.842 6.898 CG2 12A 35 12A HOP3 3HOP H 0 0 N N N 16.819 19.310 -1.187 -3.490 1.461 -8.541 HOP3 12A 36 12A HOP2 2HOP H 0 0 N N N 15.572 22.274 0.131 -0.632 0.647 -9.041 HOP2 12A 37 12A "H5'" 1H5* H 0 1 N N N 19.124 22.460 1.212 0.290 -0.742 -6.918 "H5'" 12A 38 12A "H5''" 2H5* H 0 0 N N N 17.525 22.713 1.695 -0.919 -1.198 -5.695 "H5''" 12A 39 12A "H4'" H4* H 0 1 N N N 17.623 20.780 3.290 1.487 0.630 -5.224 "H4'" 12A 40 12A "H3'" H3* H 0 1 N N N 19.462 23.235 3.550 0.941 -2.311 -4.787 "H3'" 12A 41 12A "HO3'" H3T H 0 0 N Y N 18.159 23.305 5.350 3.228 -2.311 -4.918 "HO3'" 12A 42 12A "H2'" H2* H 0 1 N N N 20.732 22.189 5.348 1.219 -2.155 -2.497 "H2'" 12A 43 12A "HO2'" 2HO* H 0 0 N N N 20.088 20.221 6.285 3.483 -2.153 -2.972 "HO2'" 12A 44 12A "H1'" H1* H 0 1 N N N 21.167 19.778 4.191 1.800 0.809 -2.599 "H1'" 12A 45 12A H8 H8 H 0 1 N N N 20.659 21.460 0.964 -1.606 -0.787 -1.942 H8 12A 46 12A HN6 HN6 H 0 1 N N N 25.028 24.664 1.358 -1.718 -0.382 2.868 HN6 12A 47 12A H2M1 1H2M H 0 0 N N N 26.953 23.591 6.604 4.504 1.778 4.427 H2M1 12A 48 12A H2M2 2H2M H 0 0 N N N 27.124 23.544 4.733 2.782 2.133 4.147 H2M2 12A 49 12A H2M3 3H2M H 0 0 N N N 26.063 24.657 5.337 3.329 0.446 4.301 H2M3 12A 50 12A H H H 0 1 N N N 26.668 24.629 -0.296 -2.392 -0.395 5.103 H 12A 51 12A HA HA H 0 1 N N N 28.942 23.154 -0.359 -0.471 0.931 6.879 HA 12A 52 12A HXT HXT H 0 1 N N N 29.786 24.457 3.381 -0.721 -3.134 7.309 HXT 12A 53 12A HB HB H 0 1 N N N 29.236 25.239 -1.442 -2.272 0.722 8.571 HB 12A 54 12A HG1 HG1 H 0 1 N N N 31.057 26.218 -0.347 -3.635 -0.600 6.450 HG1 12A 55 12A HG21 1HG2 H 0 0 N N N 28.948 27.486 -0.351 -3.951 2.136 7.419 HG21 12A 56 12A HG22 2HG2 H 0 0 N N N 27.429 26.461 -0.133 -2.296 2.633 6.991 HG22 12A 57 12A HG23 3HG2 H 0 0 N N N 28.443 26.641 1.208 -3.262 1.673 5.845 HG23 12A 58 # 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 12A OP3 P SING N N 1 12A OP3 HOP3 SING N N 2 12A P OP1 DOUB N N 3 12A P OP2 SING N N 4 12A P "O5'" SING N N 5 12A OP2 HOP2 SING N N 6 12A "O5'" "C5'" SING N N 7 12A "C5'" "C4'" SING N N 8 12A "C5'" "H5'" SING N N 9 12A "C5'" "H5''" SING N N 10 12A "C4'" "O4'" SING N N 11 12A "C4'" "C3'" SING N N 12 12A "C4'" "H4'" SING N N 13 12A "O4'" "C1'" SING N N 14 12A "C3'" "O3'" SING N N 15 12A "C3'" "C2'" SING N N 16 12A "C3'" "H3'" SING N N 17 12A "O3'" "HO3'" SING N N 18 12A "C2'" "O2'" SING N N 19 12A "C2'" "C1'" SING N N 20 12A "C2'" "H2'" SING N N 21 12A "O2'" "HO2'" SING N N 22 12A "C1'" N9 SING N N 23 12A "C1'" "H1'" SING N N 24 12A N9 C8 SING Y N 25 12A N9 C4 SING Y N 26 12A C8 N7 DOUB Y N 27 12A C8 H8 SING N N 28 12A N7 C5 SING Y N 29 12A C5 C6 SING Y N 30 12A C5 C4 DOUB Y N 31 12A C6 N6 SING N N 32 12A C6 N1 DOUB Y N 33 12A N6 CC SING N N 34 12A N6 HN6 SING N N 35 12A N1 C2 SING Y N 36 12A C2 N3 DOUB Y N 37 12A C2 S2 SING N N 38 12A N3 C4 SING Y N 39 12A S2 C2M SING N N 40 12A C2M H2M1 SING N N 41 12A C2M H2M2 SING N N 42 12A C2M H2M3 SING N N 43 12A CC OO DOUB N N 44 12A CC N SING N N 45 12A N CA SING N N 46 12A N H SING N N 47 12A CA C SING N N 48 12A CA CB SING N N 49 12A CA HA SING N N 50 12A C O DOUB N N 51 12A C OXT SING N N 52 12A OXT HXT SING N N 53 12A CB OG1 SING N N 54 12A CB CG2 SING N N 55 12A CB HB SING N N 56 12A OG1 HG1 SING N N 57 12A CG2 HG21 SING N N 58 12A CG2 HG22 SING N N 59 12A CG2 HG23 SING N N 60 # 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 12A SMILES ACDLabs 10.04 "O=C(O)C(NC(=O)Nc3nc(SC)nc1c3ncn1C2OC(C(O)C2O)COP(=O)(O)O)C(O)C" 12A SMILES_CANONICAL CACTVS 3.341 "CSc1nc(NC(=O)N[C@@H]([C@@H](C)O)C(O)=O)c2ncn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1" 12A SMILES CACTVS 3.341 "CSc1nc(NC(=O)N[CH]([CH](C)O)C(O)=O)c2ncn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c2n1" 12A SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]([C@@H](C(=O)O)NC(=O)Nc1c2c(nc(n1)SC)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)O" 12A SMILES "OpenEye OEToolkits" 1.5.0 "CC(C(C(=O)O)NC(=O)Nc1c2c(nc(n1)SC)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)O" 12A InChI InChI 1.03 "InChI=1S/C16H23N6O11PS/c1-5(23)7(14(26)27)18-15(28)19-11-8-12(21-16(20-11)35-2)22(4-17-8)13-10(25)9(24)6(33-13)3-32-34(29,30)31/h4-7,9-10,13,23-25H,3H2,1-2H3,(H,26,27)(H2,29,30,31)(H2,18,19,20,21,28)/t5-,6-,7+,9-,10-,13-/m1/s1" 12A InChIKey InChI 1.03 CVAJCPGRFVTHBT-DWVDDHQFSA-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 12A "SYSTEMATIC NAME" ACDLabs 10.04 "(2S,3R)-2-({[9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2-(methylsulfanyl)-9H-purin-6-yl]carbamoyl}amino)-3-hydroxybutanoic acid (non-preferred name)" 12A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R)-2-[[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2-methylsulfanyl-purin-6-yl]carbamoylamino]-3-hydroxy-butanoic 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 12A "Create component" 2000-08-09 RCSB 12A "Modify descriptor" 2011-06-04 RCSB #