data_A1JV3 # _chem_comp.id A1JV3 _chem_comp.name "(2~{R})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-$l^{3}-sulfanyl]-2-azanyl-butanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N6 O5 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(R,S)-SAM; D-SAM" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2025-11-27 _chem_comp.pdbx_modified_date 2026-09-25 _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 399.445 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JV3 _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 9SQ1 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1JV3 N N1 N 0 1 N N N N N N 4.140 4.555 73.620 -5.867 1.601 1.732 N A1JV3 1 A1JV3 CA C1 C 0 1 N N R N N N 2.890 4.361 72.873 -6.224 0.714 0.617 CA A1JV3 2 A1JV3 C C2 C 0 1 N N N N N N 2.787 5.376 71.737 -7.304 1.358 -0.213 C A1JV3 3 A1JV3 O O1 O 0 1 N N N N N N 1.799 6.133 71.747 -8.067 0.607 -1.023 O A1JV3 4 A1JV3 OXT O2 O 0 1 N N N N N N 3.687 5.345 70.861 -7.484 2.552 -0.149 OXT A1JV3 5 A1JV3 CB C3 C 0 1 N N N N N N 2.774 2.922 72.363 -4.990 0.467 -0.254 CB A1JV3 6 A1JV3 CG C4 C 0 1 N N N N N N 1.971 2.081 73.342 -3.941 -0.299 0.553 CG A1JV3 7 A1JV3 SD S1 S 1 1 N N S N N N 2.686 0.518 73.906 -2.478 -0.591 -0.479 SD A1JV3 8 A1JV3 CE C5 C 0 1 N N N N N N 1.515 0.453 75.256 -3.040 -1.877 -1.628 CE A1JV3 9 A1JV3 "C5'" C6 C 0 1 N N N N N N 4.137 0.838 74.997 -1.367 -1.494 0.633 "C5'" A1JV3 10 A1JV3 "C4'" C7 C 0 1 N N S N N N 4.678 -0.459 75.576 -0.065 -1.821 -0.101 "C4'" A1JV3 11 A1JV3 "O4'" O3 O 0 1 N N N N N N 3.607 -1.185 76.224 0.649 -0.608 -0.393 "O4'" A1JV3 12 A1JV3 "C3'" C8 C 0 1 N N S N N N 5.270 -1.430 74.557 0.843 -2.681 0.800 "C3'" A1JV3 13 A1JV3 "O3'" O4 O 0 1 N N N N N N 6.658 -1.190 74.345 1.115 -3.940 0.180 "O3'" A1JV3 14 A1JV3 "C2'" C9 C 0 1 N N R N N N 5.023 -2.786 75.220 2.143 -1.851 0.932 "C2'" A1JV3 15 A1JV3 "O2'" O5 O 0 1 N N N N N N 5.996 -3.059 76.224 3.296 -2.692 0.854 "O2'" A1JV3 16 A1JV3 "C1'" C10 C 0 1 N N R N N N 3.651 -2.553 75.854 2.057 -0.914 -0.300 "C1'" A1JV3 17 A1JV3 N9 N2 N 0 1 Y N N N N N 2.526 -2.841 74.977 2.837 0.306 -0.077 N9 A1JV3 18 A1JV3 C8 C11 C 0 1 Y N N N N N 2.561 -3.012 73.613 2.361 1.492 0.395 C8 A1JV3 19 A1JV3 N7 N3 N 0 1 Y N N N N N 1.408 -3.309 73.075 3.328 2.359 0.475 N7 A1JV3 20 A1JV3 C5 C12 C 0 1 Y N N N N N 0.536 -3.338 74.158 4.483 1.786 0.061 C5 A1JV3 21 A1JV3 C6 C13 C 0 1 Y N N N N N -0.842 -3.598 74.258 5.812 2.222 -0.068 C6 A1JV3 22 A1JV3 N6 N4 N 0 1 N N N N N N -1.618 -3.918 73.216 6.169 3.516 0.270 N6 A1JV3 23 A1JV3 N1 N5 N 0 1 Y N N N N N -1.402 -3.543 75.487 6.720 1.364 -0.522 N1 A1JV3 24 A1JV3 C2 C14 C 0 1 Y N N N N N -0.626 -3.250 76.536 6.389 0.127 -0.848 C2 A1JV3 25 A1JV3 N3 N6 N 0 1 Y N N N N N 0.685 -2.989 76.561 5.157 -0.325 -0.743 N3 A1JV3 26 A1JV3 C4 C15 C 0 1 Y N N N N N 1.212 -3.051 75.329 4.182 0.461 -0.298 C4 A1JV3 27 A1JV3 HN1 H1 H 0 1 N N N N N N 4.194 3.884 74.360 -5.191 1.164 2.340 HN1 A1JV3 28 A1JV3 H3 H2 H 0 1 N N N N N N 4.918 4.435 73.004 -5.528 2.489 1.393 H3 A1JV3 29 A1JV3 HA H4 H 0 1 N N N N N N 2.047 4.540 73.557 -6.586 -0.236 1.010 HA A1JV3 30 A1JV3 H1 H5 H 0 1 N N N N N N 1.823 6.696 70.982 -8.747 1.066 -1.535 H1 A1JV3 31 A1JV3 HB2 H6 H 0 1 N N N N N N 2.269 2.923 71.386 -5.274 -0.118 -1.129 HB2 A1JV3 32 A1JV3 HB1 H7 H 0 1 N N N N N N 3.781 2.492 72.256 -4.576 1.423 -0.575 HB1 A1JV3 33 A1JV3 HG2 H8 H 0 1 N N N N N N 1.792 2.699 74.234 -3.657 0.286 1.428 HG2 A1JV3 34 A1JV3 HG1 H9 H 0 1 N N N N N N 1.011 1.846 72.860 -4.355 -1.254 0.874 HG1 A1JV3 35 A1JV3 HE1 H10 H 0 1 N N N N N N 1.690 -0.456 75.850 -3.890 -1.507 -2.201 HE1 A1JV3 36 A1JV3 HE3 H11 H 0 1 N N N N N N 1.643 1.339 75.895 -2.228 -2.136 -2.309 HE3 A1JV3 37 A1JV3 HE2 H12 H 0 1 N N N N N N 0.492 0.436 74.853 -3.339 -2.761 -1.066 HE2 A1JV3 38 A1JV3 "H5'1" H13 H 0 0 N N N N N N 4.928 1.328 74.410 -1.147 -0.879 1.506 "H5'1" A1JV3 39 A1JV3 "H5'2" H14 H 0 0 N N N N N N 3.829 1.499 75.821 -1.846 -2.420 0.952 "H5'2" A1JV3 40 A1JV3 "H4'" H15 H 0 1 N N N N N N 5.455 -0.214 76.315 -0.284 -2.353 -1.026 "H4'" A1JV3 41 A1JV3 "H3'" H16 H 0 1 N N N N N N 4.706 -1.369 73.614 0.383 -2.828 1.777 "H3'" A1JV3 42 A1JV3 "HO3'" H17 H 0 0 N N N N N N 6.774 -0.342 73.933 1.728 -4.498 0.676 "HO3'" A1JV3 43 A1JV3 "H2'" H18 H 0 1 N N N N N N 4.970 -3.583 74.464 2.145 -1.276 1.858 "H2'" A1JV3 44 A1JV3 "HO2'" H19 H 0 0 N N N N N N 5.817 -3.905 76.617 3.346 -3.356 1.555 "HO2'" A1JV3 45 A1JV3 "H1'" H20 H 0 1 N N N N N N 3.577 -3.182 76.753 2.397 -1.430 -1.198 "H1'" A1JV3 46 A1JV3 H8 H21 H 0 1 N N N N N N 3.467 -2.909 73.034 1.332 1.685 0.664 H8 A1JV3 47 A1JV3 HN61 H22 H 0 0 N N N N N N -2.553 -4.077 73.533 5.498 4.133 0.601 HN61 A1JV3 48 A1JV3 HN62 H23 H 0 0 N N N N N N -1.613 -3.168 72.554 7.090 3.805 0.177 HN62 A1JV3 49 A1JV3 H2 H24 H 0 1 N N N N N N -1.126 -3.220 77.493 7.157 -0.538 -1.213 H2 A1JV3 50 # 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 A1JV3 OXT C DOUB N N 1 A1JV3 C O SING N N 2 A1JV3 C CA SING N N 3 A1JV3 CB CA SING N N 4 A1JV3 CB CG SING N N 5 A1JV3 CA N SING N N 6 A1JV3 N7 C8 DOUB Y N 7 A1JV3 N7 C5 SING Y N 8 A1JV3 N6 C6 SING N N 9 A1JV3 CG SD SING N N 10 A1JV3 C8 N9 SING Y N 11 A1JV3 SD "C5'" SING N N 12 A1JV3 SD CE SING N N 13 A1JV3 C5 C6 DOUB Y N 14 A1JV3 C5 C4 SING Y N 15 A1JV3 C6 N1 SING Y N 16 A1JV3 "O3'" "C3'" SING N N 17 A1JV3 "C3'" "C2'" SING N N 18 A1JV3 "C3'" "C4'" SING N N 19 A1JV3 N9 C4 SING Y N 20 A1JV3 N9 "C1'" SING N N 21 A1JV3 "C5'" "C4'" SING N N 22 A1JV3 "C2'" "C1'" SING N N 23 A1JV3 "C2'" "O2'" SING N N 24 A1JV3 C4 N3 DOUB Y N 25 A1JV3 N1 C2 DOUB Y N 26 A1JV3 "C4'" "O4'" SING N N 27 A1JV3 "C1'" "O4'" SING N N 28 A1JV3 C2 N3 SING Y N 29 A1JV3 N HN1 SING N N 30 A1JV3 N H3 SING N N 31 A1JV3 CA HA SING N N 32 A1JV3 O H1 SING N N 33 A1JV3 CB HB2 SING N N 34 A1JV3 CB HB1 SING N N 35 A1JV3 CG HG2 SING N N 36 A1JV3 CG HG1 SING N N 37 A1JV3 CE HE1 SING N N 38 A1JV3 CE HE3 SING N N 39 A1JV3 CE HE2 SING N N 40 A1JV3 "C5'" "H5'1" SING N N 41 A1JV3 "C5'" "H5'2" SING N N 42 A1JV3 "C4'" "H4'" SING N N 43 A1JV3 "C3'" "H3'" SING N N 44 A1JV3 "O3'" "HO3'" SING N N 45 A1JV3 "C2'" "H2'" SING N N 46 A1JV3 "O2'" "HO2'" SING N N 47 A1JV3 "C1'" "H1'" SING N N 48 A1JV3 C8 H8 SING N N 49 A1JV3 N6 HN61 SING N N 50 A1JV3 N6 HN62 SING N N 51 A1JV3 C2 H2 SING N N 52 # 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 A1JV3 InChI InChI 1.06 "InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8-,10-,11-,14-,27+/m1/s1" A1JV3 InChIKey InChI 1.06 MEFKEPWMEQBLKI-XSNYTKKPSA-O A1JV3 SMILES_CANONICAL CACTVS 3.385 "C[S@@+](CC[C@@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" A1JV3 SMILES CACTVS 3.385 "C[S+](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" A1JV3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[S@@+](CC[C@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" A1JV3 SMILES "OpenEye OEToolkits" 2.0.7 "C[S+](CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O" # _pdbx_chem_comp_identifier.comp_id A1JV3 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{R})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-methyl-sulfanium" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 A1JV3 "(R,S)-SAM" AUTHOR ? 2 A1JV3 D-SAM AUTHOR ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JV3 "Create component" 2025-11-27 PDBE A1JV3 "Initial release" 2026-09-30 RCSB #