data_SMM # _chem_comp.id SMM _chem_comp.name "S-ADENOSYLMETHIONINE METHYL ESTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H26 N6 O5 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-03-13 _chem_comp.pdbx_modified_date 2024-09-27 _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 414.480 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SMM _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 1I7B _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 SMM N N N 0 1 N N N N N N -21.977 -9.558 9.544 -2.916 5.902 -1.167 N SMM 1 SMM CA CA C 0 1 N N S N N N -20.895 -8.636 9.533 -3.949 4.964 -0.804 CA SMM 2 SMM CB CB C 0 1 N N N N N N -20.283 -8.665 8.164 -3.396 3.849 0.089 CB SMM 3 SMM CG CG C 0 1 N N N N N N -18.648 -8.685 8.274 -2.914 4.366 1.439 CG SMM 4 SMM SD SD S 0 1 N N N N N N -17.957 -8.389 6.783 -2.311 3.051 2.450 SD SMM 5 SMM CE CE C 0 1 N N N N N N -17.803 -9.685 6.052 -1.734 3.796 3.944 CE SMM 6 SMM "C5'" C5* C 0 1 N N N N N N -16.449 -7.671 7.017 -0.881 2.428 1.621 "C5'" SMM 7 SMM "C4'" C4* C 0 1 N N S N N N -15.668 -7.537 5.726 -0.199 1.333 2.429 "C4'" SMM 8 SMM "O4'" O4* O 0 1 N N N N N N -16.526 -6.984 4.688 -1.128 0.236 2.584 "O4'" SMM 9 SMM "C1'" C1* C 0 1 N N R N N N -16.011 -5.736 4.255 -0.616 -0.910 1.877 "C1'" SMM 10 SMM N9 N9 N 0 1 Y N N N N N -17.138 -4.840 4.011 -1.713 -1.611 1.213 N9 SMM 11 SMM C4 C4 C 0 1 Y N N N N N -18.157 -4.573 4.892 -1.815 -2.957 0.996 C4 SMM 12 SMM N3 N3 N 0 1 Y N N N N N -18.317 -5.077 6.128 -0.937 -3.909 1.343 N3 SMM 13 SMM C2 C2 C 0 1 Y N N N N N -19.416 -4.588 6.695 -1.384 -5.125 0.960 C2 SMM 14 SMM N1 N1 N 0 1 Y N N N N N -20.305 -3.714 6.206 -2.532 -5.444 0.316 N1 SMM 15 SMM C6 C6 C 0 1 Y N N N N N -20.114 -3.224 4.961 -3.373 -4.431 -0.004 C6 SMM 16 SMM N6 N6 N 0 1 N N N N N N -20.997 -2.346 4.475 -4.580 -4.698 -0.672 N6 SMM 17 SMM C5 C5 C 0 1 Y N N N N N -18.985 -3.670 4.250 -3.023 -3.129 0.339 C5 SMM 18 SMM N7 N7 N 0 1 Y N N N N N -18.503 -3.378 2.979 -3.651 -1.923 0.154 N7 SMM 19 SMM C8 C8 C 0 1 Y N N N N N -17.409 -4.096 2.886 -2.841 -1.034 0.689 C8 SMM 20 SMM "C2'" C2* C 0 1 N N R N N N -15.097 -5.263 5.385 0.447 -0.380 0.926 "C2'" SMM 21 SMM "O2'" O2* O 0 1 N N N N N N -14.146 -4.326 4.921 1.399 -1.370 0.596 "O2'" SMM 22 SMM "C3'" C3* C 0 1 N N S N N N -14.478 -6.584 5.814 1.032 0.761 1.734 "C3'" SMM 23 SMM "O3'" O3* O 0 1 N N N N N N -13.463 -6.970 4.888 1.918 0.238 2.725 "O3'" SMM 24 SMM C C C 0 1 N N N N N N -21.372 -7.198 9.806 -5.108 5.665 -0.107 C SMM 25 SMM O O O 0 1 N N N N N N -20.913 -6.273 9.092 -5.089 6.861 0.169 O SMM 26 SMM OXT OXT O 0 1 N N N N N N -22.224 -7.028 10.714 -6.139 4.817 0.166 OXT SMM 27 SMM CXT CXT C 0 1 N N N N N N -21.899 -6.139 11.623 -7.268 5.400 0.825 CXT SMM 28 SMM HN1 1HN H 0 1 N N N N N N -22.393 -9.538 10.475 -2.458 6.427 -0.442 HN1 SMM 29 SMM HN2 2HN H 0 1 N N N N N N -21.701 -10.496 9.253 -2.813 6.164 -2.132 HN2 SMM 30 SMM HA1 1HA H 0 1 N N N N N N -20.170 -8.927 10.328 -4.341 4.558 -1.743 HA1 SMM 31 SMM HB1 1HB H 0 1 N N N N N N -20.669 -9.513 7.553 -2.562 3.347 -0.417 HB1 SMM 32 SMM HB2 2HB H 0 1 N N N N N N -20.647 -7.825 7.527 -4.163 3.078 0.243 HB2 SMM 33 SMM HG1 1HG H 0 1 N N N N N N -18.276 -7.976 9.050 -3.720 4.847 2.000 HG1 SMM 34 SMM HG2 2HG H 0 1 N N N N N N -18.274 -9.635 8.722 -2.091 5.078 1.320 HG2 SMM 35 SMM HD1 1HD H 0 1 N N N N N N -18.709 -7.592 6.083 -3.236 2.100 2.672 HD1 SMM 36 SMM HE1 1HE H 0 1 N N N N N N -17.341 -9.487 5.056 -0.657 3.943 3.862 HE1 SMM 37 SMM HE2 2HE H 0 1 N N N N N N -17.232 -10.440 6.641 -2.243 4.752 4.071 HE2 SMM 38 SMM HE3 3HE H 0 1 N N N N N N -18.764 -10.243 5.971 -1.966 3.126 4.774 HE3 SMM 39 SMM "H5'1" 1H5* H 0 0 N N N N N N -16.547 -6.686 7.531 -1.211 2.050 0.649 "H5'1" SMM 40 SMM "H5'2" 2H5* H 0 0 N N N N N N -15.858 -8.217 7.789 -0.207 3.274 1.461 "H5'2" SMM 41 SMM "H4'" H4* H 0 1 N N N N N N -15.301 -8.566 5.504 0.033 1.713 3.429 "H4'" SMM 42 SMM "H1'" H1* H 0 1 N N N N N N -15.429 -5.782 3.304 -0.213 -1.625 2.603 "H1'" SMM 43 SMM H2 H2 H 0 1 N N N N N N -19.618 -4.959 7.713 -0.735 -5.961 1.201 H2 SMM 44 SMM HN61 1HN6 H 0 0 N N N N N N -20.852 -1.976 3.535 -4.567 -4.889 -1.656 HN61 SMM 45 SMM HN62 2HN6 H 0 0 N N N N N N -21.081 -1.566 5.127 -5.448 -4.601 -0.179 HN62 SMM 46 SMM H8 H8 H 0 1 N N N N N N -16.791 -4.076 1.972 -3.013 0.033 0.727 H8 SMM 47 SMM "H2'" H2* H 0 1 N N N N N N -15.605 -4.718 6.214 -0.005 0.000 0.002 "H2'" SMM 48 SMM "HO2'" *HO2 H 0 0 N N N N N N -13.577 -4.032 5.623 0.913 -2.125 0.219 "HO2'" SMM 49 SMM "H3'" H3* H 0 1 N N N N N N -13.995 -6.557 6.818 1.592 1.484 1.136 "H3'" SMM 50 SMM "HO3'" *HO3 H 0 0 N N N N N N -12.722 -6.377 4.942 2.712 -0.055 2.254 "HO3'" SMM 51 SMM HXT1 1HXT H 0 0 N N N N N N -22.654 -5.988 12.428 -7.391 6.434 0.493 HXT1 SMM 52 SMM HXT2 2HXT H 0 0 N N N N N N -20.907 -6.389 12.068 -7.116 5.369 1.907 HXT2 SMM 53 SMM HXT3 3HXT H 0 0 N N N N N N -21.654 -5.165 11.138 -8.164 4.828 0.568 HXT3 SMM 54 # 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 SMM N CA SING N N 1 SMM N HN1 SING N N 2 SMM N HN2 SING N N 3 SMM CA CB SING N N 4 SMM CA C SING N N 5 SMM CA HA1 SING N N 6 SMM CB CG SING N N 7 SMM CB HB1 SING N N 8 SMM CB HB2 SING N N 9 SMM CG SD SING N N 10 SMM CG HG1 SING N N 11 SMM CG HG2 SING N N 12 SMM SD CE SING N N 13 SMM SD "C5'" SING N N 14 SMM SD HD1 SING N N 15 SMM CE HE1 SING N N 16 SMM CE HE2 SING N N 17 SMM CE HE3 SING N N 18 SMM "C5'" "C4'" SING N N 19 SMM "C5'" "H5'1" SING N N 20 SMM "C5'" "H5'2" SING N N 21 SMM "C4'" "O4'" SING N N 22 SMM "C4'" "C3'" SING N N 23 SMM "C4'" "H4'" SING N N 24 SMM "O4'" "C1'" SING N N 25 SMM "C1'" N9 SING N N 26 SMM "C1'" "C2'" SING N N 27 SMM "C1'" "H1'" SING N N 28 SMM N9 C4 SING Y N 29 SMM N9 C8 SING Y N 30 SMM C4 N3 DOUB Y N 31 SMM C4 C5 SING Y N 32 SMM N3 C2 SING Y N 33 SMM C2 N1 DOUB Y N 34 SMM C2 H2 SING N N 35 SMM N1 C6 SING Y N 36 SMM C6 N6 SING N N 37 SMM C6 C5 DOUB Y N 38 SMM N6 HN61 SING N N 39 SMM N6 HN62 SING N N 40 SMM C5 N7 SING Y N 41 SMM N7 C8 DOUB Y N 42 SMM C8 H8 SING N N 43 SMM "C2'" "O2'" SING N N 44 SMM "C2'" "C3'" SING N N 45 SMM "C2'" "H2'" SING N N 46 SMM "O2'" "HO2'" SING N N 47 SMM "C3'" "O3'" SING N N 48 SMM "C3'" "H3'" SING N N 49 SMM "O3'" "HO3'" SING N N 50 SMM C O DOUB N N 51 SMM C OXT SING N N 52 SMM OXT CXT SING N N 53 SMM CXT HXT1 SING N N 54 SMM CXT HXT2 SING N N 55 SMM CXT HXT3 SING N N 56 # 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 SMM SMILES ACDLabs 10.04 "O=C(OC)C(N)CCS(C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O" SMM SMILES_CANONICAL CACTVS 3.341 "COC(=O)[C@@H](N)CC[SH](C)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" SMM SMILES CACTVS 3.341 "COC(=O)[CH](N)CC[SH](C)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" SMM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "COC(=O)[C@H](CC[S@H](C)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N" SMM SMILES "OpenEye OEToolkits" 1.5.0 "COC(=O)C(CCS(C)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N" SMM InChI InChI 1.03 "InChI=1S/C16H26N6O5S/c1-26-16(25)8(17)3-4-28(2)5-9-11(23)12(24)15(27-9)22-7-21-10-13(18)19-6-20-14(10)22/h6-9,11-12,15,23-24,28H,3-5,17H2,1-2H3,(H2,18,19,20)/t8-,9+,11+,12+,15+/m0/s1" SMM InChIKey InChI 1.03 NAKVRMNIKCRDOL-OPYVMVOTSA-N # _pdbx_chem_comp_identifier.comp_id SMM _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program ACDLabs _pdbx_chem_comp_identifier.program_version 10.04 _pdbx_chem_comp_identifier.identifier "5'-[(S)-[(3S)-3-amino-4-methoxy-4-oxobutyl](methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SMM "Create component" 2001-03-13 RCSB SMM "Modify descriptor" 2011-06-04 RCSB SMM "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id SMM _pdbx_chem_comp_pcm.modified_residue_id PYR _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid backbone" _pdbx_chem_comp_pcm.polypeptide_position N-terminal _pdbx_chem_comp_pcm.comp_id_linking_atom N _pdbx_chem_comp_pcm.modified_residue_id_linking_atom CA _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #