data_S7M
#
_chem_comp.id S7M
_chem_comp.name
;[(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}ethyls
ulfonium
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H25 N6 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "S-ADENOSYL ETHIONINE"
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2013-06-07
_chem_comp.pdbx_modified_date 2020-06-17
_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 413.472
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S7M
_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 4L2Z
_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
S7M C1 C1 C 0 1 N N N 29.045 50.450 7.946 -2.717 2.902 1.532 C1 S7M 1
S7M S2 S2 S 1 1 N N S 30.633 49.812 8.371 -2.514 1.182 0.992 S2 S7M 2
S7M C3 C3 C 0 1 N N N 30.525 49.066 9.990 -4.199 0.700 0.522 C3 S7M 3
S7M C4 C4 C 0 1 N N N 30.153 49.929 11.181 -4.225 -0.789 0.174 C4 S7M 4
S7M C5 C5 C 0 1 N N S 30.770 51.307 11.284 -5.613 -1.167 -0.347 C5 S7M 5
S7M C6 C6 C 0 1 N N N 29.969 52.184 12.197 -5.605 -2.603 -0.804 C6 S7M 6
S7M O7 O7 O 0 1 N N N 30.521 52.800 13.149 -5.104 -2.920 -2.009 O7 S7M 7
S7M O8 O8 O 0 1 N N N 28.730 52.327 12.011 -6.049 -3.468 -0.087 O8 S7M 8
S7M N9 N9 N 0 1 N N N 32.124 51.213 11.746 -6.601 -1.002 0.729 N9 S7M 9
S7M C10 C10 C 0 1 N N N 31.169 48.578 7.187 -1.676 1.352 -0.608 C10 S7M 10
S7M C11 C11 C 0 1 N N S 31.306 48.890 5.751 -0.220 1.761 -0.380 C11 S7M 11
S7M C12 C12 C 0 1 N N S 32.079 50.145 5.446 0.490 1.996 -1.731 C12 S7M 12
S7M C13 C13 C 0 1 N N R 31.670 50.414 4.074 1.920 1.455 -1.503 C13 S7M 13
S7M C14 C14 C 0 1 N N R 30.270 50.109 4.130 1.904 0.958 -0.041 C14 S7M 14
S7M O15 O15 O 0 1 N N N 30.038 49.142 5.143 0.513 0.684 0.243 O15 S7M 15
S7M N16 N16 N 0 1 Y N N 29.558 51.350 4.397 2.702 -0.263 0.091 N16 S7M 16
S7M C17 C17 C 0 1 Y N N 30.042 52.465 5.001 2.234 -1.543 0.042 C17 S7M 17
S7M N18 N18 N 0 1 Y N N 29.058 53.385 5.021 3.216 -2.382 0.195 N18 S7M 18
S7M C19 C19 C 0 1 Y N N 27.945 52.851 4.420 4.374 -1.697 0.351 C19 S7M 19
S7M C20 C20 C 0 1 Y N N 28.264 51.554 4.021 4.059 -0.330 0.281 C20 S7M 20
S7M N21 N21 N 0 1 Y N N 27.329 50.800 3.385 5.035 0.565 0.401 N21 S7M 21
S7M C22 C22 C 0 1 Y N N 26.094 51.279 3.131 6.281 0.179 0.580 C22 S7M 22
S7M N23 N23 N 0 1 Y N N 25.758 52.522 3.516 6.626 -1.094 0.649 N23 S7M 23
S7M C24 C24 C 0 1 Y N N 26.636 53.326 4.149 5.718 -2.059 0.548 C24 S7M 24
S7M N25 N25 N 0 1 N N N 26.253 54.651 4.540 6.089 -3.390 0.623 N25 S7M 25
S7M O26 O26 O 0 1 N N N 32.280 49.560 3.114 2.883 2.498 -1.667 O26 S7M 26
S7M O27 O27 O 0 1 N N N 33.448 49.999 5.568 0.526 3.390 -2.043 O27 S7M 27
S7M C28 C28 C 0 1 N N N 27.945 49.458 7.687 -3.581 2.942 2.794 C28 S7M 28
S7M H1 H1 H 0 1 N N N 29.166 51.054 7.034 -1.739 3.333 1.747 H1 S7M 29
S7M H2 H2 H 0 1 N N N 28.717 51.097 8.773 -3.201 3.476 0.741 H2 S7M 30
S7M H3 H3 H 0 1 N N N 29.772 48.266 9.925 -4.877 0.891 1.354 H3 S7M 31
S7M H4 H4 H 0 1 N N N 31.510 48.626 10.207 -4.514 1.282 -0.345 H4 S7M 32
S7M H5 H5 H 0 1 N N N 29.061 50.061 11.160 -3.480 -0.996 -0.595 H5 S7M 33
S7M H6 H6 H 0 1 N N N 30.438 49.375 12.087 -3.999 -1.375 1.065 H6 S7M 34
S7M H7 H7 H 0 1 N N N 30.763 51.758 10.281 -5.876 -0.520 -1.184 H7 S7M 35
S7M H8 H8 H 0 1 N N N 29.871 53.314 13.613 -5.120 -3.854 -2.259 H8 S7M 36
S7M H9 H9 H 0 1 N N N 32.519 52.129 11.809 -6.379 -1.591 1.517 H9 S7M 37
S7M H10 H10 H 0 1 N N N 32.139 50.780 12.647 -6.672 -0.035 1.009 H10 S7M 38
S7M H12 H12 H 0 1 N N N 30.449 47.749 7.256 -1.708 0.400 -1.137 H12 S7M 39
S7M H13 H13 H 0 1 N N N 32.158 48.234 7.525 -2.180 2.115 -1.202 H13 S7M 40
S7M H14 H14 H 0 1 N N N 31.796 48.045 5.246 -0.171 2.659 0.236 H14 S7M 41
S7M H15 H15 H 0 1 N N N 31.717 50.952 6.101 -0.008 1.441 -2.526 H15 S7M 42
S7M H16 H16 H 0 1 N N N 31.832 51.473 3.822 2.128 0.631 -2.185 H16 S7M 43
S7M H17 H17 H 0 1 N N N 29.944 49.710 3.158 2.282 1.732 0.627 H17 S7M 44
S7M H18 H18 H 0 1 N N N 31.039 52.592 5.396 1.199 -1.818 -0.102 H18 S7M 45
S7M H19 H19 H 0 1 N N N 25.373 50.662 2.616 7.049 0.932 0.673 H19 S7M 46
S7M H20 H20 H 0 1 N N N 25.305 54.818 4.269 7.021 -3.628 0.750 H20 S7M 47
S7M H21 H21 H 0 1 N N N 26.337 54.743 5.532 5.417 -4.086 0.547 H21 S7M 48
S7M H22 H22 H 0 1 N N N 33.209 49.750 3.065 2.935 2.848 -2.567 H22 S7M 49
S7M H23 H23 H 0 1 N N N 33.669 49.826 6.476 0.961 3.595 -2.882 H23 S7M 50
S7M H24 H24 H 0 1 N N N 27.018 49.995 7.435 -4.586 2.594 2.557 H24 S7M 51
S7M H25 H25 H 0 1 N N N 28.230 48.805 6.849 -3.142 2.297 3.555 H25 S7M 52
S7M H26 H26 H 0 1 N N N 27.782 48.848 8.588 -3.629 3.965 3.168 H26 S7M 53
# #
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
S7M O26 C13 SING N N 1
S7M C22 N21 DOUB Y N 2
S7M C22 N23 SING Y N 3
S7M N21 C20 SING Y N 4
S7M N23 C24 DOUB Y N 5
S7M C20 N16 SING Y N 6
S7M C20 C19 DOUB Y N 7
S7M C13 C14 SING N N 8
S7M C13 C12 SING N N 9
S7M C14 N16 SING N N 10
S7M C14 O15 SING N N 11
S7M C24 C19 SING Y N 12
S7M C24 N25 SING N N 13
S7M N16 C17 SING Y N 14
S7M C19 N18 SING Y N 15
S7M C17 N18 DOUB Y N 16
S7M O15 C11 SING N N 17
S7M C12 O27 SING N N 18
S7M C12 C11 SING N N 19
S7M C11 C10 SING N N 20
S7M C10 S2 SING N N 21
S7M C28 C1 SING N N 22
S7M C1 S2 SING N N 23
S7M S2 C3 SING N N 24
S7M C3 C4 SING N N 25
S7M C4 C5 SING N N 26
S7M C5 N9 SING N N 27
S7M C5 C6 SING N N 28
S7M O8 C6 DOUB N N 29
S7M C6 O7 SING N N 30
S7M C1 H1 SING N N 31
S7M C1 H2 SING N N 32
S7M C3 H3 SING N N 33
S7M C3 H4 SING N N 34
S7M C4 H5 SING N N 35
S7M C4 H6 SING N N 36
S7M C5 H7 SING N N 37
S7M O7 H8 SING N N 38
S7M N9 H9 SING N N 39
S7M N9 H10 SING N N 40
S7M C10 H12 SING N N 41
S7M C10 H13 SING N N 42
S7M C11 H14 SING N N 43
S7M C12 H15 SING N N 44
S7M C13 H16 SING N N 45
S7M C14 H17 SING N N 46
S7M C17 H18 SING N N 47
S7M C22 H19 SING N N 48
S7M N25 H20 SING N N 49
S7M N25 H21 SING N N 50
S7M O26 H22 SING N N 51
S7M O27 H23 SING N N 52
S7M C28 H24 SING N N 53
S7M C28 H25 SING N N 54
S7M C28 H26 SING N N 55
# #
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
S7M SMILES ACDLabs 12.01 "O=C(O)C(N)CC[S+](CC)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O"
S7M InChI InChI 1.03 "InChI=1S/C16H24N6O5S/c1-2-28(4-3-8(17)16(25)26)5-9-11(23)12(24)15(27-9)22-7-21-10-13(18)19-6-20-14(10)22/h6-9,11-12,15,23-24H,2-5,17H2,1H3,(H2-,18,19,20,25,26)/p+1/t8-,9+,11+,12+,15+,28-/m0/s1"
S7M InChIKey InChI 1.03 UBQZUBPODLPCFG-XIFWJBDBSA-O
S7M SMILES_CANONICAL CACTVS 3.370 "CC[S@@+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"
S7M SMILES CACTVS 3.370 "CC[S+](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"
S7M SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC[S+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O"
S7M SMILES "OpenEye OEToolkits" 1.7.6 "CC[S+](CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O"
# #
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
S7M "SYSTEMATIC NAME" ACDLabs 12.01 "[(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}ethylsulfonium (non-preferred name)"
S7M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3S)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-ethyl-sulfanium"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S7M "Create component" 2013-06-07 RCSB
S7M "Initial release" 2013-06-19 RCSB
S7M "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id S7M
_pdbx_chem_comp_synonyms.name "S-ADENOSYL ETHIONINE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##