data_A1MAL
# 
_chem_comp.id                                    A1MAL 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methylsulfanyl-butanoyl]sulfamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H23 N7 O7 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "sulfamate analog of methionyl adenylate (Met-AMS)" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-07-01 
_chem_comp.pdbx_modified_date                    2025-09-19 
_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                        477.516 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1MAL 
_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        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_chem_comp.pdbx_pcm                              ? 
# 
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 
A1MAL N2    N1  N 0 1 N N N N N N ? ? ? -2.936 2.229  -0.724 N2    A1MAL 1  
A1MAL CA    C1  C 0 1 N N S N N N ? ? ? -3.508 1.079  -0.012 CA    A1MAL 2  
A1MAL CB    C2  C 0 1 N N N N N N ? ? ? -5.034 1.117  -0.125 CB    A1MAL 3  
A1MAL CG    C3  C 0 1 N N N N N N ? ? ? -5.569 2.351  0.604  CG    A1MAL 4  
A1MAL SD    S1  S 0 1 N N N N N N ? ? ? -7.377 2.396  0.470  SD    A1MAL 5  
A1MAL CE    C4  C 0 1 N N N N N N ? ? ? -7.817 3.903  1.379  CE    A1MAL 6  
A1MAL C9    C5  C 0 1 N N N N N N ? ? ? -2.991 -0.198 -0.622 C9    A1MAL 7  
A1MAL N8    N2  N 0 1 N N N N N N ? ? ? -3.038 -1.347 0.080  N8    A1MAL 8  
A1MAL S1    S2  S 0 1 N N N N N N ? ? ? -2.469 -2.751 -0.591 S1    A1MAL 9  
A1MAL O1S   O1  O 0 1 N N N N N N ? ? ? -2.624 -3.760 0.398  O1S   A1MAL 10 
A1MAL O2S   O2  O 0 1 N N N N N N ? ? ? -3.044 -2.838 -1.887 O2S   A1MAL 11 
A1MAL "O5'" O3  O 0 1 N N N N N N ? ? ? -0.971 -2.577 -0.796 "O5'" A1MAL 12 
A1MAL "C5'" C6  C 0 1 N N N N N N ? ? ? -0.205 -2.664 0.408  "C5'" A1MAL 13 
A1MAL "C4'" C7  C 0 1 N N R N N N ? ? ? 1.278  -2.476 0.083  "C4'" A1MAL 14 
A1MAL "O4'" O4  O 0 1 N N N N N N ? ? ? 1.537  -1.111 -0.311 "O4'" A1MAL 15 
A1MAL "C3'" C8  C 0 1 N N S N N N ? ? ? 2.137  -2.691 1.350  "C3'" A1MAL 16 
A1MAL "O3'" O5  O 0 1 N N N N N N ? ? ? 2.680  -4.012 1.368  "O3'" A1MAL 17 
A1MAL "C2'" C9  C 0 1 N N R N N N ? ? ? 3.265  -1.643 1.220  "C2'" A1MAL 18 
A1MAL "O2'" O6  O 0 1 N N N N N N ? ? ? 4.540  -2.285 1.155  "O2'" A1MAL 19 
A1MAL "C1'" C10 C 0 1 N N R N N N ? ? ? 2.954  -0.919 -0.109 "C1'" A1MAL 20 
A1MAL N9    N3  N 0 1 Y N N N N N ? ? ? 3.265  0.508  0.003  N9    A1MAL 21 
A1MAL C8    C11 C 0 1 Y N N N N N ? ? ? 2.401  1.494  0.377  C8    A1MAL 22 
A1MAL N7    N4  N 0 1 Y N N N N N ? ? ? 3.010  2.645  0.369  N7    A1MAL 23 
A1MAL C5    C12 C 0 1 Y N N N N N ? ? ? 4.299  2.470  -0.010 C5    A1MAL 24 
A1MAL C6    C13 C 0 1 Y N N N N N ? ? ? 5.399  3.325  -0.195 C6    A1MAL 25 
A1MAL N6    N5  N 0 1 N N N N N N ? ? ? 5.283  4.686  0.026  N6    A1MAL 26 
A1MAL N1    N6  N 0 1 Y N N N N N ? ? ? 6.553  2.795  -0.586 N1    A1MAL 27 
A1MAL C2    C14 C 0 1 Y N N N N N ? ? ? 6.673  1.498  -0.799 C2    A1MAL 28 
A1MAL N3    N7  N 0 1 Y N N N N N ? ? ? 5.671  0.660  -0.639 N3    A1MAL 29 
A1MAL C4    C15 C 0 1 Y N N N N N ? ? ? 4.479  1.097  -0.244 C4    A1MAL 30 
A1MAL O1    O7  O 0 1 N N N N N N ? ? ? -2.532 -0.191 -1.745 O1    A1MAL 31 
A1MAL H1    H1  H 0 1 N N N N N N ? ? ? -1.934 2.263  -0.610 H1    A1MAL 32 
A1MAL H2    H2  H 0 1 N N N N N N ? ? ? -3.189 2.212  -1.701 H2    A1MAL 33 
A1MAL H4    H4  H 0 1 N N N N N N ? ? ? -3.221 1.123  1.039  H4    A1MAL 34 
A1MAL H5    H5  H 0 1 N N N N N N ? ? ? -5.319 1.163  -1.176 H5    A1MAL 35 
A1MAL H6    H6  H 0 1 N N N N N N ? ? ? -5.454 0.218  0.327  H6    A1MAL 36 
A1MAL H7    H7  H 0 1 N N N N N N ? ? ? -5.283 2.305  1.655  H7    A1MAL 37 
A1MAL H8    H8  H 0 1 N N N N N N ? ? ? -5.149 3.250  0.153  H8    A1MAL 38 
A1MAL H9    H9  H 0 1 N N N N N N ? ? ? -7.340 4.763  0.908  H9    A1MAL 39 
A1MAL H10   H10 H 0 1 N N N N N N ? ? ? -8.899 4.034  1.364  H10   A1MAL 40 
A1MAL H11   H11 H 0 1 N N N N N N ? ? ? -7.475 3.818  2.410  H11   A1MAL 41 
A1MAL H12   H12 H 0 1 N N N N N N ? ? ? -3.404 -1.353 0.978  H12   A1MAL 42 
A1MAL H13   H13 H 0 1 N N N N N N ? ? ? -0.527 -1.887 1.100  H13   A1MAL 43 
A1MAL H14   H14 H 0 1 N N N N N N ? ? ? -0.356 -3.642 0.864  H14   A1MAL 44 
A1MAL H15   H15 H 0 1 N N N N N N ? ? ? 1.584  -3.165 -0.704 H15   A1MAL 45 
A1MAL H16   H16 H 0 1 N N N N N N ? ? ? 1.546  -2.507 2.247  H16   A1MAL 46 
A1MAL H17   H17 H 0 1 N N N N N N ? ? ? 3.228  -4.201 2.142  H17   A1MAL 47 
A1MAL H18   H18 H 0 1 N N N N N N ? ? ? 3.233  -0.943 2.055  H18   A1MAL 48 
A1MAL H19   H19 H 0 1 N N N N N N ? ? ? 4.759  -2.804 1.940  H19   A1MAL 49 
A1MAL H20   H20 H 0 1 N N N N N N ? ? ? 3.519  -1.367 -0.927 H20   A1MAL 50 
A1MAL H21   H21 H 0 1 N N N N N N ? ? ? 1.365  1.343  0.642  H21   A1MAL 51 
A1MAL H22   H22 H 0 1 N N N N N N ? ? ? 4.435  5.061  0.312  H22   A1MAL 52 
A1MAL H23   H23 H 0 1 N N N N N N ? ? ? 6.049  5.266  -0.105 H23   A1MAL 53 
A1MAL H24   H24 H 0 1 N N N N N N ? ? ? 7.628  1.110  -1.121 H24   A1MAL 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 
A1MAL C2    N3    SING Y N 1  
A1MAL C2    N1    DOUB Y N 2  
A1MAL N3    C4    DOUB Y N 3  
A1MAL N1    C6    SING Y N 4  
A1MAL "O4'" "C4'" SING N N 5  
A1MAL "O4'" "C1'" SING N N 6  
A1MAL "O3'" "C3'" SING N N 7  
A1MAL "C4'" "C5'" SING N N 8  
A1MAL "C4'" "C3'" SING N N 9  
A1MAL C4    N9    SING Y N 10 
A1MAL C4    C5    SING Y N 11 
A1MAL "C1'" N9    SING N N 12 
A1MAL "C1'" "C2'" SING N N 13 
A1MAL "C5'" "O5'" SING N N 14 
A1MAL "C3'" "C2'" SING N N 15 
A1MAL C6    C5    DOUB Y N 16 
A1MAL C6    N6    SING N N 17 
A1MAL N9    C8    SING Y N 18 
A1MAL C5    N7    SING Y N 19 
A1MAL SD    CE    SING N N 20 
A1MAL SD    CG    SING N N 21 
A1MAL "C2'" "O2'" SING N N 22 
A1MAL "O5'" S1    SING N N 23 
A1MAL C8    N7    DOUB Y N 24 
A1MAL CB    CG    SING N N 25 
A1MAL CB    CA    SING N N 26 
A1MAL O1S   S1    DOUB N N 27 
A1MAL S1    N8    SING N N 28 
A1MAL S1    O2S   DOUB N N 29 
A1MAL N8    C9    SING N N 30 
A1MAL N2    CA    SING N N 31 
A1MAL C9    CA    SING N N 32 
A1MAL C9    O1    DOUB N N 33 
A1MAL N2    H1    SING N N 34 
A1MAL N2    H2    SING N N 35 
A1MAL CA    H4    SING N N 36 
A1MAL CB    H5    SING N N 37 
A1MAL CB    H6    SING N N 38 
A1MAL CG    H7    SING N N 39 
A1MAL CG    H8    SING N N 40 
A1MAL CE    H9    SING N N 41 
A1MAL CE    H10   SING N N 42 
A1MAL CE    H11   SING N N 43 
A1MAL N8    H12   SING N N 44 
A1MAL "C5'" H13   SING N N 45 
A1MAL "C5'" H14   SING N N 46 
A1MAL "C4'" H15   SING N N 47 
A1MAL "C3'" H16   SING N N 48 
A1MAL "O3'" H17   SING N N 49 
A1MAL "C2'" H18   SING N N 50 
A1MAL "O2'" H19   SING N N 51 
A1MAL "C1'" H20   SING N N 52 
A1MAL C8    H21   SING N N 53 
A1MAL N6    H22   SING N N 54 
A1MAL N6    H23   SING N N 55 
A1MAL C2    H24   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 
A1MAL InChI            InChI                1.06  "InChI=1S/C15H23N7O7S2/c1-30-3-2-7(16)14(25)21-31(26,27)28-4-8-10(23)11(24)15(29-8)22-6-20-9-12(17)18-5-19-13(9)22/h5-8,10-11,15,23-24H,2-4,16H2,1H3,(H,21,25)(H2,17,18,19)/t7-,8+,10+,11+,15+/m0/s1" 
A1MAL InChIKey         InChI                1.06  PBPVXRRYIIRSNJ-JVEUSOJLSA-N                                                                                                                                                                           
A1MAL SMILES_CANONICAL CACTVS               3.385 "CSCC[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"                                                                                                                       
A1MAL SMILES           CACTVS               3.385 "CSCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                                             
A1MAL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CSCC[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N"                                                                                                                       
A1MAL SMILES           "OpenEye OEToolkits" 2.0.7 "CSCCC(C(=O)NS(=O)(=O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N"                                                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           A1MAL 
_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~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methylsulfanyl-butanoyl]sulfamate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1MAL "Create component"   2025-07-01 PDBJ 
A1MAL "Modify synonyms"    2025-07-09 PDBJ 
A1MAL "Modify coordinates" 2025-09-15 RCSB 
A1MAL "Initial release"    2025-09-24 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1MAL 
_pdbx_chem_comp_synonyms.name         "sulfamate analog of methionyl adenylate (Met-AMS)" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
