data_VMX
# 
_chem_comp.id                                    VMX 
_chem_comp.name                                  "5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H21 N7 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-12-30 
_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                        387.415 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VMX 
_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        3KYD 
_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 
VMX S      S    S 0 1 N N N N N N 21.741 25.303 19.920 -4.212 0.360  0.944  S    VMX 1  
VMX N1     N1   N 0 1 Y N N N N N 21.675 14.743 22.519 6.477  -0.961 0.184  N1   VMX 2  
VMX C2     C2   C 0 1 Y N N N N N 20.843 15.348 21.653 6.102  0.302  0.272  C2   VMX 3  
VMX N3     N3   N 0 1 Y N N N N N 20.696 16.684 21.609 4.836  0.664  0.279  N3   VMX 4  
VMX C4     C4   C 0 1 Y N N N N N 21.398 17.483 22.450 3.871  -0.246 0.198  C4   VMX 5  
VMX C5     C5   C 0 1 Y N N N N N 22.278 16.941 23.371 4.219  -1.604 0.103  C5   VMX 6  
VMX C6     C6   C 0 1 Y N N N N N 22.412 15.462 23.390 5.583  -1.940 0.098  C6   VMX 7  
VMX N6     N6   N 0 1 N N N N N N 23.245 14.848 24.262 5.987  -3.261 0.006  N6   VMX 8  
VMX N7     N7   N 0 1 Y N N N N N 22.842 17.954 24.080 3.064  -2.309 0.034  N7   VMX 9  
VMX C8     C8   C 0 1 Y N N N N N 22.342 19.129 23.626 2.054  -1.490 0.080  C8   VMX 10 
VMX N9     N9   N 0 1 Y N N N N N 21.490 18.787 22.659 2.500  -0.205 0.182  N9   VMX 11 
VMX "C1'"  C1*  C 0 1 N N R N N N 20.765 19.698 21.944 1.667  0.998  0.259  C1*  VMX 12 
VMX C10    C10  C 0 1 N N N N N N 23.354 27.310 20.490 -5.846 -1.367 -0.408 C10  VMX 13 
VMX C11    C11  C 0 1 N N N N N N 24.821 27.567 20.155 -5.982 -2.502 -1.425 C11  VMX 14 
VMX N12    N12  N 0 1 N N N N N N 25.561 27.621 21.401 -7.397 -2.868 -1.565 N12  VMX 15 
VMX C1S    C1S  C 0 1 N N N N N N 23.132 25.812 20.673 -4.372 -0.985 -0.262 C1S  VMX 16 
VMX "C2'"  C2*  C 0 1 N N R N N N 19.723 20.353 22.810 1.481  1.624  -1.147 C2*  VMX 17 
VMX "O2'"  O2*  O 0 1 N N N N N N 18.579 19.504 22.937 2.559  2.510  -1.456 O2*  VMX 18 
VMX O2S    O2S  O 0 1 N N N N N N 20.583 25.906 20.529 -4.779 1.559  0.432  O2S  VMX 19 
VMX "C3'"  C3*  C 0 1 N N S N N N 19.358 21.670 22.151 0.155  2.405  -0.981 C3*  VMX 20 
VMX "O3'"  O3*  O 0 1 N N N N N N 18.056 21.608 21.563 0.416  3.784  -0.712 O3*  VMX 21 
VMX O3S    O3S  O 0 1 N N N N N N 21.794 25.649 18.524 -4.529 -0.101 2.250  O3S  VMX 22 
VMX "C4'"  C4*  C 0 1 N N R N N N 20.389 21.890 21.065 -0.527 1.739  0.230  C4*  VMX 23 
VMX "O4'"  O4*  O 0 1 N N N N N N 21.254 20.756 21.068 0.321  0.660  0.657  O4*  VMX 24 
VMX "C5'"  C5*  C 0 1 N N N N N N 21.207 23.138 21.338 -1.897 1.194  -0.178 C5*  VMX 25 
VMX "N5'"  N5*  N 0 1 N N N N N N 21.645 23.713 20.083 -2.586 0.670  1.003  N5*  VMX 26 
VMX H2     H2   H 0 1 N N N N N N 20.272 14.739 20.968 6.861  1.067  0.340  H2   VMX 27 
VMX HN6    HN6  H 0 1 N N N N N N 23.196 13.858 24.130 6.932  -3.480 0.004  HN6  VMX 28 
VMX HN6A   HN6A H 0 0 N N N N N N 24.182 15.159 24.103 5.325  -3.967 -0.056 HN6A VMX 29 
VMX H8     H8   H 0 1 N N N N N N 22.581 20.124 23.972 1.015  -1.784 0.043  H8   VMX 30 
VMX "H1'"  H1*  H 0 1 N N N N N N 20.501 18.946 21.186 2.103  1.721  0.947  H1*  VMX 31 
VMX H10    H10  H 0 1 N N N N N N 23.092 27.836 21.420 -6.413 -0.502 -0.751 H10  VMX 32 
VMX H10A   H10A H 0 0 N N N N N N 22.720 27.678 19.670 -6.234 -1.696 0.556  H10A VMX 33 
VMX H11    H11  H 0 1 N N N N N N 25.210 26.756 19.522 -5.594 -2.173 -2.390 H11  VMX 34 
VMX H11A   H11A H 0 0 N N N N N N 24.922 28.521 19.616 -5.414 -3.367 -1.082 H11A VMX 35 
VMX HN12   HN12 H 0 0 N N N N N N 26.528 27.789 21.208 -7.513 -3.616 -2.232 HN12 VMX 36 
VMX HN1A   HN1A H 0 0 N Y N N N N 25.202 28.360 21.970 -7.797 -3.115 -0.672 HN1A VMX 37 
VMX H1S    H1S  H 0 1 N N N N N N 23.052 25.595 21.748 -3.985 -0.656 -1.227 H1S  VMX 38 
VMX H1SA   H1SA H 0 0 N N N N N N 23.987 25.272 20.240 -3.805 -1.850 0.081  H1SA VMX 39 
VMX "H2'"  H2*  H 0 1 N N N N N N 20.107 20.530 23.826 1.385  0.850  -1.908 H2*  VMX 40 
VMX "HO2'" HO2* H 0 0 N N N N N N 17.929 19.928 23.485 2.488  2.927  -2.326 HO2* VMX 41 
VMX "H3'"  H3*  H 0 1 N N N N N N 19.346 22.485 22.890 -0.463 2.302  -1.873 H3*  VMX 42 
VMX "HO3'" HO3* H 0 0 N N N N N N 17.851 22.442 21.158 0.896  4.238  -1.418 HO3* VMX 43 
VMX "H4'"  H4*  H 0 1 N N N N N N 19.888 22.017 20.094 -0.639 2.464  1.037  H4*  VMX 44 
VMX "H5'"  H5*  H 0 1 N N N N N N 20.590 23.869 21.881 -2.490 1.996  -0.620 H5*  VMX 45 
VMX "H5'A" H5*A H 0 0 N N N N N N 22.085 22.875 21.947 -1.767 0.395  -0.908 H5*A VMX 46 
VMX "HN5'" HN5* H 0 0 N N N N N N 20.991 23.403 19.393 -2.091 0.506  1.821  HN5* VMX 47 
# 
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 
VMX S     C1S    SING N N 1  
VMX S     O2S    DOUB N N 2  
VMX S     O3S    DOUB N N 3  
VMX S     "N5'"  SING N N 4  
VMX N1    C2     DOUB Y N 5  
VMX N1    C6     SING Y N 6  
VMX C2    N3     SING Y N 7  
VMX N3    C4     DOUB Y N 8  
VMX C4    C5     SING Y N 9  
VMX C4    N9     SING Y N 10 
VMX C5    C6     DOUB Y N 11 
VMX C5    N7     SING Y N 12 
VMX C6    N6     SING N N 13 
VMX N7    C8     DOUB Y N 14 
VMX C8    N9     SING Y N 15 
VMX N9    "C1'"  SING N N 16 
VMX "C1'" "C2'"  SING N N 17 
VMX "C1'" "O4'"  SING N N 18 
VMX C10   C11    SING N N 19 
VMX C10   C1S    SING N N 20 
VMX C11   N12    SING N N 21 
VMX "C2'" "O2'"  SING N N 22 
VMX "C2'" "C3'"  SING N N 23 
VMX "C3'" "O3'"  SING N N 24 
VMX "C3'" "C4'"  SING N N 25 
VMX "C4'" "O4'"  SING N N 26 
VMX "C4'" "C5'"  SING N N 27 
VMX "C5'" "N5'"  SING N N 28 
VMX C2    H2     SING N N 29 
VMX N6    HN6    SING N N 30 
VMX N6    HN6A   SING N N 31 
VMX C8    H8     SING N N 32 
VMX "C1'" "H1'"  SING N N 33 
VMX C10   H10    SING N N 34 
VMX C10   H10A   SING N N 35 
VMX C11   H11    SING N N 36 
VMX C11   H11A   SING N N 37 
VMX N12   HN12   SING N N 38 
VMX N12   HN1A   SING N N 39 
VMX C1S   H1S    SING N N 40 
VMX C1S   H1SA   SING N N 41 
VMX "C2'" "H2'"  SING N N 42 
VMX "O2'" "HO2'" SING N N 43 
VMX "C3'" "H3'"  SING N N 44 
VMX "O3'" "HO3'" SING N N 45 
VMX "C4'" "H4'"  SING N N 46 
VMX "C5'" "H5'"  SING N N 47 
VMX "C5'" "H5'A" SING N N 48 
VMX "N5'" "HN5'" SING N N 49 
# 
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 
VMX SMILES_CANONICAL CACTVS               3.352 "NCCC[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"                                                                                                      
VMX SMILES           CACTVS               3.352 "NCCC[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                           
VMX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNS(=O)(=O)CCCN)O)O)N"                                                                                                 
VMX SMILES           "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CNS(=O)(=O)CCCN)O)O)N"                                                                                                                   
VMX InChI            InChI                1.03  "InChI=1S/C13H21N7O5S/c14-2-1-3-26(23,24)19-4-7-9(21)10(22)13(25-7)20-6-18-8-11(15)16-5-17-12(8)20/h5-7,9-10,13,19,21-22H,1-4,14H2,(H2,15,16,17)/t7-,9-,10-,13-/m1/s1" 
VMX InChIKey         InChI                1.03  GCNSCCULRVBOML-QYVSTXNMSA-N                                                                                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           VMX 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   1.6.1 
_pdbx_chem_comp_identifier.identifier        "N-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-3-azanyl-propane-1-sulfonamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VMX "Create component"     2009-12-30 RCSB 
VMX "Modify aromatic_flag" 2011-06-04 RCSB 
VMX "Modify descriptor"    2011-06-04 RCSB 
VMX "Modify PCM"           2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 VMX GLY None "Covalent chemical modification" "Amino-acid backbone"   C-terminal     N12 C  ? ? 
2 VMX CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C10 SG ? ? 
# 
