data_VE8
#

_chem_comp.id                                   VE8
_chem_comp.name                                 "Non-hydrolasable alarmone analogue"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H19 N6 O19 P5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-05-11
_chem_comp.pdbx_modified_date                   2022-05-27
_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                       682.155
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VE8
_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       7OHG
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
VE8  O17  O1   O  0  1  N  N  N  58.857  51.008  -2.980  -2.761   0.854  -1.905  O17  VE8   1  
VE8  P2   P1   P  0  1  N  N  N  59.911  50.069  -2.539  -2.858   0.835  -0.428  P2   VE8   2  
VE8  O9   O2   O  0  1  N  N  N  59.474  48.606  -2.421  -3.165   2.321   0.109  O9   VE8   3  
VE8  O10  O3   O  0  1  N  N  N  61.178  50.100  -3.509  -4.048  -0.154   0.019  O10  VE8   4  
VE8  P3   P2   P  0  1  N  N  N  61.434  50.420  -5.051  -5.525  -0.453  -0.547  P3   VE8   5  
VE8  O16  O4   O  0  1  N  N  N  61.604  49.169  -5.831  -6.160   0.817  -0.964  O16  VE8   6  
VE8  O15  O5   O  0  1  N  N  N  60.288  51.351  -5.516  -5.425  -1.443  -1.812  O15  VE8   7  
VE8  O11  O6   O  0  1  N  N  N  62.779  51.287  -5.023  -6.412  -1.143   0.606  O11  VE8   8  
VE8  P4   P3   P  0  1  N  N  N  63.630  52.183  -6.046  -7.989  -1.403   0.799  P4   VE8   9  
VE8  O14  O7   O  0  1  N  N  N  62.854  53.385  -6.501  -8.716  -0.021   1.193  O14  VE8  10  
VE8  O13  O8   O  0  1  N  N  N  64.008  51.221  -7.192  -8.562  -1.920  -0.463  O13  VE8  11  
VE8  O12  O9   O  0  1  N  N  N  64.910  52.549  -5.271  -8.215  -2.482   1.973  O12  VE8  12  
VE8  O8   O10  O  0  1  N  N  N  60.474  50.487  -1.093  -1.467   0.316   0.194  O8   VE8  13  
VE8  C7   C1   C  0  1  N  N  N  61.022  51.776  -0.740  -0.207   0.920  -0.104  C7   VE8  14  
VE8  C6   C2   C  0  1  N  N  S  62.504  51.789  -1.025   0.903   0.185   0.650  C6   VE8  15  
VE8  C5   C3   C  0  1  N  N  S  63.401  51.128   0.032   2.258   0.897   0.441  C5   VE8  16  
VE8  N1   N1   N  0  1  N  N  N  63.680  49.694  -0.213   2.565   1.765   1.587  N1   VE8  17  
VE8  P    P4   P  0  1  N  N  N  64.146  48.563   0.895   3.373   3.155   1.091  P    VE8  18  
VE8  O7   O11  O  0  1  N  N  N  64.798  47.393   0.307   3.665   4.003   2.269  O7   VE8  19  
VE8  O6   O12  O  0  1  N  N  N  65.232  49.235   1.845   4.753   2.746   0.369  O6   VE8  20  
VE8  O2   O13  O  0  1  N  N  N  62.886  48.108   1.835   2.449   3.973   0.057  O2   VE8  21  
VE8  P1   P5   P  0  1  N  N  N  61.366  47.627   1.665   2.631   5.348  -0.760  P1   VE8  22  
VE8  O5   O14  O  0  1  N  N  N  60.387  48.709   2.051   1.188   5.901  -1.210  O5   VE8  23  
VE8  O4   O15  O  0  1  N  N  N  61.257  47.189   0.184   3.295   6.351   0.103  O4   VE8  24  
VE8  O3   O16  O  0  1  N  N  N  61.249  46.377   2.560   3.535   5.081  -2.065  O3   VE8  25  
VE8  C4   C4   C  0  1  N  N  R  64.616  52.081   0.205   3.279  -0.258   0.348  C4   VE8  26  
VE8  O1   O17  O  0  1  N  N  N  65.863  51.414   0.023   4.242  -0.162   1.400  O1   VE8  27  
VE8  O18  O18  O  0  1  N  N  N  62.968  53.152  -1.084   1.093  -1.137   0.101  O18  VE8  28  
VE8  C3   C5   C  0  1  N  N  R  64.363  53.137  -0.875   2.421  -1.532   0.511  C3   VE8  29  
VE8  N    N2   N  0  1  Y  N  N  64.799  54.500  -0.517   2.925  -2.601  -0.355  N    VE8  30  
VE8  C8   C6   C  0  1  Y  N  N  65.665  55.288  -1.226   2.520  -2.865  -1.631  C8   VE8  31  
VE8  N2   N3   N  0  1  Y  N  N  65.857  56.467  -0.685   3.178  -3.884  -2.101  N2   VE8  32  
VE8  C1   C7   C  0  1  Y  N  N  65.071  56.453   0.454   4.042  -4.333  -1.158  C1   VE8  33  
VE8  C2   C8   C  0  1  Y  N  N  64.412  55.249   0.570   3.893  -3.514  -0.033  C2   VE8  34  
VE8  N3   N4   N  0  1  N  N  N  63.566  54.857   1.538   4.641  -3.737   1.054  N3   VE8  35  
VE8  C9   C9   C  0  1  N  N  N  63.389  55.787   2.475   5.519  -4.715   1.085  C9   VE8  36  
VE8  N4   N5   N  0  1  N  N  N  62.559  55.548   3.488   6.263  -4.905   2.222  N4   VE8  37  
VE8  N5   N6   N  0  1  N  N  N  64.005  57.011   2.452   5.711  -5.544   0.021  N5   VE8  38  
VE8  C    C10  C  0  1  N  N  N  64.870  57.443   1.468   4.988  -5.384  -1.110  C    VE8  39  
VE8  O    O19  O  0  1  N  N  N  65.366  58.565   1.524   5.154  -6.120  -2.067  O    VE8  40  
VE8  H1   H1   H  0  1  N  N  N  58.558  48.529  -2.659  -3.242   2.384   1.071  H1   VE8  41  
VE8  H2   H2   H  0  1  N  N  N  59.848  50.963  -6.263  -5.018  -2.297  -1.612  H2   VE8  42  
VE8  H3   H3   H  0  1  N  N  N  62.727  53.343  -7.442  -8.389   0.375   2.012  H3   VE8  43  
VE8  H4   H4   H  0  1  N  N  N  65.655  52.107  -5.662  -9.144  -2.687   2.144  H4   VE8  44  
VE8  H5   H5   H  0  1  N  N  N  60.528  52.559  -1.333  -0.020   0.859  -1.176  H5   VE8  45  
VE8  H6   H6   H  0  1  N  N  N  60.853  51.965   0.330  -0.224   1.966   0.203  H6   VE8  46  
VE8  H7   H7   H  0  1  N  N  N  62.683  51.295  -1.991   0.665   0.126   1.712  H7   VE8  47  
VE8  H8   H8   H  0  1  N  N  N  62.843  51.181   0.978   2.248   1.474  -0.484  H8   VE8  48  
VE8  H9   H9   H  0  1  N  N  N  62.836  49.333  -0.609   1.728   1.997   2.100  H9   VE8  49  
VE8  H10  H10  H  0  1  N  N  N  66.037  48.732   1.812   4.637   2.189  -0.413  H10  VE8  50  
VE8  H11  H11  H  0  1  N  N  N  59.858  48.941   1.297   1.221   6.729  -1.709  H11  VE8  51  
VE8  H12  H12  H  0  1  N  N  N  61.135  45.607   2.016   3.160   4.433  -2.677  H12  VE8  52  
VE8  H13  H13  H  0  1  N  N  N  64.565  52.553   1.197   3.774  -0.253  -0.623  H13  VE8  53  
VE8  H14  H14  H  0  1  N  N  N  65.981  50.770   0.711   4.908  -0.863   1.389  H14  VE8  54  
VE8  H15  H15  H  0  1  N  N  N  64.879  52.823  -1.795   2.416  -1.857   1.551  H15  VE8  55  
VE8  H16  H16  H  0  1  N  N  N  66.143  54.970  -2.141   1.765  -2.311  -2.170  H16  VE8  56  
VE8  H17  H17  H  0  1  N  N  N  62.074  54.675   3.542   6.137  -4.323   2.987  H17  VE8  57  
VE8  H18  H18  H  0  1  N  N  N  62.421  56.241   4.195   6.915  -5.623   2.260  H18  VE8  58  
VE8  H19  H19  H  0  1  N  N  N  63.813  57.639   3.206   6.368  -6.256   0.076  H19  VE8  59  
#   #
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
VE8  O13  P4   DOUB  N  N   1  
VE8  O14  P4   SING  N  N   2  
VE8  P4   O12  SING  N  N   3  
VE8  P4   O11  SING  N  N   4  
VE8  O16  P3   DOUB  N  N   5  
VE8  O15  P3   SING  N  N   6  
VE8  P3   O11  SING  N  N   7  
VE8  P3   O10  SING  N  N   8  
VE8  O10  P2   SING  N  N   9  
VE8  O17  P2   DOUB  N  N  10  
VE8  P2   O9   SING  N  N  11  
VE8  P2   O8   SING  N  N  12  
VE8  C8   N2   DOUB  Y  N  13  
VE8  C8   N    SING  Y  N  14  
VE8  O8   C7   SING  N  N  15  
VE8  O18  C6   SING  N  N  16  
VE8  O18  C3   SING  N  N  17  
VE8  C6   C7   SING  N  N  18  
VE8  C6   C5   SING  N  N  19  
VE8  C3   N    SING  N  N  20  
VE8  C3   C4   SING  N  N  21  
VE8  N2   C1   SING  Y  N  22  
VE8  N    C2   SING  Y  N  23  
VE8  N1   C5   SING  N  N  24  
VE8  N1   P    SING  N  N  25  
VE8  O1   C4   SING  N  N  26  
VE8  C5   C4   SING  N  N  27  
VE8  O4   P1   DOUB  N  N  28  
VE8  O7   P    DOUB  N  N  29  
VE8  C1   C2   DOUB  Y  N  30  
VE8  C1   C    SING  N  N  31  
VE8  C2   N3   SING  N  N  32  
VE8  P    O2   SING  N  N  33  
VE8  P    O6   SING  N  N  34  
VE8  C    O    DOUB  N  N  35  
VE8  C    N5   SING  N  N  36  
VE8  N3   C9   DOUB  N  N  37  
VE8  P1   O2   SING  N  N  38  
VE8  P1   O5   SING  N  N  39  
VE8  P1   O3   SING  N  N  40  
VE8  N5   C9   SING  N  N  41  
VE8  C9   N4   SING  N  N  42  
VE8  O9   H1   SING  N  N  43  
VE8  O15  H2   SING  N  N  44  
VE8  O14  H3   SING  N  N  45  
VE8  O12  H4   SING  N  N  46  
VE8  C7   H5   SING  N  N  47  
VE8  C7   H6   SING  N  N  48  
VE8  C6   H7   SING  N  N  49  
VE8  C5   H8   SING  N  N  50  
VE8  N1   H9   SING  N  N  51  
VE8  O6   H10  SING  N  N  52  
VE8  O5   H11  SING  N  N  53  
VE8  O3   H12  SING  N  N  54  
VE8  C4   H13  SING  N  N  55  
VE8  O1   H14  SING  N  N  56  
VE8  C3   H15  SING  N  N  57  
VE8  C8   H16  SING  N  N  58  
VE8  N4   H17  SING  N  N  59  
VE8  N4   H18  SING  N  N  60  
VE8  N5   H19  SING  N  N  61  
#   #
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
VE8  InChI             InChI                 1.03   "InChI=1S/C10H19N6O19P5/c11-10-13-7-5(8(18)14-10)12-2-16(7)9-6(17)4(15-36(19,20)33-37(21,22)23)3(32-9)1-31-39(27,28)35-40(29,30)34-38(24,25)26/h2-4,6,9,17H,1H2,(H,27,28)(H,29,30)(H2,15,19,20)(H2,21,22,23)(H2,24,25,26)(H3,11,13,14,18)/t3-,4-,6-,9-/m1/s1"  
VE8  InChIKey          InChI                 1.03   IZNYESBVRGWINY-DXTOWSMRSA-N  
VE8  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](N[P](O)(=O)O[P](O)(O)=O)[C@H]3O"  
VE8  SMILES            CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](N[P](O)(=O)O[P](O)(O)=O)[CH]3O"  
VE8  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)NP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N"  
VE8  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)NP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N"  
#
_pdbx_chem_comp_identifier.comp_id          VE8
_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       "~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VE8
_pdbx_chem_comp_synonyms.name        "~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VE8  "Create component"  2021-05-11  PDBE  
VE8  "Initial release"   2022-06-01  RCSB  
##
