data_XKB
# 
_chem_comp.id                                    XKB 
_chem_comp.name                                  
;5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl 2-aminoethenoadenosine
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H24 N8 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "[(2~{R},3~{S},4~{R},5~{R})-5-(5-azanylimidazo[2,1-f]purin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[2-(1~{H}-indol-3-yl)ethyl]carbamate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-07 
_chem_comp.pdbx_modified_date                    2023-06-09 
_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                        492.487 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XKB 
_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        8PA6 
_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 
XKB C2    C1  C 0 1 Y N N 9.806  5.513  -1.000 7.083   0.322  -0.636 C2    XKB 1  
XKB C4    C2  C 0 1 Y N N 7.880  5.537  0.218  4.810   0.417  -0.173 C4    XKB 2  
XKB C5    C3  C 0 1 Y N N 7.058  5.199  -0.847 4.899   1.772  0.154  C5    XKB 3  
XKB C6    C4  C 0 1 Y N N 7.660  5.032  -2.078 6.210   2.414  0.064  C6    XKB 4  
XKB N6    N1  N 0 1 Y N N 7.163  4.707  -3.289 6.649   3.635  0.291  N6    XKB 5  
XKB C11   C5  C 0 1 N N N 4.826  4.966  7.661  -2.641  -1.544 0.052  C11   XKB 6  
XKB N12   N2  N 0 1 N N N 4.643  5.773  8.703  -3.566  -1.027 -0.782 N12   XKB 7  
XKB "O5'" O1  O 0 1 N N N 5.802  5.453  6.863  -1.381  -1.741 -0.380 "O5'" XKB 8  
XKB "C5'" C6  C 0 1 N N N 5.942  4.803  5.587  -0.438  -2.301 0.572  "C5'" XKB 9  
XKB "C4'" C7  C 0 1 N N R 6.955  5.572  4.819  0.931   -2.452 -0.095 "C4'" XKB 10 
XKB "O4'" O2  O 0 1 N N N 7.062  4.987  3.518  1.475   -1.155 -0.392 "O4'" XKB 11 
XKB "C3'" C8  C 0 1 N N S 6.668  7.080  4.664  1.908   -3.153 0.868  "C3'" XKB 12 
XKB "O3'" O3  O 0 1 N N N 7.677  7.829  5.362  2.386   -4.372 0.296  "O3'" XKB 13 
XKB "C2'" C9  C 0 1 N N R 6.619  7.255  3.140  3.068   -2.141 1.035  "C2'" XKB 14 
XKB "O2'" O4  O 0 1 N N N 7.126  8.506  2.729  4.332   -2.809 1.032  "O2'" XKB 15 
XKB "C1'" C10 C 0 1 N N R 7.423  6.031  2.635  2.907   -1.251 -0.229 "C1'" XKB 16 
XKB N9    N3  N 0 1 Y N N 7.080  5.622  1.280  3.492   0.073  -0.006 N9    XKB 17 
XKB C8    C11 C 0 1 Y N N 5.783  5.369  0.853  2.828   1.189  0.406  C8    XKB 18 
XKB N7    N4  N 0 1 Y N N 5.721  5.109  -0.439 3.660   2.187  0.499  N7    XKB 19 
XKB N1    N5  N 0 1 Y N N 9.038  5.224  -2.117 7.275   1.642  -0.337 N1    XKB 20 
XKB N3    N6  N 0 1 Y N N 9.210  5.708  0.177  5.907   -0.251 -0.555 N3    XKB 21 
XKB C9    C12 C 0 1 Y N N 8.268  4.724  -4.113 7.965   3.683  0.047  C9    XKB 22 
XKB C10   C13 C 0 1 Y N N 9.419  4.982  -3.433 8.377   2.460  -0.342 C10   XKB 23 
XKB O11   O5  O 0 1 N N N 4.173  3.956  7.428  -2.944  -1.831 1.192  O11   XKB 24 
XKB C12   C14 C 0 1 N N N 5.280  7.104  8.874  -4.937  -0.813 -0.312 C12   XKB 25 
XKB C13   C15 C 0 1 N N N 4.529  8.233  8.286  -5.777  -0.222 -1.446 C13   XKB 26 
XKB C14   C16 C 0 1 Y N N 3.072  8.286  8.613  -7.188  -0.001 -0.962 C14   XKB 27 
XKB C15   C17 C 0 1 Y N N 2.062  7.868  7.810  -8.222  -0.844 -1.106 C15   XKB 28 
XKB N15   N7  N 0 1 Y N N 0.854  8.051  8.426  -9.345  -0.304 -0.541 N15   XKB 29 
XKB C16   C18 C 0 1 Y N N 1.052  8.634  9.651  -9.054  0.931  -0.006 C16   XKB 30 
XKB C21   C19 C 0 1 Y N N 2.446  8.795  9.818  -7.688  1.172  -0.241 C21   XKB 31 
XKB C20   C20 C 0 1 Y N N 2.907  9.332  11.030 -7.104  2.361  0.202  C20   XKB 32 
XKB C19   C21 C 0 1 Y N N 2.003  9.736  11.997 -7.863  3.283  0.866  C19   XKB 33 
XKB C18   C22 C 0 1 Y N N 0.627  9.595  11.780 -9.210  3.047  1.104  C18   XKB 34 
XKB C17   C23 C 0 1 Y N N 0.133  9.026  10.625 -9.809  1.885  0.667  C17   XKB 35 
XKB N2    N8  N 0 1 N N N 11.113 5.659  -1.160 8.161   -0.431 -1.041 N2    XKB 36 
XKB H1    H1  H 0 1 N N N 4.029  5.459  9.427  -3.323  -0.798 -1.693 H1    XKB 37 
XKB H2    H2  H 0 1 N N N 4.980  4.806  5.053  -0.352  -1.637 1.431  H2    XKB 38 
XKB H3    H3  H 0 1 N N N 6.280  3.766  5.726  -0.791  -3.278 0.901  H3    XKB 39 
XKB H4    H4  H 0 1 N N N 7.922  5.472  5.334  0.834   -3.032 -1.013 H4    XKB 40 
XKB H5    H5  H 0 1 N N N 5.674  7.298  5.081  1.427   -3.345 1.827  H5    XKB 41 
XKB H6    H6  H 0 1 N N N 7.619  7.648  6.293  3.006   -4.855 0.860  H6    XKB 42 
XKB H7    H7  H 0 1 N N N 5.576  7.142  2.810  2.944   -1.552 1.943  H7    XKB 43 
XKB H8    H8  H 0 1 N N N 6.580  9.200  3.079  4.443   -3.443 1.753  H8    XKB 44 
XKB H9    H9  H 0 1 N N N 8.498  6.253  2.707  3.359   -1.731 -1.097 H9    XKB 45 
XKB H10   H10 H 0 1 N N N 4.922  5.383  1.505  1.771   1.239  0.623  H10   XKB 46 
XKB H11   H11 H 0 1 N N N 8.225  4.552  -5.178 8.593   4.556  0.148  H11   XKB 47 
XKB H12   H12 H 0 1 N N N 10.422 4.996  -3.833 9.384   2.176  -0.609 H12   XKB 48 
XKB H13   H13 H 0 1 N N N 6.273  7.071  8.402  -5.366  -1.764 0.001  H13   XKB 49 
XKB H14   H14 H 0 1 N N N 5.393  7.293  9.952  -4.927  -0.123 0.532  H14   XKB 50 
XKB H15   H15 H 0 1 N N N 4.627  8.170  7.192  -5.347  0.730  -1.759 H15   XKB 51 
XKB H16   H16 H 0 1 N N N 4.989  9.166  8.643  -5.786  -0.912 -2.289 H16   XKB 52 
XKB H17   H17 H 0 1 N N N 2.193  7.450  6.823  -8.175  -1.805 -1.595 H17   XKB 53 
XKB H18   H18 H 0 1 N N N -0.035 7.799  8.043  -10.218 -0.728 -0.520 H18   XKB 54 
XKB H19   H19 H 0 1 N N N 3.968  9.430  11.208 -6.056  2.550  0.021  H19   XKB 55 
XKB H20   H20 H 0 1 N N N 2.360  10.162 12.923 -7.411  4.201  1.209  H20   XKB 56 
XKB H21   H21 H 0 1 N N N -0.064 9.940  12.535 -9.797  3.786  1.630  H21   XKB 57 
XKB H22   H22 H 0 1 N N N -0.928 8.889  10.479 -10.857 1.711  0.859  H22   XKB 58 
XKB H23   H23 H 0 1 N N N 11.528 5.924  -0.290 8.043   -1.368 -1.261 H23   XKB 59 
XKB H24   H24 H 0 1 N N N 11.509 4.795  -1.469 9.039   -0.024 -1.107 H24   XKB 60 
# 
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 
XKB C9    C10   DOUB Y N 1  
XKB C9    N6    SING Y N 2  
XKB C10   N1    SING Y N 3  
XKB N6    C6    DOUB Y N 4  
XKB N1    C6    SING Y N 5  
XKB N1    C2    SING Y N 6  
XKB C6    C5    SING Y N 7  
XKB N2    C2    SING N N 8  
XKB C2    N3    DOUB Y N 9  
XKB C5    N7    SING Y N 10 
XKB C5    C4    DOUB Y N 11 
XKB N7    C8    DOUB Y N 12 
XKB N3    C4    SING Y N 13 
XKB C4    N9    SING Y N 14 
XKB C8    N9    SING Y N 15 
XKB N9    "C1'" SING N N 16 
XKB "C1'" "C2'" SING N N 17 
XKB "C1'" "O4'" SING N N 18 
XKB "O2'" "C2'" SING N N 19 
XKB "C2'" "C3'" SING N N 20 
XKB "O4'" "C4'" SING N N 21 
XKB "C3'" "C4'" SING N N 22 
XKB "C3'" "O3'" SING N N 23 
XKB "C4'" "C5'" SING N N 24 
XKB "C5'" "O5'" SING N N 25 
XKB "O5'" C11   SING N N 26 
XKB O11   C11   DOUB N N 27 
XKB C11   N12   SING N N 28 
XKB C15   N15   SING Y N 29 
XKB C15   C14   DOUB Y N 30 
XKB C13   C14   SING N N 31 
XKB C13   C12   SING N N 32 
XKB N15   C16   SING Y N 33 
XKB C14   C21   SING Y N 34 
XKB N12   C12   SING N N 35 
XKB C16   C21   DOUB Y N 36 
XKB C16   C17   SING Y N 37 
XKB C21   C20   SING Y N 38 
XKB C17   C18   DOUB Y N 39 
XKB C20   C19   DOUB Y N 40 
XKB C18   C19   SING Y N 41 
XKB N12   H1    SING N N 42 
XKB "C5'" H2    SING N N 43 
XKB "C5'" H3    SING N N 44 
XKB "C4'" H4    SING N N 45 
XKB "C3'" H5    SING N N 46 
XKB "O3'" H6    SING N N 47 
XKB "C2'" H7    SING N N 48 
XKB "O2'" H8    SING N N 49 
XKB "C1'" H9    SING N N 50 
XKB C8    H10   SING N N 51 
XKB C9    H11   SING N N 52 
XKB C10   H12   SING N N 53 
XKB C12   H13   SING N N 54 
XKB C12   H14   SING N N 55 
XKB C13   H15   SING N N 56 
XKB C13   H16   SING N N 57 
XKB C15   H17   SING N N 58 
XKB N15   H18   SING N N 59 
XKB C20   H19   SING N N 60 
XKB C19   H20   SING N N 61 
XKB C18   H21   SING N N 62 
XKB C17   H22   SING N N 63 
XKB N2    H23   SING N N 64 
XKB N2    H24   SING N N 65 
# 
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 
XKB InChI            InChI                1.06  "InChI=1S/C23H24N8O5/c24-22-29-20-16(19-25-7-8-30(19)22)28-11-31(20)21-18(33)17(32)15(36-21)10-35-23(34)26-6-5-12-9-27-14-4-2-1-3-13(12)14/h1-4,7-9,11,15,17-18,21,27,32-33H,5-6,10H2,(H2,24,29)(H,26,34)/t15-,17-,18-,21-/m1/s1" 
XKB InChIKey         InChI                1.06  PHVKAGZMQNJNJY-QTQZEZTPSA-N                                                                                                                                                                                                       
XKB SMILES_CANONICAL CACTVS               3.385 "Nc1nc2n(cnc2c3nccn13)[C@@H]4O[C@H](COC(=O)NCCc5c[nH]c6ccccc56)[C@@H](O)[C@H]4O"                                                                                                                                                  
XKB SMILES           CACTVS               3.385 "Nc1nc2n(cnc2c3nccn13)[CH]4O[CH](COC(=O)NCCc5c[nH]c6ccccc56)[CH](O)[CH]4O"                                                                                                                                                        
XKB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)c(c[nH]2)CCNC(=O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4nc(n6c5ncc6)N)O)O"                                                                                                                                            
XKB SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)c(c[nH]2)CCNC(=O)OCC3C(C(C(O3)n4cnc5c4nc(n6c5ncc6)N)O)O"                                                                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           XKB 
_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-(5-azanylimidazo[2,1-f]purin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[2-(1~{H}-indol-3-yl)ethyl]carbamate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
XKB "Create component" 2023-06-07 PDBE 
XKB "Initial release"  2023-06-14 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      XKB 
_pdbx_chem_comp_synonyms.name         "[(2~{R},3~{S},4~{R},5~{R})-5-(5-azanylimidazo[2,1-f]purin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[2-(1~{H}-indol-3-yl)ethyl]carbamate" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
