data_XKO
# 
_chem_comp.id                                    XKO 
_chem_comp.name                                  
;5'-O-[N-(3-Indolepropionic acid)sulfamoyl] N2-methyl-2-aminoethenoadenosine
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H26 N8 O7 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "[(2~{R},3~{S},4~{R},5~{R})-5-[5-(methylamino)imidazo[2,1-f]purin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[3-(1~{H}-indol-3-yl)propanoyl]sulfamate" 
_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                        570.578 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XKO 
_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        8PAI 
_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 
XKO "O5'" O1  O 0 1 N N N 5.908  5.162  7.007  -1.811 -3.694 -0.608 "O5'" XKO 1  
XKO "C5'" C1  C 0 1 N N N 5.787  4.673  5.654  -0.978 -3.692 0.554  "C5'" XKO 2  
XKO "C4'" C2  C 0 1 N N R 6.703  5.461  4.785  0.486  -3.549 0.131  "C4'" XKO 3  
XKO "O4'" O2  O 0 1 N N N 6.506  4.930  3.465  0.703  -2.251 -0.447 "O4'" XKO 4  
XKO "C3'" C3  C 0 1 N N S 6.436  6.977  4.740  1.401  -3.664 1.365  "C3'" XKO 5  
XKO "O3'" O3  O 0 1 N N N 7.518  7.695  5.337  2.300  -4.765 1.221  "O3'" XKO 6  
XKO "C2'" C4  C 0 1 N N R 6.234  7.261  3.252  2.181  -2.327 1.385  "C2'" XKO 7  
XKO "O2'" O4  O 0 1 N N N 6.889  8.432  2.787  3.552  -2.541 1.726  "O2'" XKO 8  
XKO N9    N1  N 0 1 Y N N 6.086  5.736  1.275  2.186  -0.393 -0.173 N9    XKO 9  
XKO C8    C5  C 0 1 Y N N 4.704  5.804  1.081  1.172  0.518  -0.176 C8    XKO 10 
XKO N7    N2  N 0 1 Y N N 4.343  5.660  -0.184 1.663  1.722  -0.263 N7    XKO 11 
XKO C5    C6  C 0 1 Y N N 5.544  5.512  -0.871 3.012  1.653  -0.321 C5    XKO 12 
XKO C6    C7  C 0 1 Y N N 5.835  5.283  -2.234 4.087  2.639  -0.424 C6    XKO 13 
XKO N6    N3  N 0 1 Y N N 5.074  5.173  -3.324 4.120  3.954  -0.497 N6    XKO 14 
XKO N1    N4  N 0 1 Y N N 7.196  5.155  -2.549 5.381  2.174  -0.459 N1    XKO 15 
XKO C2    C8  C 0 1 Y N N 8.212  5.241  -1.575 5.622  0.830  -0.398 C2    XKO 16 
XKO N3    N5  N 0 1 Y N N 7.926  5.445  -0.301 4.657  -0.051 -0.306 N3    XKO 17 
XKO C4    C9  C 0 1 Y N N 6.623  5.562  0.017  3.365  0.303  -0.259 C4    XKO 18 
XKO C9    C10 C 0 1 Y N N 5.978  4.978  -4.358 5.393  4.360  -0.577 C9    XKO 19 
XKO C10   C11 C 0 1 Y N N 7.256  4.967  -3.931 6.194  3.275  -0.556 C10   XKO 20 
XKO N2    N6  N 0 1 N N N 9.495  5.111  -1.947 6.924  0.387  -0.435 N2    XKO 21 
XKO S1    S1  S 0 1 N N N 4.738  4.772  8.004  -3.296 -3.832 -0.304 S1    XKO 22 
XKO O2    O5  O 0 1 N N N 3.933  3.775  7.355  -3.945 -4.017 -1.554 O2    XKO 23 
XKO O3    O6  O 0 1 N N N 5.324  4.476  9.250  -3.402 -4.754 0.772  O3    XKO 24 
XKO N4    N7  N 0 1 N N N 3.744  6.138  8.005  -3.814 -2.371 0.280  N4    XKO 25 
XKO C7    C12 C 0 1 N N N 3.937  7.447  7.780  -3.799 -1.283 -0.515 C7    XKO 26 
XKO C11   C13 C 0 1 N N N 2.734  8.332  7.987  -4.271 0.045  0.016  C11   XKO 27 
XKO C12   C14 C 0 1 N N N 2.896  9.069  9.311  -4.151 1.105  -1.081 C12   XKO 28 
XKO C13   C15 C 0 1 Y N N 1.846  10.106 9.592  -4.623 2.434  -0.549 C13   XKO 29 
XKO C14   C16 C 0 1 Y N N 1.552  11.275 8.789  -3.823 3.407  0.199  C14   XKO 30 
XKO C15   C17 C 0 1 Y N N 0.530  11.987 9.462  -4.683 4.484  0.479  C15   XKO 31 
XKO N16   N8  N 0 1 Y N N 0.235  11.296 10.611 -5.910 4.176  -0.064 N16   XKO 32 
XKO C17   C18 C 0 1 Y N N 1.029  10.183 10.681 -5.854 2.954  -0.677 C17   XKO 33 
XKO O24   O7  O 0 1 N N N 4.989  7.920  7.455  -3.406 -1.374 -1.659 O24   XKO 34 
XKO C25   C19 C 0 1 Y N N 2.035  11.783 7.575  -2.497 3.443  0.634  C25   XKO 35 
XKO C26   C20 C 0 1 Y N N 1.500  12.952 7.077  -2.041 4.526  1.331  C26   XKO 36 
XKO C27   C21 C 0 1 Y N N 0.489  13.634 7.759  -2.885 5.592  1.609  C27   XKO 37 
XKO C28   C22 C 0 1 Y N N -0.011 13.170 8.955  -4.197 5.577  1.189  C28   XKO 38 
XKO C16   C23 C 0 1 N N R 6.775  5.983  2.564  2.043  -1.849 -0.087 C16   XKO 39 
XKO C1    C24 C 0 1 N N N 10.597 5.246  -1.026 7.211  -1.048 -0.371 C1    XKO 40 
XKO H1    H1  H 0 1 N N N 4.750  4.794  5.307  -1.253 -2.856 1.197  H1    XKO 41 
XKO H2    H2  H 0 1 N N N 6.064  3.609  5.617  -1.110 -4.628 1.097  H2    XKO 42 
XKO H3    H3  H 0 1 N N N 7.742  5.296  5.107  0.740  -4.324 -0.592 H3    XKO 43 
XKO H4    H4  H 0 1 N N N 5.498  7.187  5.274  0.807  -3.774 2.272  H4    XKO 44 
XKO H5    H5  H 0 1 N N N 7.580  7.467  6.257  2.900  -4.884 1.970  H5    XKO 45 
XKO H6    H6  H 0 1 N N N 5.154  7.329  3.053  1.719  -1.616 2.070  H6    XKO 46 
XKO H7    H7  H 0 1 N N N 6.532  9.192  3.230  3.684  -2.925 2.603  H7    XKO 47 
XKO H8    H8  H 0 1 N N N 3.999  5.959  1.885  0.121  0.278  -0.115 H8    XKO 48 
XKO H9    H9  H 0 1 N N N 5.689  4.849  -5.391 5.724  5.385  -0.648 H9    XKO 49 
XKO H10   H10 H 0 1 N N N 8.143  4.839  -4.533 7.273  3.273  -0.605 H10   XKO 50 
XKO H11   H11 H 0 1 N N N 9.576  4.196  -2.342 7.651  1.024  -0.503 H11   XKO 51 
XKO H12   H12 H 0 1 N N N 2.793  5.921  8.224  -4.128 -2.299 1.195  H12   XKO 52 
XKO H13   H13 H 0 1 N N N 2.662  9.059  7.164  -5.311 -0.037 0.330  H13   XKO 53 
XKO H14   H14 H 0 1 N N N 1.822  7.718  8.014  -3.656 0.335  0.869  H14   XKO 54 
XKO H15   H15 H 0 1 N N N 2.867  8.326  10.121 -3.111 1.188  -1.395 H15   XKO 55 
XKO H16   H16 H 0 1 N N N 3.876  9.568  9.306  -4.766 0.816  -1.934 H16   XKO 56 
XKO H17   H17 H 0 1 N N N -0.450 11.563 11.289 -6.696 4.742  -0.022 H17   XKO 57 
XKO H18   H18 H 0 1 N N N 1.011  9.465  11.488 -6.678 2.477  -1.186 H18   XKO 58 
XKO H19   H19 H 0 1 N N N 2.816  11.266 7.037  -1.834 2.617  0.421  H19   XKO 59 
XKO H20   H20 H 0 1 N N N 1.869  13.348 6.142  -1.015 4.554  1.667  H20   XKO 60 
XKO H21   H21 H 0 1 N N N 0.091  14.546 7.339  -2.510 6.441  2.161  H21   XKO 61 
XKO H22   H22 H 0 1 N N N -0.791 13.700 9.480  -4.847 6.411  1.411  H22   XKO 62 
XKO H23   H23 H 0 1 N N N 7.857  6.094  2.397  2.777  -2.344 -0.723 H23   XKO 63 
XKO H24   H24 H 0 1 N N N 11.545 5.098  -1.564 6.820  -1.456 0.562  H24   XKO 64 
XKO H25   H25 H 0 1 N N N 10.582 6.252  -0.581 6.738  -1.552 -1.214 H25   XKO 65 
XKO H26   H26 H 0 1 N N N 10.505 4.492  -0.231 8.289  -1.205 -0.412 H26   XKO 66 
# 
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 
XKO C9    C10   DOUB Y N 1  
XKO C9    N6    SING Y N 2  
XKO C10   N1    SING Y N 3  
XKO N6    C6    DOUB Y N 4  
XKO N1    C6    SING Y N 5  
XKO N1    C2    SING Y N 6  
XKO C6    C5    SING Y N 7  
XKO N2    C2    SING N N 8  
XKO N2    C1    SING N N 9  
XKO C2    N3    DOUB Y N 10 
XKO C5    N7    SING Y N 11 
XKO C5    C4    DOUB Y N 12 
XKO N3    C4    SING Y N 13 
XKO N7    C8    DOUB Y N 14 
XKO C4    N9    SING Y N 15 
XKO C8    N9    SING Y N 16 
XKO N9    C16   SING N N 17 
XKO C16   "C2'" SING N N 18 
XKO C16   "O4'" SING N N 19 
XKO "O2'" "C2'" SING N N 20 
XKO "C2'" "C3'" SING N N 21 
XKO "O4'" "C4'" SING N N 22 
XKO "C3'" "C4'" SING N N 23 
XKO "C3'" "O3'" SING N N 24 
XKO "C4'" "C5'" SING N N 25 
XKO "C5'" "O5'" SING N N 26 
XKO "O5'" S1    SING N N 27 
XKO C26   C25   DOUB Y N 28 
XKO C26   C27   SING Y N 29 
XKO O2    S1    DOUB N N 30 
XKO O24   C7    DOUB N N 31 
XKO C25   C14   SING Y N 32 
XKO C27   C28   DOUB Y N 33 
XKO C7    C11   SING N N 34 
XKO C7    N4    SING N N 35 
XKO C11   C12   SING N N 36 
XKO S1    N4    SING N N 37 
XKO S1    O3    DOUB N N 38 
XKO C14   C15   DOUB Y N 39 
XKO C14   C13   SING Y N 40 
XKO C28   C15   SING Y N 41 
XKO C12   C13   SING N N 42 
XKO C15   N16   SING Y N 43 
XKO C13   C17   DOUB Y N 44 
XKO N16   C17   SING Y N 45 
XKO "C5'" H1    SING N N 46 
XKO "C5'" H2    SING N N 47 
XKO "C4'" H3    SING N N 48 
XKO "C3'" H4    SING N N 49 
XKO "O3'" H5    SING N N 50 
XKO "C2'" H6    SING N N 51 
XKO "O2'" H7    SING N N 52 
XKO C8    H8    SING N N 53 
XKO C9    H9    SING N N 54 
XKO C10   H10   SING N N 55 
XKO N2    H11   SING N N 56 
XKO N4    H12   SING N N 57 
XKO C11   H13   SING N N 58 
XKO C11   H14   SING N N 59 
XKO C12   H15   SING N N 60 
XKO C12   H16   SING N N 61 
XKO N16   H17   SING N N 62 
XKO C17   H18   SING N N 63 
XKO C25   H19   SING N N 64 
XKO C26   H20   SING N N 65 
XKO C27   H21   SING N N 66 
XKO C28   H22   SING N N 67 
XKO C16   H23   SING N N 68 
XKO C1    H24   SING N N 69 
XKO C1    H25   SING N N 70 
XKO C1    H26   SING N N 71 
# 
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 
XKO InChI            InChI                1.06  "InChI=1S/C24H26N8O7S/c1-25-24-29-22-18(21-26-8-9-31(21)24)28-12-32(22)23-20(35)19(34)16(39-23)11-38-40(36,37)30-17(33)7-6-13-10-27-15-5-3-2-4-14(13)15/h2-5,8-10,12,16,19-20,23,27,34-35H,6-7,11H2,1H3,(H,25,29)(H,30,33)/t16-,19-,20-,23-/m1/s1" 
XKO InChIKey         InChI                1.06  MCGJNWYQNXMIEN-UGTJMOTHSA-N                                                                                                                                                                                                                        
XKO SMILES_CANONICAL CACTVS               3.385 "CNc1nc2n(cnc2c3nccn13)[C@@H]4O[C@H](CO[S](=O)(=O)NC(=O)CCc5c[nH]c6ccccc56)[C@@H](O)[C@H]4O"                                                                                                                                                       
XKO SMILES           CACTVS               3.385 "CNc1nc2n(cnc2c3nccn13)[CH]4O[CH](CO[S](=O)(=O)NC(=O)CCc5c[nH]c6ccccc56)[CH](O)[CH]4O"                                                                                                                                                             
XKO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNc1nc2c(c3n1ccn3)ncn2[C@H]4[C@@H]([C@@H]([C@H](O4)COS(=O)(=O)NC(=O)CCc5c[nH]c6c5cccc6)O)O"                                                                                                                                                       
XKO SMILES           "OpenEye OEToolkits" 2.0.7 "CNc1nc2c(c3n1ccn3)ncn2C4C(C(C(O4)COS(=O)(=O)NC(=O)CCc5c[nH]c6c5cccc6)O)O"                                                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           XKO 
_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-(methylamino)imidazo[2,1-f]purin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[3-(1~{H}-indol-3-yl)propanoyl]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 
XKO "Create component" 2023-06-07 PDBE 
XKO "Initial release"  2023-06-14 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      XKO 
_pdbx_chem_comp_synonyms.name         "[(2~{R},3~{S},4~{R},5~{R})-5-[5-(methylamino)imidazo[2,1-f]purin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[3-(1~{H}-indol-3-yl)propanoyl]sulfamate" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
