data_XKF
# 
_chem_comp.id                                    XKF 
_chem_comp.name                                  
;5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl N2-methyl-2-aminoethenoadenosine
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H26 N8 O5" 
_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}-[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                        506.514 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XKF 
_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        8PA9 
_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 
XKF N1    N1  N 0 1 Y N N 7.493  5.231  -2.423 7.033   -1.786 0.274  N1    XKF 1  
XKF C2    C1  C 0 1 Y N N 8.428  5.321  -1.408 6.861   -0.458 0.548  C2    XKF 2  
XKF C3    C2  C 0 1 N N N 10.711 5.473  -0.625 7.799   1.715  1.222  C3    XKF 3  
XKF N2    N2  N 0 1 N N N 9.731  5.278  -1.665 7.954   0.289  0.923  N2    XKF 4  
XKF C4    C3  C 0 1 Y N N 6.753  5.542  0.121  4.583   -0.531 0.107  C4    XKF 5  
XKF C5    C4  C 0 1 Y N N 5.738  5.465  -0.829 4.651   -1.893 -0.194 C5    XKF 6  
XKF C6    C5  C 0 1 Y N N 6.121  5.293  -2.182 5.954   -2.551 -0.103 C6    XKF 7  
XKF N3    N3  N 0 1 Y N N 8.060  5.493  -0.136 5.693   0.129  0.465  N3    XKF 8  
XKF C8    C6  C 0 1 Y N N 4.790  5.677  1.084  2.586   -1.288 -0.440 C8    XKF 9  
XKF C9    C7  C 0 1 Y N N 6.402  5.065  -4.303 7.694   -3.841 -0.086 C9    XKF 10 
XKF C10   C8  C 0 1 Y N N 7.650  5.078  -3.801 8.125   -2.617 0.279  C10   XKF 11 
XKF C11   C9  C 0 1 N N N 4.979  5.542  8.131  -2.842  1.526  -0.093 C11   XKF 12 
XKF N12   N4  N 0 1 N N N 4.171  6.550  8.535  -3.767  1.038  0.758  N12   XKF 13 
XKF "O5'" O1  O 0 1 N N N 5.600  5.915  6.984  -1.576  1.714  0.325  "O5'" XKF 14 
XKF "C5'" C10 C 0 1 N N N 5.879  4.915  5.968  -0.634  2.243  -0.646 "C5'" XKF 15 
XKF "C4'" C11 C 0 1 N N R 6.680  5.569  4.877  0.742   2.388  0.006  "C4'" XKF 16 
XKF "O4'" O2  O 0 1 N N N 6.298  4.980  3.604  1.272   1.089  0.324  "O4'" XKF 17 
XKF "C3'" C12 C 0 1 N N S 6.495  7.091  4.719  1.720   3.057  -0.978 "C3'" XKF 18 
XKF "O3'" O3  O 0 1 N N N 7.560  7.824  5.338  2.220   4.280  -0.434 "O3'" XKF 19 
XKF "C2'" C13 C 0 1 N N R 6.351  7.272  3.201  2.865   2.027  -1.135 "C2'" XKF 20 
XKF "O2'" O4  O 0 1 N N N 7.095  8.383  2.746  4.137   2.677  -1.156 "O2'" XKF 21 
XKF "C1'" C14 C 0 1 N N R 6.779  5.906  2.642  2.703   1.163  0.147  "C1'" XKF 22 
XKF N9    N5  N 0 1 Y N N 6.143  5.668  1.339  3.269   -0.173 -0.056 N9    XKF 23 
XKF N7    N6  N 0 1 Y N N 4.510  5.552  -0.197 3.404   -2.299 -0.520 N7    XKF 24 
XKF N6    N7  N 0 1 Y N N 5.440  5.189  -3.316 6.375   -3.782 -0.308 N6    XKF 25 
XKF O11   O5  O 0 1 N N N 5.315  4.609  8.850  -3.152  1.795  -1.236 O11   XKF 26 
XKF C12   C15 C 0 1 N N N 4.468  7.957  8.283  -5.144  0.832  0.304  C12   XKF 27 
XKF C13   C16 C 0 1 N N N 3.335  8.749  7.672  -5.983  0.274  1.456  C13   XKF 28 
XKF C14   C17 C 0 1 Y N N 2.498  9.520  8.652  -7.400  0.063  0.989  C14   XKF 29 
XKF C15   C18 C 0 1 Y N N 1.997  9.090  9.849  -8.424  0.921  1.130  C15   XKF 30 
XKF N15   N8  N 0 1 Y N N 1.248  10.074 10.444 -9.558  0.387  0.582  N15   XKF 31 
XKF C16   C19 C 0 1 Y N N 1.237  11.178 9.633  -9.286  -0.859 0.062  C16   XKF 32 
XKF C21   C20 C 0 1 Y N N 2.010  10.874 8.486  -7.921  -1.114 0.289  C21   XKF 33 
XKF C20   C21 C 0 1 Y N N 2.158  11.855 7.497  -7.356  -2.316 -0.141 C20   XKF 34 
XKF C19   C22 C 0 1 Y N N 1.556  13.080 7.677  -8.132  -3.238 -0.784 C19   XKF 35 
XKF C18   C23 C 0 1 Y N N 0.795  13.354 8.814  -9.479  -2.990 -1.014 C18   XKF 36 
XKF C17   C24 C 0 1 Y N N 0.624  12.419 9.809  -10.058 -1.814 -0.591 C17   XKF 37 
XKF H1    H1  H 0 1 N N N 11.721 5.397  -1.054 7.416   2.232  0.342  H1    XKF 38 
XKF H2    H2  H 0 1 N N N 10.577 6.468  -0.177 7.099   1.839  2.049  H2    XKF 39 
XKF H3    H3  H 0 1 N N N 10.583 4.702  0.149  8.766   2.135  1.499  H3    XKF 40 
XKF H4    H4  H 0 1 N N N 9.912  4.376  -2.057 8.827   -0.128 0.989  H4    XKF 41 
XKF H5    H5  H 0 1 N N N 4.038  5.776  1.853  1.527   -1.328 -0.647 H5    XKF 42 
XKF H6    H6  H 0 1 N N N 6.177  4.969  -5.355 8.310   -4.723 -0.180 H6    XKF 43 
XKF H7    H7  H 0 1 N N N 8.577  4.989  -4.348 9.139   -2.341 0.526  H7    XKF 44 
XKF H8    H8  H 0 1 N N N 3.332  6.320  9.029  -3.520  0.822  1.671  H8    XKF 45 
XKF H9    H9  H 0 1 N N N 4.935  4.528  5.557  -0.565  1.561  -1.493 H9    XKF 46 
XKF H10   H10 H 0 1 N N N 6.454  4.087  6.408  -0.977  3.218  -0.991 H10   XKF 47 
XKF H11   H11 H 0 1 N N N 7.747  5.372  5.061  0.661   2.987  0.913  H11   XKF 48 
XKF H12   H12 H 0 1 N N N 5.539  7.368  5.188  1.233   3.238  -1.936 H12   XKF 49 
XKF H13   H13 H 0 1 N N N 7.566  7.647  6.271  2.840   4.744  -1.012 H13   XKF 50 
XKF H14   H14 H 0 1 N N N 5.285  7.418  2.972  2.725   1.423  -2.031 H14   XKF 51 
XKF H15   H15 H 0 1 N N N 6.757  9.176  3.145  4.251   3.296  -1.890 H15   XKF 52 
XKF H16   H16 H 0 1 N N N 7.875  5.865  2.555  3.169   1.653  1.001  H16   XKF 53 
XKF H17   H17 H 0 1 N N N 5.328  8.007  7.598  -5.564  1.783  -0.024 H17   XKF 54 
XKF H18   H18 H 0 1 N N N 4.735  8.427  9.241  -5.152  0.126  -0.526 H18   XKF 55 
XKF H19   H19 H 0 1 N N N 3.766  9.463  6.955  -5.563  -0.677 1.784  H19   XKF 56 
XKF H20   H20 H 0 1 N N N 2.677  8.047  7.139  -5.976  0.981  2.286  H20   XKF 57 
XKF H21   H21 H 0 1 N N N 2.167  8.110  10.269 -8.361  1.888  1.605  H21   XKF 58 
XKF H22   H22 H 0 1 N N N 0.785  9.997  11.327 -10.425 0.821  0.563  H22   XKF 59 
XKF H23   H23 H 0 1 N N N 2.736  11.653 6.607  -6.309  -2.516 0.033  H23   XKF 60 
XKF H24   H24 H 0 1 N N N 1.675  13.844 6.923  -7.694  -4.168 -1.117 H24   XKF 61 
XKF H25   H25 H 0 1 N N N 0.329  14.323 8.916  -10.079 -3.729 -1.524 H25   XKF 62 
XKF H26   H26 H 0 1 N N N 0.039  12.637 10.690 -11.106 -1.630 -0.775 H26   XKF 63 
# 
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 
XKF C9    C10   DOUB Y N 1  
XKF C9    N6    SING Y N 2  
XKF C10   N1    SING Y N 3  
XKF N6    C6    DOUB Y N 4  
XKF N1    C6    SING Y N 5  
XKF N1    C2    SING Y N 6  
XKF C6    C5    SING Y N 7  
XKF N2    C2    SING N N 8  
XKF N2    C3    SING N N 9  
XKF C2    N3    DOUB Y N 10 
XKF C5    N7    SING Y N 11 
XKF C5    C4    DOUB Y N 12 
XKF N7    C8    DOUB Y N 13 
XKF N3    C4    SING Y N 14 
XKF C4    N9    SING Y N 15 
XKF C8    N9    SING Y N 16 
XKF N9    "C1'" SING N N 17 
XKF "C1'" "C2'" SING N N 18 
XKF "C1'" "O4'" SING N N 19 
XKF "O2'" "C2'" SING N N 20 
XKF "C2'" "C3'" SING N N 21 
XKF "O4'" "C4'" SING N N 22 
XKF "C3'" "C4'" SING N N 23 
XKF "C3'" "O3'" SING N N 24 
XKF "C4'" "C5'" SING N N 25 
XKF "C5'" "O5'" SING N N 26 
XKF "O5'" C11   SING N N 27 
XKF C20   C19   DOUB Y N 28 
XKF C20   C21   SING Y N 29 
XKF C13   C12   SING N N 30 
XKF C13   C14   SING N N 31 
XKF C19   C18   SING Y N 32 
XKF C11   N12   SING N N 33 
XKF C11   O11   DOUB N N 34 
XKF C12   N12   SING N N 35 
XKF C21   C14   SING Y N 36 
XKF C21   C16   DOUB Y N 37 
XKF C14   C15   DOUB Y N 38 
XKF C18   C17   DOUB Y N 39 
XKF C16   C17   SING Y N 40 
XKF C16   N15   SING Y N 41 
XKF C15   N15   SING Y N 42 
XKF C3    H1    SING N N 43 
XKF C3    H2    SING N N 44 
XKF C3    H3    SING N N 45 
XKF N2    H4    SING N N 46 
XKF C8    H5    SING N N 47 
XKF C9    H6    SING N N 48 
XKF C10   H7    SING N N 49 
XKF N12   H8    SING N N 50 
XKF "C5'" H9    SING N N 51 
XKF "C5'" H10   SING N N 52 
XKF "C4'" H11   SING N N 53 
XKF "C3'" H12   SING N N 54 
XKF "O3'" H13   SING N N 55 
XKF "C2'" H14   SING N N 56 
XKF "O2'" H15   SING N N 57 
XKF "C1'" H16   SING N N 58 
XKF C12   H17   SING N N 59 
XKF C12   H18   SING N N 60 
XKF C13   H19   SING N N 61 
XKF C13   H20   SING N N 62 
XKF C15   H21   SING N N 63 
XKF N15   H22   SING N N 64 
XKF C20   H23   SING N N 65 
XKF C19   H24   SING N N 66 
XKF C18   H25   SING N N 67 
XKF C17   H26   SING N N 68 
# 
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 
XKF InChI            InChI                1.06  "InChI=1S/C24H26N8O5/c1-25-23-30-21-17(20-26-8-9-31(20)23)29-12-32(21)22-19(34)18(33)16(37-22)11-36-24(35)27-7-6-13-10-28-15-5-3-2-4-14(13)15/h2-5,8-10,12,16,18-19,22,28,33-34H,6-7,11H2,1H3,(H,25,30)(H,27,35)/t16-,18-,19-,22-/m1/s1" 
XKF InChIKey         InChI                1.06  CBOHRQLNXCBGQM-WGQQHEPDSA-N                                                                                                                                                                                                              
XKF SMILES_CANONICAL CACTVS               3.385 "CNc1nc2n(cnc2c3nccn13)[C@@H]4O[C@H](COC(=O)NCCc5c[nH]c6ccccc56)[C@@H](O)[C@H]4O"                                                                                                                                                        
XKF SMILES           CACTVS               3.385 "CNc1nc2n(cnc2c3nccn13)[CH]4O[CH](COC(=O)NCCc5c[nH]c6ccccc56)[CH](O)[CH]4O"                                                                                                                                                              
XKF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNc1nc2c(c3n1ccn3)ncn2[C@H]4[C@@H]([C@@H]([C@H](O4)COC(=O)NCCc5c[nH]c6c5cccc6)O)O"                                                                                                                                                      
XKF SMILES           "OpenEye OEToolkits" 2.0.7 "CNc1nc2c(c3n1ccn3)ncn2C4C(C(C(O4)COC(=O)NCCc5c[nH]c6c5cccc6)O)O"                                                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           XKF 
_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}-[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 
XKF "Create component" 2023-06-07 PDBE 
XKF "Initial release"  2023-06-14 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      XKF 
_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}-[2-(1~{H}-indol-3-yl)ethyl]carbamate" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
