data_ZNL
# 
_chem_comp.id                                    ZNL 
_chem_comp.name                                  "N-{7-methyl-1-[(3S)-1-(prop-2-enoyl)azepan-3-yl]-1H-benzimidazol-2-yl}-5-(prop-2-enamido)thiophene-3-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H27 N5 O3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-09-28 
_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                        477.579 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ZNL 
_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        8EME 
_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 
ZNL C16 C1  C 0 1 Y N N N N N -10.468 -24.151 12.652 1.124   -1.469 -0.097 C16 ZNL 1  
ZNL C12 C2  C 0 1 N N N N N N -10.654 -23.518 5.679  4.252   2.149  1.770  C12 ZNL 2  
ZNL C11 C3  C 0 1 N N N N N N -11.342 -23.304 6.975  3.476   3.145  1.015  C11 ZNL 3  
ZNL C15 C4  C 0 1 N N N N N N -12.202 -24.097 9.145  1.913   1.404  0.468  C15 ZNL 4  
ZNL C13 C5  C 0 1 N N N N N N -9.408  -23.093 5.455  5.392   2.500  2.358  C13 ZNL 5  
ZNL C01 C6  C 0 1 N N N N N N -14.266 -22.118 10.581 5.435   -0.641 -0.607 C01 ZNL 6  
ZNL C02 C7  C 0 1 Y N N N N N -13.470 -21.955 11.819 4.679   -1.907 -0.294 C02 ZNL 7  
ZNL C03 C8  C 0 1 Y N N N N N -12.304 -22.767 12.202 3.297   -1.884 -0.189 C03 ZNL 8  
ZNL C05 C9  C 0 1 N N S N N N -11.583 -24.739 10.412 2.590   0.523  -0.611 C05 ZNL 9  
ZNL C06 C10 C 0 1 N N N N N N -12.119 -26.156 10.683 2.050   0.840  -1.942 C06 ZNL 10 
ZNL C07 C11 C 0 1 N N N N N N -11.754 -27.109 9.544  2.314   2.270  -2.403 C07 ZNL 11 
ZNL C08 C12 C 0 1 N N N N N N -10.567 -26.624 8.718  1.240   3.178  -1.855 C08 ZNL 12 
ZNL C09 C13 C 0 1 N N N N N N -10.994 -25.727 7.539  1.684   3.766  -0.503 C09 ZNL 13 
ZNL C18 C14 C 0 1 N N N N N N -8.403  -25.678 13.285 -1.234  -1.483 0.083  C18 ZNL 14 
ZNL C19 C15 C 0 1 Y N N N N N -7.466  -26.850 12.933 -2.525  -0.778 0.041  C19 ZNL 15 
ZNL C20 C16 C 0 1 Y N N N N N -7.599  -27.591 11.791 -2.645  0.551  -0.220 C20 ZNL 16 
ZNL C22 C17 C 0 1 Y N N N N N -5.656  -28.493 13.061 -4.832  -0.592 0.178  C22 ZNL 17 
ZNL C24 C18 C 0 1 N N N N N N -3.300  -28.837 14.040 -7.140  -0.031 0.241  C24 ZNL 18 
ZNL C25 C19 C 0 1 N N N N N N -3.011  -27.378 14.286 -8.547  -0.416 0.423  C25 ZNL 19 
ZNL C26 C20 C 0 1 N N N N N N -2.219  -26.635 13.505 -9.507  0.498  0.314  C26 ZNL 20 
ZNL C28 C21 C 0 1 Y N N N N N -6.301  -27.407 13.683 -3.796  -1.429 0.266  C28 ZNL 21 
ZNL C31 C22 C 0 1 Y N N N N N -11.673 -22.449 13.449 2.595   -3.066 0.102  C31 ZNL 22 
ZNL C32 C23 C 0 1 Y N N N N N -12.138 -21.403 14.290 3.301   -4.257 0.283  C32 ZNL 23 
ZNL C33 C24 C 0 1 Y N N N N N -13.233 -20.667 13.893 4.674   -4.262 0.174  C33 ZNL 24 
ZNL C34 C25 C 0 1 Y N N N N N -13.873 -20.946 12.685 5.361   -3.093 -0.112 C34 ZNL 25 
ZNL N04 N1  N 0 1 Y N N N N N -11.496 -23.897 11.690 2.341   -0.889 -0.310 N04 ZNL 26 
ZNL N10 N2  N 0 1 N N N N N N -11.511 -24.361 7.889  2.373   2.768  0.338  N10 ZNL 27 
ZNL N17 N3  N 0 1 N N N N N N -9.499  -25.228 12.439 -0.090  -0.807 -0.137 N17 ZNL 28 
ZNL N23 N4  N 0 1 N N N N N N -4.538  -29.280 13.466 -6.168  -0.957 0.351  N23 ZNL 29 
ZNL N30 N5  N 0 1 Y N N N N N -10.567 -23.312 13.691 1.275   -2.747 0.144  N30 ZNL 30 
ZNL O14 O1  O 0 1 N N N N N N -11.772 -22.194 7.266  3.831   4.308  1.001  O14 ZNL 31 
ZNL O27 O2  O 0 1 N N N N N N -2.436  -29.651 14.342 -6.854  1.124  -0.010 O27 ZNL 32 
ZNL O29 O3  O 0 1 N N N N N N -8.234  -25.078 14.329 -1.200  -2.676 0.318  O29 ZNL 33 
ZNL S21 S1  S 0 1 Y N N N N N -6.473  -28.835 11.588 -4.279  1.033  -0.190 S21 ZNL 34 
ZNL H1  H1  H 0 1 N N N N N N -11.179 -24.035 4.889  3.895   1.132  1.848  H1  ZNL 35 
ZNL H2  H2  H 0 1 N N N N N N -12.221 -23.008 9.295  0.831   1.372  0.336  H2  ZNL 36 
ZNL H3  H3  H 0 1 N N N N N N -13.232 -24.472 9.047  2.169   1.027  1.458  H3  ZNL 37 
ZNL H4  H4  H 0 1 N N N N N N -8.942  -23.269 4.497  5.961   1.768  2.912  H4  ZNL 38 
ZNL H5  H5  H 0 1 N N N N N N -8.867  -22.574 6.232  5.749   3.516  2.280  H5  ZNL 39 
ZNL H6  H6  H 0 1 N N N N N N -15.088 -22.826 10.763 5.582   -0.071 0.310  H6  ZNL 40 
ZNL H7  H7  H 0 1 N N N N N N -14.681 -21.144 10.281 6.403   -0.893 -1.038 H7  ZNL 41 
ZNL H8  H8  H 0 1 N N N N N N -13.620 -22.504 9.778  4.864   -0.044 -1.319 H8  ZNL 42 
ZNL H9  H9  H 0 1 N N N N N N -10.532 -24.905 10.133 3.665   0.707  -0.604 H9  ZNL 43 
ZNL H10 H10 H 0 1 N N N N N N -13.214 -26.114 10.779 2.493   0.156  -2.667 H10 ZNL 44 
ZNL H11 H11 H 0 1 N N N N N N -11.683 -26.532 11.620 0.973   0.676  -1.926 H11 ZNL 45 
ZNL H12 H12 H 0 1 N N N N N N -12.625 -27.211 8.880  3.287   2.596  -2.038 H12 ZNL 46 
ZNL H13 H13 H 0 1 N N N N N N -11.504 -28.090 9.974  2.302   2.309  -3.492 H13 ZNL 47 
ZNL H14 H14 H 0 1 N N N N N N -10.033 -27.500 8.320  1.058   3.989  -2.560 H14 ZNL 48 
ZNL H15 H15 H 0 1 N N N N N N -9.894  -26.050 9.372  0.322   2.608  -1.714 H15 ZNL 49 
ZNL H16 H16 H 0 1 N N N N N N -11.788 -26.254 6.989  2.360   4.602  -0.686 H16 ZNL 50 
ZNL H17 H17 H 0 1 N N N N N N -10.119 -25.596 6.885  0.806   4.133  0.028  H17 ZNL 51 
ZNL H18 H18 H 0 1 N N N N N N -8.374  -27.394 11.065 -1.815  1.213  -0.419 H18 ZNL 52 
ZNL H19 H19 H 0 1 N N N N N N -3.470  -26.906 15.142 -8.802  -1.442 0.646  H19 ZNL 53 
ZNL H20 H20 H 0 1 N N N N N N -2.054  -25.594 13.738 -10.541 0.215  0.449  H20 ZNL 54 
ZNL H21 H21 H 0 1 N N N N N N -1.745  -27.077 12.641 -9.253  1.524  0.092  H21 ZNL 55 
ZNL H22 H22 H 0 1 N N N N N N -5.977  -27.006 14.632 -3.896  -2.483 0.482  H22 ZNL 56 
ZNL H23 H23 H 0 1 N N N N N N -11.642 -21.188 15.225 2.772   -5.172 0.507  H23 ZNL 57 
ZNL H24 H24 H 0 1 N N N N N N -13.599 -19.868 14.521 5.219   -5.184 0.314  H24 ZNL 58 
ZNL H25 H25 H 0 1 N N N N N N -14.727 -20.346 12.408 6.438   -3.110 -0.195 H25 ZNL 59 
ZNL H26 H26 H 0 1 N N N N N N -9.607  -25.731 11.582 -0.117  0.145  -0.324 H26 ZNL 60 
ZNL H27 H27 H 0 1 N N N N N N -4.628  -30.267 13.333 -6.396  -1.879 0.551  H27 ZNL 61 
# 
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 
ZNL C13 C12 DOUB N N 1  
ZNL C12 C11 SING N N 2  
ZNL C11 O14 DOUB N N 3  
ZNL C11 N10 SING N N 4  
ZNL C09 N10 SING N N 5  
ZNL C09 C08 SING N N 6  
ZNL N10 C15 SING N N 7  
ZNL C08 C07 SING N N 8  
ZNL C15 C05 SING N N 9  
ZNL C07 C06 SING N N 10 
ZNL C05 C06 SING N N 11 
ZNL C05 N04 SING N N 12 
ZNL C01 C02 SING N N 13 
ZNL S21 C20 SING Y N 14 
ZNL S21 C22 SING Y N 15 
ZNL N04 C03 SING Y N 16 
ZNL N04 C16 SING Y N 17 
ZNL C20 C19 DOUB Y N 18 
ZNL C02 C03 DOUB Y N 19 
ZNL C02 C34 SING Y N 20 
ZNL C03 C31 SING Y N 21 
ZNL N17 C16 SING N N 22 
ZNL N17 C18 SING N N 23 
ZNL C16 N30 DOUB Y N 24 
ZNL C34 C33 DOUB Y N 25 
ZNL C19 C18 SING N N 26 
ZNL C19 C28 SING Y N 27 
ZNL C22 N23 SING N N 28 
ZNL C22 C28 DOUB Y N 29 
ZNL C18 O29 DOUB N N 30 
ZNL C31 N30 SING Y N 31 
ZNL C31 C32 DOUB Y N 32 
ZNL N23 C24 SING N N 33 
ZNL C26 C25 DOUB N N 34 
ZNL C33 C32 SING Y N 35 
ZNL C24 C25 SING N N 36 
ZNL C24 O27 DOUB N N 37 
ZNL C12 H1  SING N N 38 
ZNL C15 H2  SING N N 39 
ZNL C15 H3  SING N N 40 
ZNL C13 H4  SING N N 41 
ZNL C13 H5  SING N N 42 
ZNL C01 H6  SING N N 43 
ZNL C01 H7  SING N N 44 
ZNL C01 H8  SING N N 45 
ZNL C05 H9  SING N N 46 
ZNL C06 H10 SING N N 47 
ZNL C06 H11 SING N N 48 
ZNL C07 H12 SING N N 49 
ZNL C07 H13 SING N N 50 
ZNL C08 H14 SING N N 51 
ZNL C08 H15 SING N N 52 
ZNL C09 H16 SING N N 53 
ZNL C09 H17 SING N N 54 
ZNL C20 H18 SING N N 55 
ZNL C25 H19 SING N N 56 
ZNL C26 H20 SING N N 57 
ZNL C26 H21 SING N N 58 
ZNL C28 H22 SING N N 59 
ZNL C32 H23 SING N N 60 
ZNL C33 H24 SING N N 61 
ZNL C34 H25 SING N N 62 
ZNL N17 H26 SING N N 63 
ZNL N23 H27 SING N N 64 
# 
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 
ZNL SMILES           ACDLabs              12.01 "O=C(Nc1nc2cccc(C)c2n1C1CCCCN(C1)C(=O)C=C)c1cc(NC(=O)C=C)sc1"                                                                                                                                                  
ZNL InChI            InChI                1.06  "InChI=1S/C25H27N5O3S/c1-4-20(31)27-21-13-17(15-34-21)24(33)28-25-26-19-11-8-9-16(3)23(19)30(25)18-10-6-7-12-29(14-18)22(32)5-2/h4-5,8-9,11,13,15,18H,1-2,6-7,10,12,14H2,3H3,(H,27,31)(H,26,28,33)/t18-/m0/s1" 
ZNL InChIKey         InChI                1.06  DZTGCJZKRUDIGP-SFHVURJKSA-N                                                                                                                                                                                    
ZNL SMILES_CANONICAL CACTVS               3.385 "Cc1cccc2nc(NC(=O)c3csc(NC(=O)C=C)c3)n([C@H]4CCCCN(C4)C(=O)C=C)c12"                                                                                                                                            
ZNL SMILES           CACTVS               3.385 "Cc1cccc2nc(NC(=O)c3csc(NC(=O)C=C)c3)n([CH]4CCCCN(C4)C(=O)C=C)c12"                                                                                                                                             
ZNL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cccc2c1n(c(n2)NC(=O)c3cc(sc3)NC(=O)C=C)[C@H]4CCCCN(C4)C(=O)C=C"                                                                                                                                            
ZNL SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cccc2c1n(c(n2)NC(=O)c3cc(sc3)NC(=O)C=C)C4CCCCN(C4)C(=O)C=C"                                                                                                                                                
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
ZNL "SYSTEMATIC NAME" ACDLabs              12.01 "N-{7-methyl-1-[(3S)-1-(prop-2-enoyl)azepan-3-yl]-1H-benzimidazol-2-yl}-5-(prop-2-enamido)thiophene-3-carboxamide"    
ZNL "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[7-methyl-1-[(3~{S})-1-prop-2-enoylazepan-3-yl]benzimidazol-2-yl]-5-(prop-2-enoylamino)thiophene-3-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
ZNL "Create component" 2022-09-28 RCSB 
ZNL "Initial release"  2023-10-18 RCSB 
ZNL "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 ZNL CYS None Crosslinker "Amino-acid side chain" "Any position" C13 SG ? ? 
2 ZNL CYS None Crosslinker "Amino-acid side chain" "Any position" C26 SG ? ? 
# 
