data_VYN
# 
_chem_comp.id                                    VYN 
_chem_comp.name                                  "8-(4-azanylbutyl)-2-[1,3-bis(oxidanyl)propan-2-ylamino]-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]pyrido[2,3-d]pyrimidin-7-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H29 Cl N6 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-09-20 
_chem_comp.pdbx_modified_date                    2023-11-03 
_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                        509.000 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VYN 
_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        8QLR 
_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.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 
VYN N1  N1  N  0 1 N N N N N N 42.400 14.326 42.709 5.511   -1.212 -0.338 N1  VYN 1  
VYN C2  C1  C  0 1 Y N N N N N 37.376 19.822 55.441 -9.066  -0.386 0.976  C2  VYN 2  
VYN N3  N2  N  0 1 N N N N N N 42.428 15.801 47.093 1.361   0.933  -0.551 N3  VYN 3  
VYN C4  C2  C  0 1 Y N N N N N 36.877 19.264 53.177 -6.906  -0.332 1.979  C4  VYN 4  
VYN C5  C3  C  0 1 Y N N N N N 38.184 18.812 53.043 -6.357  -0.357 0.698  C5  VYN 5  
VYN C6  C4  C  0 1 Y N N N N N 38.696 18.271 51.758 -4.884  -0.343 0.530  C6  VYN 6  
VYN C8  C5  C  0 1 Y N N N N N 40.067 18.498 49.781 -2.686  -0.284 1.494  C8  VYN 7  
VYN C24 C6  C  0 1 Y N N N N N 38.905 16.452 50.195 -2.960  -0.354 -0.908 C24 VYN 8  
VYN CL  CL1 CL 0 0 N N N N N N 38.453 14.837 49.747 -2.269  -0.385 -2.500 CL  VYN 9  
VYN C25 C7  C  0 1 Y N N N N N 38.378 16.973 51.361 -4.329  -0.368 -0.750 C25 VYN 10 
VYN C3  C8  C  0 1 Y N N N N N 36.477 19.783 54.394 -8.282  -0.346 2.121  C3  VYN 11 
VYN N5  N3  N  0 1 Y N N N N N 39.072 18.840 54.060 -7.142  -0.400 -0.371 N5  VYN 12 
VYN C1  C9  C  0 1 Y N N N N N 38.665 19.332 55.248 -8.455  -0.414 -0.264 C1  VYN 13 
VYN C   C10 C  0 1 N N N N N N 39.663 19.291 56.368 -9.302  -0.462 -1.509 C   VYN 14 
VYN C9  C11 C  0 1 Y N N N N N 39.766 17.191 49.391 -2.129  -0.315 0.215  C9  VYN 15 
VYN C7  C12 C  0 1 Y N N N N N 39.539 19.022 50.947 -4.054  -0.298 1.650  C7  VYN 16 
VYN C10 C13 C  0 1 N N N N N N 40.412 16.632 48.175 -0.658  -0.300 0.047  C10 VYN 17 
VYN C23 C14 C  0 1 N N N N N N 41.828 16.277 48.251 0.023   0.919  -0.398 C23 VYN 18 
VYN O2  O1  O  0 1 N N N N N N 42.494 16.363 49.269 -0.625  1.924  -0.631 O2  VYN 19 
VYN C19 C15 C  0 1 N N N N N N 43.868 15.541 47.158 2.026   2.159  -0.997 C19 VYN 20 
VYN C20 C16 C  0 1 N N N N N N 44.706 16.666 46.554 2.411   3.003  0.220  C20 VYN 21 
VYN C21 C17 C  0 1 N N N N N N 44.740 17.917 47.446 3.106   4.283  -0.245 C21 VYN 22 
VYN C22 C18 C  0 1 N N N N N N 45.606 19.022 46.865 3.490   5.127  0.972  C22 VYN 23 
VYN N4  N4  N  0 1 N N N N N N 45.518 20.279 47.639 4.158   6.357  0.525  N4  VYN 24 
VYN C18 C19 C  0 1 Y N N N N N 41.744 15.619 45.904 2.107   -0.188 -0.289 C18 VYN 25 
VYN C12 C20 C  0 1 Y N N N N N 40.375 15.941 45.834 1.482   -1.378 0.142  C12 VYN 26 
VYN C11 C21 C  0 1 N N N N N N 39.742 16.469 47.011 0.079   -1.425 0.306  C11 VYN 27 
VYN N2  N5  N  0 1 Y N N N N N 42.433 15.128 44.867 3.428   -0.177 -0.433 N2  VYN 28 
VYN C14 C22 C  0 1 Y N N N N N 41.737 14.929 43.740 4.141   -1.263 -0.176 C14 VYN 29 
VYN N   N6  N  0 1 Y N N N N N 40.433 15.181 43.551 3.587   -2.399 0.231  N   VYN 30 
VYN C13 C23 C  0 1 Y N N N N N 39.769 15.688 44.599 2.282   -2.501 0.401  C13 VYN 31 
VYN C15 C24 C  0 1 N N N N N N 43.604 14.841 42.067 6.326   -2.399 -0.067 C15 VYN 32 
VYN C17 C25 C  0 1 N N N N N N 44.016 13.850 40.988 7.626   -2.319 -0.870 C17 VYN 33 
VYN O1  O2  O  0 1 N N N N N N 44.187 12.564 41.567 8.404   -1.214 -0.408 O1  VYN 34 
VYN C16 C26 C  0 1 N N N N N N 44.765 14.871 43.044 6.652   -2.464 1.426  C16 VYN 35 
VYN O   O3  O  0 1 N N N N N N 45.838 15.623 42.504 7.475   -1.352 1.783  O   VYN 36 
VYN H1  H1  H  0 1 N N N N N N 41.726 14.237 41.976 5.934   -0.391 -0.635 H1  VYN 37 
VYN H2  H2  H  0 1 N N N N N N 37.083 20.228 56.398 -10.143 -0.398 1.054  H2  VYN 38 
VYN H3  H3  H  0 1 N N N N N N 36.188 19.211 52.347 -6.266  -0.302 2.849  H3  VYN 39 
VYN H4  H4  H  0 1 N N N N N N 40.717 19.104 49.167 -2.044  -0.250 2.362  H4  VYN 40 
VYN H5  H5  H  0 1 N N N N N N 37.717 16.372 51.968 -4.972  -0.399 -1.617 H5  VYN 41 
VYN H6  H6  H  0 1 N N N N N N 35.471 20.154 54.525 -8.737  -0.327 3.101  H6  VYN 42 
VYN H7  H7  H  0 1 N N N N N N 40.601 18.844 56.008 -9.492  -1.501 -1.779 H7  VYN 43 
VYN H8  H8  H  0 1 N N N N N N 39.857 20.314 56.724 -10.248 0.045  -1.324 H8  VYN 44 
VYN H9  H9  H  0 1 N N N N N N 39.262 18.685 57.194 -8.776  0.034  -2.325 H9  VYN 45 
VYN H10 H10 H  0 1 N N N N N N 39.786 20.034 51.233 -4.485  -0.274 2.640  H10 VYN 46 
VYN H11 H11 H  0 1 N N N N N N 44.081 14.612 46.609 2.924   1.902  -1.559 H11 VYN 47 
VYN H12 H12 H  0 1 N N N N N N 44.155 15.418 48.213 1.350   2.729  -1.635 H12 VYN 48 
VYN H13 H13 H  0 1 N N N N N N 45.735 16.304 46.415 1.513   3.260  0.782  H13 VYN 49 
VYN H14 H14 H  0 1 N N N N N N 44.278 16.940 45.578 3.087   2.433  0.858  H14 VYN 50 
VYN H15 H15 H  0 1 N N N N N N 43.714 18.296 47.561 4.004   4.026  -0.807 H15 VYN 51 
VYN H16 H16 H  0 1 N N N N N N 45.140 17.637 48.432 2.430   4.853  -0.883 H16 VYN 52 
VYN H17 H17 H  0 1 N N N N N N 46.653 18.684 46.860 2.592   5.384  1.534  H17 VYN 53 
VYN H18 H18 H  0 1 N N N N N N 45.280 19.220 45.833 4.166   4.557  1.610  H18 VYN 54 
VYN H19 H19 H  0 1 N N N N N N 46.103 20.972 47.218 3.575   6.870  -0.119 H19 VYN 55 
VYN H20 H20 H  0 1 N N N N N N 44.571 20.601 47.645 4.421   6.931  1.312  H20 VYN 56 
VYN H22 H22 H  0 1 N N N N N N 38.699 16.744 46.965 -0.405  -2.333 0.636  H22 VYN 57 
VYN H23 H23 H  0 1 N N N N N N 38.719 15.911 44.485 1.840   -3.429 0.732  H23 VYN 58 
VYN H24 H24 H  0 1 N N N N N N 43.436 15.838 41.633 5.773   -3.292 -0.358 H24 VYN 59 
VYN H25 H25 H  0 1 N N N N N N 44.963 14.176 40.533 8.191   -3.242 -0.738 H25 VYN 60 
VYN H26 H26 H  0 1 N N N N N N 43.235 13.803 40.215 7.393   -2.184 -1.926 H26 VYN 61 
VYN H27 H27 H  0 1 N N N N N N 44.444 11.945 40.894 9.244   -1.102 -0.873 H27 VYN 62 
VYN H28 H28 H  0 1 N N N N N N 44.435 15.333 43.986 5.727   -2.431 2.002  H28 VYN 63 
VYN H29 H29 H  0 1 N N N N N N 45.103 13.843 43.238 7.181   -3.392 1.642  H29 VYN 64 
VYN H30 H30 H  0 1 N N N N N N 46.559 15.636 43.122 7.721   -1.329 2.718  H30 VYN 65 
# 
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 
VYN C17 O1  SING N N 1  
VYN C17 C15 SING N N 2  
VYN C15 N1  SING N N 3  
VYN C15 C16 SING N N 4  
VYN O   C16 SING N N 5  
VYN N1  C14 SING N N 6  
VYN N   C14 DOUB Y N 7  
VYN N   C13 SING Y N 8  
VYN C14 N2  SING Y N 9  
VYN C13 C12 DOUB Y N 10 
VYN N2  C18 DOUB Y N 11 
VYN C12 C18 SING Y N 12 
VYN C12 C11 SING N N 13 
VYN C18 N3  SING N N 14 
VYN C20 C19 SING N N 15 
VYN C20 C21 SING N N 16 
VYN C22 C21 SING N N 17 
VYN C22 N4  SING N N 18 
VYN C11 C10 DOUB N N 19 
VYN N3  C19 SING N N 20 
VYN N3  C23 SING N N 21 
VYN C10 C23 SING N N 22 
VYN C10 C9  SING N N 23 
VYN C23 O2  DOUB N N 24 
VYN C9  C8  DOUB Y N 25 
VYN C9  C24 SING Y N 26 
VYN CL  C24 SING N N 27 
VYN C8  C7  SING Y N 28 
VYN C24 C25 DOUB Y N 29 
VYN C7  C6  DOUB Y N 30 
VYN C25 C6  SING Y N 31 
VYN C6  C5  SING N N 32 
VYN C5  C4  DOUB Y N 33 
VYN C5  N5  SING Y N 34 
VYN C4  C3  SING Y N 35 
VYN N5  C1  DOUB Y N 36 
VYN C3  C2  DOUB Y N 37 
VYN C1  C2  SING Y N 38 
VYN C1  C   SING N N 39 
VYN N1  H1  SING N N 40 
VYN C2  H2  SING N N 41 
VYN C4  H3  SING N N 42 
VYN C8  H4  SING N N 43 
VYN C25 H5  SING N N 44 
VYN C3  H6  SING N N 45 
VYN C   H7  SING N N 46 
VYN C   H8  SING N N 47 
VYN C   H9  SING N N 48 
VYN C7  H10 SING N N 49 
VYN C19 H11 SING N N 50 
VYN C19 H12 SING N N 51 
VYN C20 H13 SING N N 52 
VYN C20 H14 SING N N 53 
VYN C21 H15 SING N N 54 
VYN C21 H16 SING N N 55 
VYN C22 H17 SING N N 56 
VYN C22 H18 SING N N 57 
VYN N4  H19 SING N N 58 
VYN N4  H20 SING N N 59 
VYN C11 H22 SING N N 60 
VYN C13 H23 SING N N 61 
VYN C15 H24 SING N N 62 
VYN C17 H25 SING N N 63 
VYN C17 H26 SING N N 64 
VYN O1  H27 SING N N 65 
VYN C16 H28 SING N N 66 
VYN C16 H29 SING N N 67 
VYN O   H30 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 
VYN InChI            InChI                1.06  "InChI=1S/C26H29ClN6O3/c1-16-5-4-6-23(30-16)17-7-8-20(22(27)12-17)21-11-18-13-29-26(31-19(14-34)15-35)32-24(18)33(25(21)36)10-3-2-9-28/h4-8,11-13,19,34-35H,2-3,9-10,14-15,28H2,1H3,(H,29,31,32)" 
VYN InChIKey         InChI                1.06  PIJSEUOSRTYUJM-UHFFFAOYSA-N                                                                                                                                                                       
VYN SMILES_CANONICAL CACTVS               3.385 "Cc1cccc(n1)c2ccc(c(Cl)c2)C3=Cc4cnc(NC(CO)CO)nc4N(CCCCN)C3=O"                                                                                                                                     
VYN SMILES           CACTVS               3.385 "Cc1cccc(n1)c2ccc(c(Cl)c2)C3=Cc4cnc(NC(CO)CO)nc4N(CCCCN)C3=O"                                                                                                                                     
VYN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cccc(n1)c2ccc(c(c2)Cl)C3=Cc4cnc(nc4N(C3=O)CCCCN)NC(CO)CO"                                                                                                                                     
VYN SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cccc(n1)c2ccc(c(c2)Cl)C3=Cc4cnc(nc4N(C3=O)CCCCN)NC(CO)CO"                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           VYN 
_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        "8-(4-azanylbutyl)-2-[1,3-bis(oxidanyl)propan-2-ylamino]-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]pyrido[2,3-d]pyrimidin-7-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VYN "Create component" 2023-09-20 PDBE 
VYN "Initial release"  2023-11-08 RCSB 
# 
