data_D5W
# 
_chem_comp.id                                    D5W 
_chem_comp.name                                  "(2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H28 Cl2 N6 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-12-26 
_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                        479.403 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D5W 
_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        6FDU 
_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 
D5W C4  C1  C  0 1 Y N N N N N -40.356 -2.290 155.694 4.922  -0.645 0.683  C4  D5W 1  
D5W C5  C2  C  0 1 Y N N N N N -41.384 -3.012 155.052 5.909  0.114  1.296  C5  D5W 2  
D5W C6  C3  C  0 1 Y N N N N N -41.146 -3.697 153.856 7.206  0.034  0.810  C6  D5W 3  
D5W N1  N1  N  0 1 Y N N N N N -39.922 -3.658 153.305 7.462  -0.758 -0.216 N1  D5W 4  
D5W N3  N2  N  0 1 Y N N N N N -39.144 -2.267 155.113 5.247  -1.421 -0.337 N3  D5W 5  
D5W CAJ C4  C  0 1 Y N N N N N -44.969 -4.195 163.323 -3.560 -0.485 1.282  CAJ D5W 6  
D5W CAK C5  C  0 1 Y N N N N N -45.951 -5.051 163.884 -3.902 -1.812 1.476  CAK D5W 7  
D5W CLA CL1 CL 0 0 N N N N N N -46.496 -6.589 163.125 -3.905 -2.482 3.078  CLA D5W 8  
D5W CAL C6  C  0 1 Y N N N N N -46.574 -4.743 165.084 -4.242 -2.604 0.394  CAL D5W 9  
D5W CAM C7  C  0 1 Y N N N N N -46.239 -3.584 165.748 -4.240 -2.070 -0.881 CAM D5W 10 
D5W CLB CL2 CL 0 0 N N N N N N -47.105 -3.269 167.294 -4.666 -3.063 -2.240 CLB D5W 11 
D5W CAN C8  C  0 1 Y N N N N N -45.261 -2.730 165.202 -3.898 -0.743 -1.075 CAN D5W 12 
D5W CAI C9  C  0 1 Y N N N N N -44.592 -2.975 163.955 -3.558 0.048  0.007  CAI D5W 13 
D5W CAH C10 C  0 1 N N S N N N -43.521 -1.982 163.412 -3.187 1.493  -0.204 CAH D5W 14 
D5W NAU N3  N  0 1 N N N N N N -43.985 -0.568 163.108 -4.068 2.082  -1.221 NAU D5W 15 
D5W CAW C11 C  0 1 N N N N N N -42.819 0.366  163.025 -5.480 1.935  -0.842 CAW D5W 16 
D5W CAV C12 C  0 1 N N N N N N -44.968 0.042  164.052 -3.731 3.493  -1.457 CAV D5W 17 
D5W CAG C13 C  0 1 N N N N N N -42.687 -2.406 162.173 -1.756 1.581  -0.669 CAG D5W 18 
D5W OAQ O1  O  0 1 N N N N N N -41.453 -2.391 162.227 -1.507 1.678  -1.852 OAQ D5W 19 
D5W N   N4  N  0 1 N N N N N N -43.308 -2.718 161.015 -0.752 1.552  0.230  N   D5W 20 
D5W CA  C14 C  0 1 N N S N N N -42.636 -3.189 159.780 0.640  1.530  -0.226 CA  D5W 21 
D5W CB  C15 C  0 1 N N S N N N -43.449 -4.450 159.333 1.224  2.942  -0.148 CB  D5W 22 
D5W CG2 C16 C  0 1 N N N N N N -44.787 -4.134 158.630 0.546  3.833  -1.191 CG2 D5W 23 
D5W CG1 C17 C  0 1 N N N N N N -42.633 -5.471 158.500 0.982  3.517  1.249  CG1 D5W 24 
D5W CD1 C18 C  0 1 N N N N N N -41.642 -6.318 159.288 1.796  2.726  2.274  CD1 D5W 25 
D5W C   C19 C  0 1 N N N N N N -42.325 -2.191 158.635 1.442  0.605  0.652  C   D5W 26 
D5W O   O2  O  0 1 N N N N N N -43.124 -1.336 158.229 0.915  0.058  1.597  O   D5W 27 
D5W NAF N5  N  0 1 N N N N N N -41.098 -2.332 158.072 2.746  0.386  0.387  NAF D5W 28 
D5W CAX C20 C  0 1 N N N N N N -40.583 -1.513 156.980 3.500  -0.590 1.177  CAX D5W 29 
D5W C2  C21 C  0 1 Y N N N N N -38.949 -2.936 153.942 6.496  -1.470 -0.780 C2  D5W 30 
D5W CBE C22 C  0 1 N N N N N N -37.580 -2.892 153.371 6.820  -2.347 -1.928 CBE D5W 31 
D5W NBF N6  N  0 1 N N N N N N -37.375 -3.466 152.219 8.032  -2.411 -2.369 NBF D5W 32 
D5W H1  H1  H  0 1 N N N N N N -42.370 -3.036 155.491 5.672  0.754  2.134  H1  D5W 33 
D5W H2  H2  H  0 1 N N N N N N -41.940 -4.253 153.380 7.997  0.612  1.264  H2  D5W 34 
D5W H3  H3  H  0 1 N N N N N N -44.495 -4.475 162.394 -3.300 0.134  2.127  H3  D5W 35 
D5W H4  H4  H  0 1 N N N N N N -47.318 -5.409 165.496 -4.508 -3.640 0.546  H4  D5W 36 
D5W H5  H5  H  0 1 N N N N N N -44.999 -1.839 165.753 -3.895 -0.326 -2.071 H5  D5W 37 
D5W H6  H6  H  0 1 N N N N N N -42.789 -1.880 164.227 -3.298 2.038  0.733  H6  D5W 38 
D5W H8  H8  H  0 1 N N N N N N -43.178 1.382  162.804 -5.672 2.498  0.072  H8  D5W 39 
D5W H9  H9  H  0 1 N N N N N N -42.281 0.367  163.985 -6.113 2.316  -1.643 H9  D5W 40 
D5W H10 H10 H  0 1 N N N N N N -42.141 0.035  162.225 -5.703 0.882  -0.673 H10 D5W 41 
D5W H11 H11 H  0 1 N N N N N N -45.846 -0.615 164.143 -2.711 3.563  -1.836 H11 D5W 42 
D5W H12 H12 H  0 1 N N N N N N -44.499 0.167  165.039 -4.421 3.914  -2.189 H12 D5W 43 
D5W H13 H13 H  0 1 N N N N N N -45.283 1.024  163.669 -3.810 4.047  -0.522 H13 D5W 44 
D5W H14 H14 H  0 1 N N N N N N -44.303 -2.624 160.988 -0.951 1.544  1.179  H14 D5W 45 
D5W H15 H15 H  0 1 N N N N N N -41.657 -3.578 160.098 0.679  1.178  -1.257 H15 D5W 46 
D5W H16 H16 H  0 1 N N N N N N -43.717 -4.972 160.263 2.296  2.904  -0.344 H16 D5W 47 
D5W H17 H17 H  0 1 N N N N N N -45.355 -3.409 159.231 -0.505 3.959  -0.933 H17 D5W 48 
D5W H18 H18 H  0 1 N N N N N N -44.587 -3.709 157.635 1.035  4.807  -1.209 H18 D5W 49 
D5W H19 H19 H  0 1 N N N N N N -45.372 -5.059 158.522 0.626  3.368  -2.173 H19 D5W 50 
D5W H20 H20 H  0 1 N N N N N N -42.070 -4.913 157.737 1.289  4.563  1.270  H20 D5W 51 
D5W H21 H21 H  0 1 N N N N N N -43.343 -6.151 158.007 -0.078 3.445  1.493  H21 D5W 52 
D5W H22 H22 H  0 1 N N N N N N -41.120 -7.004 158.604 1.856  3.290  3.205  H22 D5W 53 
D5W H23 H23 H  0 1 N N N N N N -40.908 -5.662 159.779 1.312  1.767  2.461  H23 D5W 54 
D5W H24 H24 H  0 1 N N N N N N -42.182 -6.900 160.050 2.801  2.556  1.888  H24 D5W 55 
D5W H25 H25 H  0 1 N N N N N N -40.503 -3.050 158.432 3.184  0.875  -0.327 H25 D5W 56 
D5W H26 H26 H  0 1 N N N N N N -39.625 -1.075 157.296 3.041  -1.574 1.073  H26 D5W 57 
D5W H27 H27 H  0 1 N N N N N N -41.305 -0.708 156.778 3.490  -0.294 2.226  H27 D5W 58 
D5W H28 H28 H  0 1 N N N N N N -36.776 -2.398 153.896 6.043  -2.933 -2.397 H28 D5W 59 
D5W H29 H29 H  0 1 N N N N N N -36.424 -3.381 151.922 8.244  -2.985 -3.121 H29 D5W 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 
D5W NBF CBE DOUB N N 1  
D5W N1  C6  DOUB Y N 2  
D5W N1  C2  SING Y N 3  
D5W CBE C2  SING N N 4  
D5W C6  C5  SING Y N 5  
D5W C2  N3  DOUB Y N 6  
D5W C5  C4  DOUB Y N 7  
D5W N3  C4  SING Y N 8  
D5W C4  CAX SING N N 9  
D5W CAX NAF SING N N 10 
D5W NAF C   SING N N 11 
D5W O   C   DOUB N N 12 
D5W CG1 CD1 SING N N 13 
D5W CG1 CB  SING N N 14 
D5W CG2 CB  SING N N 15 
D5W C   CA  SING N N 16 
D5W CB  CA  SING N N 17 
D5W CA  N   SING N N 18 
D5W N   CAG SING N N 19 
D5W CAG OAQ DOUB N N 20 
D5W CAG CAH SING N N 21 
D5W CAW NAU SING N N 22 
D5W NAU CAH SING N N 23 
D5W NAU CAV SING N N 24 
D5W CLA CAK SING N N 25 
D5W CAJ CAK DOUB Y N 26 
D5W CAJ CAI SING Y N 27 
D5W CAH CAI SING N N 28 
D5W CAK CAL SING Y N 29 
D5W CAI CAN DOUB Y N 30 
D5W CAL CAM DOUB Y N 31 
D5W CAN CAM SING Y N 32 
D5W CAM CLB SING N N 33 
D5W C5  H1  SING N N 34 
D5W C6  H2  SING N N 35 
D5W CAJ H3  SING N N 36 
D5W CAL H4  SING N N 37 
D5W CAN H5  SING N N 38 
D5W CAH H6  SING N N 39 
D5W CAW H8  SING N N 40 
D5W CAW H9  SING N N 41 
D5W CAW H10 SING N N 42 
D5W CAV H11 SING N N 43 
D5W CAV H12 SING N N 44 
D5W CAV H13 SING N N 45 
D5W N   H14 SING N N 46 
D5W CA  H15 SING N N 47 
D5W CB  H16 SING N N 48 
D5W CG2 H17 SING N N 49 
D5W CG2 H18 SING N N 50 
D5W CG2 H19 SING N N 51 
D5W CG1 H20 SING N N 52 
D5W CG1 H21 SING N N 53 
D5W CD1 H22 SING N N 54 
D5W CD1 H23 SING N N 55 
D5W CD1 H24 SING N N 56 
D5W NAF H25 SING N N 57 
D5W CAX H26 SING N N 58 
D5W CAX H27 SING N N 59 
D5W CBE H28 SING N N 60 
D5W NBF H29 SING N N 61 
# 
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 
D5W InChI            InChI                1.03  "InChI=1S/C22H28Cl2N6O2/c1-5-13(2)19(21(31)27-12-17-6-7-26-18(11-25)28-17)29-22(32)20(30(3)4)14-8-15(23)10-16(24)9-14/h6-11,13,19-20,25H,5,12H2,1-4H3,(H,27,31)(H,29,32)/b25-11-/t13-,19-,20-/m0/s1" 
D5W InChIKey         InChI                1.03  XBUAFLLXSYLZPV-BFFNQEOMSA-N                                                                                                                                                                          
D5W SMILES_CANONICAL CACTVS               3.385 "CC[C@H](C)[C@H](NC(=O)[C@@H](N(C)C)c1cc(Cl)cc(Cl)c1)C(=O)NCc2ccnc(C=N)n2"                                                                                                                           
D5W SMILES           CACTVS               3.385 "CC[CH](C)[CH](NC(=O)[CH](N(C)C)c1cc(Cl)cc(Cl)c1)C(=O)NCc2ccnc(C=N)n2"                                                                                                                               
D5W SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C\c1nccc(n1)CNC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H](c2cc(cc(c2)Cl)Cl)N(C)C"                                                                                                                      
D5W SMILES           "OpenEye OEToolkits" 2.0.6 "CCC(C)C(C(=O)NCc1ccnc(n1)C=N)NC(=O)C(c2cc(cc(c2)Cl)Cl)N(C)C"                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           D5W 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.6 
_pdbx_chem_comp_identifier.identifier        "(2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
D5W "Create component" 2017-12-26 RCSB 
D5W "Initial release"  2018-08-15 RCSB 
D5W "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            D5W 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               CBE 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
