data_VR4
# 
_chem_comp.id                                    VR4 
_chem_comp.name                                  "N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H38 N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "			 GC376 alpha-ketoamide analog (bound form)" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-09-09 
_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                        538.635 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VR4 
_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        7K0H 
_chem_comp.pdbx_subcomponent_list                "P6S LEU UZ4 ABN" 
_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 
VR4 C33 C23 C 0 1 N N N N N N 20.216 23.445 -3.567 -6.098 0.298  -0.632 C21  P6S 1  
VR4 C34 C24 C 0 1 Y N N N N N 20.472 24.917 -3.316 -7.137 0.236  0.458  C22  P6S 2  
VR4 C36 C26 C 0 1 Y N N N N N 21.660 26.671 -2.096 -8.603 1.346  1.991  C24  P6S 3  
VR4 C38 C28 C 0 1 Y N N N N N 20.030 27.259 -3.738 -8.534 -1.046 1.920  C26  P6S 4  
VR4 C02 C1  C 0 1 N N N N N N 20.450 21.403 -2.364 -3.726 0.378  -0.881 C19  P6S 5  
VR4 C35 C25 C 0 1 Y N N N N N 21.415 25.312 -2.346 -7.650 1.403  0.991  C23  P6S 6  
VR4 C37 C27 C 0 1 Y N N N N N 20.961 27.647 -2.796 -9.043 0.121  2.458  C25  P6S 7  
VR4 C39 C29 C 0 1 Y N N N N N 19.788 25.913 -3.990 -7.581 -0.989 0.920  C27  P6S 8  
VR4 O32 O6  O 0 1 N N N N N N 20.669 22.752 -2.435 -4.774 0.322  -0.038 O20  P6S 9  
VR4 O01 O1  O 0 1 N N N N N N 19.719 20.813 -3.132 -3.913 0.406  -2.082 O28  P6S 10 
VR4 N03 N1  N 0 1 N N N N N N 21.107 20.845 -1.335 -2.470 0.403  -0.395 N    LEU 11 
VR4 C04 C2  C 0 1 N N S N N N 21.159 19.423 -1.160 -1.328 0.353  -1.311 CA   LEU 12 
VR4 C05 C3  C 0 1 N N N N N N 19.809 18.983 -0.599 -0.157 -0.296 -0.620 C    LEU 13 
VR4 O27 O5  O 0 1 N N N N N N 19.262 19.643 0.292  -0.172 -0.449 0.583  O    LEU 14 
VR4 C28 C19 C 0 1 N N N N N N 22.250 19.014 -0.186 -0.948 1.774  -1.732 CB   LEU 15 
VR4 C29 C20 C 0 1 N N N N N N 23.620 19.161 -0.736 0.153  1.715  -2.792 CG   LEU 16 
VR4 C30 C21 C 0 1 N N N N N N 24.648 19.070 0.408  -0.407 1.102  -4.076 CD1  LEU 17 
VR4 C31 C22 C 0 1 N N N N N N 23.890 18.072 -1.718 0.659  3.130  -3.081 CD2  LEU 18 
VR4 N06 N2  N 0 1 N N N N N N 19.205 17.823 -1.048 0.907  -0.706 -1.338 N19  UZ4 19 
VR4 C07 C4  C 0 1 N N S N N N 18.059 17.268 -0.476 1.999  -1.431 -0.683 C20  UZ4 20 
VR4 C08 C5  C 0 1 N N N N N N 16.957 17.006 -1.538 1.693  -2.930 -0.691 C21  UZ4 21 
VR4 C09 C6  C 0 1 N N S N N N 16.361 18.306 -2.045 2.762  -3.673 0.113  C22  UZ4 22 
VR4 C13 C9  C 0 1 N N N N N N 15.553 19.131 -0.992 2.568  -5.202 -0.012 C23  UZ4 23 
VR4 C12 C8  C 0 1 N N N N N N 14.300 19.656 -1.715 2.954  -5.685 1.404  C24  UZ4 24 
VR4 N11 N3  N 0 1 N N N N N N 14.208 18.812 -2.900 2.706  -4.542 2.289  N25  UZ4 25 
VR4 C10 C7  C 0 1 N N N N N N 15.336 18.043 -3.112 2.599  -3.398 1.592  C26  UZ4 26 
VR4 O14 O2  O 0 1 N N N N N N 15.447 17.270 -4.073 2.401  -2.304 2.077  O27  UZ4 27 
VR4 C15 C10 C 0 1 N N R N N N 18.512 15.951 0.332  3.306  -1.173 -1.434 C28  UZ4 28 
VR4 O26 O4  O 0 1 N N N N N N 19.733 16.261 1.018  3.178  -1.625 -2.783 O29  UZ4 29 
VR4 C16 C11 C 0 1 N N N N N N 17.532 15.479 1.383  3.607  0.304  -1.425 C31  UZ4 30 
VR4 O25 O3  O 0 1 N N N N N N 16.408 15.091 1.078  3.613  0.928  -2.466 O32  UZ4 31 
VR4 N17 N4  N 0 1 N N N N N N 17.938 15.540 2.727  3.871  0.931  -0.262 N    ABN 32 
VR4 C18 C12 C 0 1 N N N N N N 17.094 15.137 3.860  4.163  2.367  -0.254 C    ABN 33 
VR4 C19 C13 C 0 1 Y N N N N N 16.364 16.298 4.467  4.420  2.819  1.161  C1   ABN 34 
VR4 C20 C14 C 0 1 Y N N N N N 15.543 16.184 5.594  5.703  2.789  1.673  C2   ABN 35 
VR4 C21 C15 C 0 1 Y N N N N N 14.860 17.303 6.103  5.939  3.204  2.971  C3   ABN 36 
VR4 C22 C16 C 0 1 Y N N N N N 14.991 18.558 5.502  4.891  3.648  3.756  C4   ABN 37 
VR4 C23 C17 C 0 1 Y N N N N N 15.791 18.680 4.380  3.608  3.678  3.243  C5   ABN 38 
VR4 C24 C18 C 0 1 Y N N N N N 16.471 17.555 3.883  3.373  3.269  1.944  C6   ABN 39 
VR4 H27 H27 H 0 1 N N N N N N 19.140 23.268 -3.713 -6.192 -0.578 -1.274 H7   P6S 40 
VR4 H28 H28 H 0 1 N N N N N N 20.767 23.112 -4.459 -6.247 1.201  -1.225 H8   P6S 41 
VR4 H30 H30 H 0 1 N N N N N N 22.394 26.959 -1.358 -9.004 2.258  2.408  H9   P6S 42 
VR4 H32 H32 H 0 1 N N N N N N 19.482 28.011 -4.287 -8.877 -2.003 2.285  H10  P6S 43 
VR4 H29 H29 H 0 1 N N N N N N 21.955 24.561 -1.789 -7.307 2.360  0.627  H20  P6S 44 
VR4 H31 H31 H 0 1 N N N N N N 21.144 28.694 -2.606 -9.783 0.076  3.242  H21  P6S 45 
VR4 H33 H33 H 0 1 N N N N N N 19.049 25.639 -4.729 -7.183 -1.901 0.501  H22  P6S 46 
VR4 H34 H34 H 0 1 N N N N N N 21.571 21.435 -0.675 -2.321 0.455  0.562  H    LEU 47 
VR4 H1  H1  H 0 1 N N N N N N 21.329 18.923 -2.125 -1.596 -0.228 -2.194 HA   LEU 48 
VR4 H18 H18 H 0 1 N N N N N N 22.167 19.642 0.714  -1.823 2.277  -2.144 HB2  LEU 49 
VR4 H19 H19 H 0 1 N N N N N N 22.096 17.960 0.087  -0.588 2.326  -0.863 HB3  LEU 50 
VR4 H20 H20 H 0 1 N N N N N N 23.720 20.139 -1.230 0.977  1.103  -2.426 HG   LEU 51 
VR4 H21 H21 H 0 1 N N N N N N 24.457 19.870 1.138  0.395  0.989  -4.806 HD11 LEU 52 
VR4 H22 H22 H 0 1 N N N N N N 24.559 18.092 0.904  -0.837 0.125  -3.855 HD12 LEU 53 
VR4 H23 H23 H 0 1 N N N N N N 25.663 19.182 -0.001 -1.180 1.754  -4.484 HD13 LEU 54 
VR4 H24 H24 H 0 1 N N N N N N 24.907 18.186 -2.122 1.058  3.568  -2.166 HD21 LEU 55 
VR4 H25 H25 H 0 1 N N N N N N 23.802 17.097 -1.217 1.443  3.089  -3.836 HD22 LEU 56 
VR4 H26 H26 H 0 1 N N N N N N 23.160 18.130 -2.539 -0.165 3.743  -3.447 HD23 LEU 57 
VR4 H35 H35 H 0 1 N N N N N N 19.614 17.353 -1.830 0.950  -0.522 -2.290 H2   UZ4 58 
VR4 H2  H2  H 0 1 N N N N N N 17.643 17.968 0.264  2.097  -1.086 0.347  H4   UZ4 59 
VR4 H3  H3  H 0 1 N N N N N N 16.160 16.399 -1.085 0.715  -3.104 -0.243 H5   UZ4 60 
VR4 H4  H4  H 0 1 N N N N N N 17.398 16.459 -2.385 1.692  -3.295 -1.718 H6   UZ4 61 
VR4 H5  H5  H 0 1 N N N N N N 17.162 18.940 -2.452 3.758  -3.387 -0.223 H7   UZ4 62 
VR4 H8  H8  H 0 1 N N N N N N 15.263 18.489 -0.147 1.529  -5.446 -0.237 H8   UZ4 63 
VR4 H9  H9  H 0 1 N N N N N N 16.158 19.972 -0.622 3.237  -5.620 -0.764 H9   UZ4 64 
VR4 H6  H6  H 0 1 N N N N N N 14.422 20.713 -1.994 2.333  -6.531 1.697  H10  UZ4 65 
VR4 H7  H7  H 0 1 N N N N N N 13.406 19.544 -1.083 4.008  -5.964 1.432  H11  UZ4 66 
VR4 H36 H36 H 0 1 N N N N N N 13.408 18.792 -3.500 2.628  -4.603 3.254  H12  UZ4 67 
VR4 H10 H10 H 0 1 N N N N N N 18.678 15.144 -0.397 4.118  -1.712 -0.946 H13  UZ4 68 
VR4 H38 H38 H 0 1 N N N N N N 20.025 15.500 1.505  2.472  -1.187 -3.279 H14  UZ4 69 
VR4 H37 H37 H 0 1 N N N N N N 18.858 15.879 2.924  3.866  0.432  0.570  HN2  ABN 70 
VR4 H11 H11 H 0 1 N N N N N N 16.357 14.401 3.508  5.046  2.561  -0.863 H1   ABN 71 
VR4 H12 H12 H 0 1 N N N N N N 17.731 14.678 4.630  3.313  2.913  -0.661 H2A  ABN 72 
VR4 H13 H13 H 0 1 N N N N N N 15.432 15.225 6.079  6.522  2.442  1.060  H2   ABN 73 
VR4 H14 H14 H 0 1 N N N N N N 14.226 17.191 6.970  6.942  3.181  3.372  H3   ABN 74 
VR4 H15 H15 H 0 1 N N N N N N 14.477 19.417 5.906  5.075  3.972  4.769  H4   ABN 75 
VR4 H16 H16 H 0 1 N N N N N N 15.893 19.636 3.888  2.789  4.025  3.856  H5   ABN 76 
VR4 H17 H17 H 0 1 N N N N N N 17.101 17.672 3.014  2.371  3.292  1.543  H6   ABN 77 
# 
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 
VR4 O14 C10 DOUB N N 1  
VR4 C39 C38 DOUB Y N 2  
VR4 C39 C34 SING Y N 3  
VR4 C38 C37 SING Y N 4  
VR4 C33 C34 SING N N 5  
VR4 C33 O32 SING N N 6  
VR4 C34 C35 DOUB Y N 7  
VR4 O01 C02 DOUB N N 8  
VR4 C10 N11 SING N N 9  
VR4 C10 C09 SING N N 10 
VR4 N11 C12 SING N N 11 
VR4 C37 C36 DOUB Y N 12 
VR4 O32 C02 SING N N 13 
VR4 C02 N03 SING N N 14 
VR4 C35 C36 SING Y N 15 
VR4 C09 C08 SING N N 16 
VR4 C09 C13 SING N N 17 
VR4 C31 C29 SING N N 18 
VR4 C12 C13 SING N N 19 
VR4 C08 C07 SING N N 20 
VR4 N03 C04 SING N N 21 
VR4 C04 C05 SING N N 22 
VR4 C04 C28 SING N N 23 
VR4 N06 C05 SING N N 24 
VR4 N06 C07 SING N N 25 
VR4 C29 C28 SING N N 26 
VR4 C29 C30 SING N N 27 
VR4 C05 O27 DOUB N N 28 
VR4 C07 C15 SING N N 29 
VR4 C15 O26 SING N N 30 
VR4 C15 C16 SING N N 31 
VR4 O25 C16 DOUB N N 32 
VR4 C16 N17 SING N N 33 
VR4 N17 C18 SING N N 34 
VR4 C18 C19 SING N N 35 
VR4 C24 C23 DOUB Y N 36 
VR4 C24 C19 SING Y N 37 
VR4 C23 C22 SING Y N 38 
VR4 C19 C20 DOUB Y N 39 
VR4 C22 C21 DOUB Y N 40 
VR4 C20 C21 SING Y N 41 
VR4 C04 H1  SING N N 42 
VR4 C07 H2  SING N N 43 
VR4 C08 H3  SING N N 44 
VR4 C08 H4  SING N N 45 
VR4 C09 H5  SING N N 46 
VR4 C12 H6  SING N N 47 
VR4 C12 H7  SING N N 48 
VR4 C13 H8  SING N N 49 
VR4 C13 H9  SING N N 50 
VR4 C15 H10 SING N N 51 
VR4 C18 H11 SING N N 52 
VR4 C18 H12 SING N N 53 
VR4 C20 H13 SING N N 54 
VR4 C21 H14 SING N N 55 
VR4 C22 H15 SING N N 56 
VR4 C23 H16 SING N N 57 
VR4 C24 H17 SING N N 58 
VR4 C28 H18 SING N N 59 
VR4 C28 H19 SING N N 60 
VR4 C29 H20 SING N N 61 
VR4 C30 H21 SING N N 62 
VR4 C30 H22 SING N N 63 
VR4 C30 H23 SING N N 64 
VR4 C31 H24 SING N N 65 
VR4 C31 H25 SING N N 66 
VR4 C31 H26 SING N N 67 
VR4 C33 H27 SING N N 68 
VR4 C33 H28 SING N N 69 
VR4 C35 H29 SING N N 70 
VR4 C36 H30 SING N N 71 
VR4 C37 H31 SING N N 72 
VR4 C38 H32 SING N N 73 
VR4 C39 H33 SING N N 74 
VR4 N03 H34 SING N N 75 
VR4 N06 H35 SING N N 76 
VR4 N11 H36 SING N N 77 
VR4 N17 H37 SING N N 78 
VR4 O26 H38 SING N N 79 
# 
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 
VR4 SMILES           ACDLabs              12.01 "C(c1ccccc1)OC(NC(C(=O)NC(C(O)C(NCc2ccccc2)=O)CC3CCNC3=O)CC(C)C)=O"                                                                                                                                                                      
VR4 InChI            InChI                1.03  "InChI=1S/C29H38N4O6/c1-19(2)15-24(33-29(38)39-18-21-11-7-4-8-12-21)27(36)32-23(16-22-13-14-30-26(22)35)25(34)28(37)31-17-20-9-5-3-6-10-20/h3-12,19,22-25,34H,13-18H2,1-2H3,(H,30,35)(H,31,37)(H,32,36)(H,33,38)/t22-,23-,24-,25+/m0/s1" 
VR4 InChIKey         InChI                1.03  MPMTWRHFCLPCDF-OJJQZRKESA-N                                                                                                                                                                                                              
VR4 SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)C(=O)NCc3ccccc3"                                                                                                                                                     
VR4 SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)C(=O)NCc3ccccc3"                                                                                                                                                            
VR4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](C(=O)NCc2ccccc2)O)NC(=O)OCc3ccccc3"                                                                                                                                                     
VR4 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(C(=O)NCc2ccccc2)O)NC(=O)OCc3ccccc3"                                                                                                                                                                        
# 
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 
VR4 "SYSTEMATIC NAME" ACDLabs              12.01 "N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide"                                                                                
VR4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(phenylmethyl) ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]pentan-2-yl]carbamate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      VR4 
_pdbx_chem_comp_synonyms.name         "GC376 alpha-ketoamide analog (bound form)" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VR4 "Create component" 2020-09-09 RCSB 
VR4 "Initial release"  2021-01-13 RCSB 
VR4 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            VR4 
_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               C15 
_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      ? 
# 
