data_V3D
# 
_chem_comp.id                                    V3D 
_chem_comp.name                                  "(3S)-3-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-2-oxo-4-[(3S)-2-oxopyrrolidin-3-yl]butyl 2-cyanobenzoate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C32 H35 N5 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-06-19 
_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                        601.650 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     V3D 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        6XHN 
_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 
V3D C1  C1  C 0 1 N N N N N N 13.209 21.513 27.692 11.271  0.590  0.132  C1  V3D 1  
V3D O2  O1  O 0 1 N N N N N N 12.955 20.131 27.395 9.853   0.698  0.277  O2  V3D 2  
V3D C3  C2  C 0 1 Y N N N N N 12.065 19.959 26.335 9.089   -0.061 -0.549 C3  V3D 3  
V3D C4  C3  C 0 1 Y N N N N N 11.553 20.998 25.527 9.684   -0.891 -1.478 C4  V3D 4  
V3D C5  C4  C 0 1 Y N N N N N 10.674 20.728 24.469 8.908   -1.670 -2.324 C5  V3D 5  
V3D C6  C5  C 0 1 Y N N N N N 10.259 19.418 24.196 7.533   -1.628 -2.254 C6  V3D 6  
V3D C7  C6  C 0 1 Y N N N N N 10.760 18.410 25.021 6.906   -0.800 -1.327 C7  V3D 7  
V3D N8  N1  N 0 1 Y N N N N N 10.535 17.051 24.974 5.586   -0.553 -1.030 N8  V3D 8  
V3D C9  C7  C 0 1 Y N N N N N 11.233 16.412 25.964 5.527   0.373  -0.005 C9  V3D 9  
V3D C10 C8  C 0 1 Y N N N N N 11.951 17.364 26.665 6.791   0.719  0.355  C10 V3D 10 
V3D C11 C9  C 0 1 Y N N N N N 11.667 18.635 26.069 7.687   -0.012 -0.460 C11 V3D 11 
V3D C12 C10 C 0 1 N N N N N N 11.120 14.991 26.141 4.295   0.899  0.599  C12 V3D 12 
V3D O13 O2  O 0 1 N N N N N N 10.421 14.319 25.394 4.359   1.714  1.499  O13 V3D 13 
V3D N14 N2  N 0 1 N N N N N N 11.790 14.476 27.213 3.094   0.477  0.155  N14 V3D 14 
V3D C15 C11 C 0 1 N N S N N N 11.693 13.051 27.508 1.866   1.002  0.757  C15 V3D 15 
V3D C17 C12 C 0 1 N N N N N N 12.720 12.624 28.543 1.489   2.321  0.080  C17 V3D 16 
V3D C18 C13 C 0 1 N N N N N N 14.144 12.687 28.021 2.563   3.370  0.374  C18 V3D 17 
V3D C19 C14 C 0 1 N N N N N N 14.463 11.539 27.089 2.252   4.651  -0.404 C19 V3D 18 
V3D C20 C15 C 0 1 N N N N N N 15.096 12.644 29.192 2.582   3.675  1.873  C20 V3D 19 
V3D C21 C16 C 0 1 N N N N N N 10.312 12.806 28.077 0.750   0.006  0.571  C21 V3D 20 
V3D O22 O3  O 0 1 N N N N N N 9.763  13.561 28.873 0.961   -1.039 -0.007 O22 V3D 21 
V3D N23 N3  N 0 1 N N N N N N 9.743  11.630 27.616 -0.481  0.276  1.047  N23 V3D 22 
V3D C24 C17 C 0 1 N N S N N N 8.437  11.204 28.110 -1.592  -0.638 0.768  C24 V3D 23 
V3D C26 C18 C 0 1 N N N N N N 7.447  10.942 26.983 -1.649  -1.717 1.851  C26 V3D 24 
V3D C27 C19 C 0 1 N N S N N N 7.041  12.265 26.354 -2.676  -2.781 1.457  C27 V3D 25 
V3D C29 C20 C 0 1 N N N N N N 6.159  13.125 27.307 -2.815  -3.839 2.576  C29 V3D 26 
V3D C30 C21 C 0 1 N N N N N N 4.979  13.641 26.486 -3.020  -5.134 1.761  C30 V3D 27 
V3D N31 N4  N 0 1 N N N N N N 4.995  12.813 25.294 -2.390  -4.882 0.460  N31 V3D 28 
V3D C32 C22 C 0 1 N N N N N N 6.107  11.997 25.190 -2.190  -3.568 0.261  C32 V3D 29 
V3D O33 O4  O 0 1 N N N N N N 6.346  11.230 24.276 -1.692  -3.084 -0.734 O33 V3D 30 
V3D C34 C23 C 0 1 N N N N N N 8.541  9.974  28.973 -2.886  0.133  0.758  C34 V3D 31 
V3D O35 O5  O 0 1 N N N N N N 7.557  9.299  29.256 -3.026  1.088  1.484  O35 V3D 32 
V3D C36 C24 C 0 1 N N N N N N 9.851  9.598  29.551 -4.006  -0.287 -0.159 C36 V3D 33 
V3D H1  H1  H 0 1 N N N N N N 13.915 21.584 28.533 11.577  -0.440 0.315  H1  V3D 34 
V3D H2  H2  H 0 1 N N N N N N 13.641 22.004 26.808 11.556  0.880  -0.879 H2  V3D 35 
V3D H3  H3  H 0 1 N N N N N N 12.265 22.009 27.963 11.760  1.247  0.851  H3  V3D 36 
V3D H4  H4  H 0 1 N N N N N N 11.844 22.019 25.728 10.761  -0.935 -1.546 H4  V3D 37 
V3D H5  H5  H 0 1 N N N N N N 10.312 21.540 23.856 9.386   -2.315 -3.046 H5  V3D 38 
V3D H6  H6  H 0 1 N N N N N N 9.582  19.198 23.384 6.940   -2.239 -2.919 H6  V3D 39 
V3D H7  H7  H 0 1 N N N N N N 9.944  16.595 24.309 4.823   -0.961 -1.468 H7  V3D 40 
V3D H8  H8  H 0 1 N N N N N N 12.604 17.183 27.506 7.063   1.422  1.128  H8  V3D 41 
V3D H9  H9  H 0 1 N N N N N N 12.344 15.073 27.793 3.043   -0.173 -0.563 H9  V3D 42 
V3D H10 H10 H 0 1 N N N N N N 11.826 12.459 26.591 2.027   1.173  1.821  H10 V3D 43 
V3D H11 H11 H 0 1 N N N N N N 12.636 13.288 29.416 1.415   2.169  -0.997 H11 V3D 44 
V3D H12 H12 H 0 1 N N N N N N 12.503 11.589 28.847 0.530   2.666  0.465  H12 V3D 45 
V3D H13 H13 H 0 1 N N N N N N 14.284 13.635 27.481 3.538   2.988  0.069  H13 V3D 46 
V3D H14 H14 H 0 1 N N N N N N 15.502 11.628 26.739 1.278   5.033  -0.099 H14 V3D 47 
V3D H15 H15 H 0 1 N N N N N N 14.337 10.586 27.624 3.018   5.398  -0.194 H15 V3D 48 
V3D H16 H16 H 0 1 N N N N N N 13.781 11.567 26.226 2.239   4.433  -1.472 H16 V3D 49 
V3D H17 H17 H 0 1 N N N N N N 14.873 13.475 29.877 2.804   2.763  2.427  H17 V3D 50 
V3D H18 H18 H 0 1 N N N N N N 14.979 11.689 29.725 3.347   4.422  2.082  H18 V3D 51 
V3D H19 H19 H 0 1 N N N N N N 16.130 12.737 28.828 1.608   4.058  2.178  H19 V3D 52 
V3D H20 H20 H 0 1 N N N N N N 10.228 11.072 26.943 -0.632  1.076  1.575  H20 V3D 53 
V3D H21 H21 H 0 1 N N N N N N 8.024  12.013 28.731 -1.440  -1.107 -0.204 H21 V3D 54 
V3D H22 H22 H 0 1 N N N N N N 6.556  10.438 27.386 -0.668  -2.180 1.955  H22 V3D 55 
V3D H23 H23 H 0 1 N N N N N N 7.917  10.302 26.222 -1.940  -1.265 2.799  H23 V3D 56 
V3D H24 H24 H 0 1 N N N N N N 7.924  12.834 26.029 -3.640  -2.319 1.247  H24 V3D 57 
V3D H25 H25 H 0 1 N N N N N N 5.796  12.509 28.143 -1.906  -3.895 3.176  H25 V3D 58 
V3D H26 H26 H 0 1 N N N N N N 6.743  13.970 27.701 -3.681  -3.631 3.204  H26 V3D 59 
V3D H27 H27 H 0 1 N N N N N N 5.116  14.701 26.228 -2.536  -5.974 2.259  H27 V3D 60 
V3D H28 H28 H 0 1 N N N N N N 4.035  13.516 27.037 -4.084  -5.335 1.633  H28 V3D 61 
V3D H29 H29 H 0 1 N N N N N N 4.267  12.831 24.609 -2.149  -5.575 -0.175 H29 V3D 62 
V3D H30 H30 H 0 1 N N N N N N 10.650 10.347 29.658 -3.680  -0.199 -1.195 H30 V3D 63 
V3D H31 H31 H 0 1 N N N N N N 9.909  8.879  30.381 -4.279  -1.321 0.050  H31 V3D 64 
V3D O1  O6  O 0 1 N N N N N N ?      ?      ?      -5.158  0.571  0.059  O1  V3D 65 
V3D C8  C25 C 0 1 N N N N N N ?      ?      ?      -6.252  0.326  -0.687 C8  V3D 66 
V3D C13 C26 C 0 1 Y N N N N N ?      ?      ?      -7.461  1.158  -0.519 C13 V3D 67 
V3D C14 C27 C 0 1 Y N N N N N ?      ?      ?      -7.474  2.197  0.410  C14 V3D 68 
V3D C16 C28 C 0 1 Y N N N N N ?      ?      ?      -8.607  2.972  0.563  C16 V3D 69 
V3D C22 C29 C 0 1 Y N N N N N ?      ?      ?      -9.734  2.725  -0.202 C22 V3D 70 
V3D C23 C30 C 0 1 Y N N N N N ?      ?      ?      -9.741  1.700  -1.128 C23 V3D 71 
V3D C25 C31 C 0 1 Y N N N N N ?      ?      ?      -8.606  0.911  -1.301 C25 V3D 72 
V3D O3  O7  O 0 1 N N N N N N ?      ?      ?      -6.245  -0.578 -1.498 O3  V3D 73 
V3D C2  C32 C 0 1 N N N N N N ?      ?      ?      -8.608  -0.153 -2.260 C2  V3D 74 
V3D N1  N5  N 0 1 N N N N N N ?      ?      ?      -8.609  -0.997 -3.021 N1  V3D 75 
V3D H32 H32 H 0 1 N N N N N N ?      ?      ?      -6.599  2.395  1.011  H32 V3D 76 
V3D H33 H33 H 0 1 N N N N N N ?      ?      ?      -8.614  3.776  1.284  H33 V3D 77 
V3D H34 H34 H 0 1 N N N N N N ?      ?      ?      -10.615 3.337  -0.073 H34 V3D 78 
V3D H35 H35 H 0 1 N N N N N N ?      ?      ?      -10.624 1.514  -1.721 H35 V3D 79 
# 
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 
V3D C6  C5  DOUB Y N 1  
V3D C6  C7  SING Y N 2  
V3D O33 C32 DOUB N N 3  
V3D C5  C4  SING Y N 4  
V3D N8  C7  SING Y N 5  
V3D N8  C9  SING Y N 6  
V3D C7  C11 DOUB Y N 7  
V3D C32 N31 SING N N 8  
V3D C32 C27 SING N N 9  
V3D N31 C30 SING N N 10 
V3D O13 C12 DOUB N N 11 
V3D C4  C3  DOUB Y N 12 
V3D C9  C12 SING N N 13 
V3D C9  C10 DOUB Y N 14 
V3D C11 C3  SING Y N 15 
V3D C11 C10 SING Y N 16 
V3D C12 N14 SING N N 17 
V3D C3  O2  SING N N 18 
V3D C27 C26 SING N N 19 
V3D C27 C29 SING N N 20 
V3D C30 C29 SING N N 21 
V3D C26 C24 SING N N 22 
V3D C19 C18 SING N N 23 
V3D N14 C15 SING N N 24 
V3D O2  C1  SING N N 25 
V3D C15 C21 SING N N 26 
V3D C15 C17 SING N N 27 
V3D N23 C21 SING N N 28 
V3D N23 C24 SING N N 29 
V3D C18 C17 SING N N 30 
V3D C18 C20 SING N N 31 
V3D C21 O22 DOUB N N 32 
V3D C24 C34 SING N N 33 
V3D C34 O35 DOUB N N 34 
V3D C34 C36 SING N N 35 
V3D C1  H1  SING N N 36 
V3D C1  H2  SING N N 37 
V3D C1  H3  SING N N 38 
V3D C4  H4  SING N N 39 
V3D C5  H5  SING N N 40 
V3D C6  H6  SING N N 41 
V3D N8  H7  SING N N 42 
V3D C10 H8  SING N N 43 
V3D N14 H9  SING N N 44 
V3D C15 H10 SING N N 45 
V3D C17 H11 SING N N 46 
V3D C17 H12 SING N N 47 
V3D C18 H13 SING N N 48 
V3D C19 H14 SING N N 49 
V3D C19 H15 SING N N 50 
V3D C19 H16 SING N N 51 
V3D C20 H17 SING N N 52 
V3D C20 H18 SING N N 53 
V3D C20 H19 SING N N 54 
V3D N23 H20 SING N N 55 
V3D C24 H21 SING N N 56 
V3D C26 H22 SING N N 57 
V3D C26 H23 SING N N 58 
V3D C27 H24 SING N N 59 
V3D C29 H25 SING N N 60 
V3D C29 H26 SING N N 61 
V3D C30 H27 SING N N 62 
V3D C30 H28 SING N N 63 
V3D N31 H29 SING N N 64 
V3D C36 H30 SING N N 65 
V3D C36 H31 SING N N 66 
V3D C36 O1  SING N N 67 
V3D O1  C8  SING N N 68 
V3D C8  C13 SING N N 69 
V3D C13 C14 SING Y N 70 
V3D C14 C16 DOUB Y N 71 
V3D C16 C22 SING Y N 72 
V3D C22 C23 DOUB Y N 73 
V3D C23 C25 SING Y N 74 
V3D C25 C13 DOUB Y N 75 
V3D C8  O3  DOUB N N 76 
V3D C25 C2  SING N N 77 
V3D C2  N1  TRIP N N 78 
V3D C14 H32 SING N N 79 
V3D C16 H33 SING N N 80 
V3D C22 H34 SING N N 81 
V3D C23 H35 SING N N 82 
# 
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 
V3D SMILES           ACDLabs              12.01 "COc1cccc2c1cc(n2)C(NC(C(=O)NC(C(=O)COC(c3ccccc3C#N)=O)CC4CCNC4=O)CC(C)C)=O"                                                                                                                                                                           
V3D InChI            InChI                1.03  "InChI=1S/C32H35N5O7/c1-18(2)13-25(37-31(41)26-15-22-23(35-26)9-6-10-28(22)43-3)30(40)36-24(14-19-11-12-34-29(19)39)27(38)17-44-32(42)21-8-5-4-7-20(21)16-33/h4-10,15,18-19,24-25,35H,11-14,17H2,1-3H3,(H,34,39)(H,36,40)(H,37,41)/t19-,24-,25-/m0/s1" 
V3D InChIKey         InChI                1.03  QDDDUZBEUKGROG-LQGLAIQGSA-N                                                                                                                                                                                                                            
V3D SMILES_CANONICAL CACTVS               3.385 "COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C(=O)COC(=O)c4ccccc4C#N"                                                                                                                                                         
V3D SMILES           CACTVS               3.385 "COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCNC3=O)C(=O)COC(=O)c4ccccc4C#N"                                                                                                                                                               
V3D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(=O)COC(=O)c2ccccc2C#N)NC(=O)c3cc4c([nH]3)cccc4OC"                                                                                                                                                         
V3D SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(=O)COC(=O)c2ccccc2C#N)NC(=O)c3cc4c([nH]3)cccc4OC"                                                                                                                                                                        
# 
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 
V3D "SYSTEMATIC NAME" ACDLabs              12.01 "(3S)-3-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-2-oxo-4-[(3S)-2-oxopyrrolidin-3-yl]butyl 2-cyanobenzoate"                                                          
V3D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butyl] 2-cyanobenzoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
V3D "Create component" 2020-06-19 RCSB 
V3D "Initial release"  2020-07-08 RCSB 
V3D "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            V3D 
_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               C36 
_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      ? 
# 
