data_Y4V
# 
_chem_comp.id                                    Y4V 
_chem_comp.name                                  "(1R,2S)-2-((S)-2-(((adamantan-1-ylmethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H41 N3 O8 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-02-03 
_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                        543.673 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y4V 
_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        7LKT 
_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 
Y4V C02 C1  C 0 1 N N N N N N -21.469 -3.730 1.855  2.235  0.692  -0.733 C02 Y4V 1  
Y4V C04 C2  C 0 1 N N S N N N -21.271 -5.533 3.561  -0.179 0.599  -1.050 C04 Y4V 2  
Y4V C05 C3  C 0 1 N N N N N N -21.916 -6.946 3.857  -0.340 0.756  -2.563 C05 Y4V 3  
Y4V C06 C4  C 0 1 N N N N N N -23.477 -6.874 3.950  -1.639 1.506  -2.863 C06 Y4V 4  
Y4V C07 C5  C 0 1 N N N N N N -23.936 -5.953 5.102  -1.544 2.930  -2.313 C07 Y4V 5  
Y4V C08 C6  C 0 1 N N N N N N -24.104 -8.282 4.108  -1.861 1.557  -4.376 C08 Y4V 6  
Y4V C09 C7  C 0 1 N N N N N N -19.732 -5.646 3.593  -1.299 -0.252 -0.511 C09 Y4V 7  
Y4V C11 C8  C 0 1 N N S N N N -17.569 -5.421 4.882  -3.565 -0.505 0.350  C11 Y4V 8  
Y4V C12 C9  C 0 1 N N N N N N -17.012 -3.946 5.022  -4.567 0.425  1.037  C12 Y4V 9  
Y4V C13 C10 C 0 1 N N S N N N -17.107 -3.219 3.680  -3.894 1.109  2.229  C13 Y4V 10 
Y4V C14 C11 C 0 1 N N N N N N -16.631 -1.781 3.800  -2.804 2.045  1.757  C14 Y4V 11 
Y4V C16 C12 C 0 1 N N N N N N -15.528 -2.672 1.977  -4.619 3.394  2.287  C16 Y4V 12 
Y4V C17 C13 C 0 1 N N N N N N -16.120 -3.837 2.662  -4.897 2.032  2.960  C17 Y4V 13 
Y4V C19 C14 C 0 1 N N R N N N -17.276 -6.262 6.190  -4.284 -1.330 -0.719 C19 Y4V 14 
Y4V C23 C15 C 0 1 N N N N N N -21.125 -2.242 -0.032 4.575  0.976  -0.357 C23 Y4V 15 
Y4V C24 C16 C 0 1 N N N N N N -21.823 -2.013 -1.439 5.792  0.163  0.088  C24 Y4V 16 
Y4V C25 C17 C 0 1 N N N N N N -21.302 -3.044 -2.431 6.009  -1.001 -0.881 C25 Y4V 17 
Y4V C26 C18 C 0 1 N N N N N N -21.937 -2.855 -3.821 7.225  -1.815 -0.436 C26 Y4V 18 
Y4V C27 C19 C 0 1 N N N N N N -21.743 -1.418 -4.303 6.986  -2.362 0.973  C27 Y4V 19 
Y4V C28 C20 C 0 1 N N N N N N -22.311 -0.390 -3.301 6.769  -1.198 1.942  C28 Y4V 20 
Y4V C29 C21 C 0 1 N N N N N N -21.675 -0.566 -1.916 5.552  -0.384 1.497  C29 Y4V 21 
Y4V C30 C22 C 0 1 N N N N N N -23.829 -0.646 -3.115 8.008  -0.301 1.947  C30 Y4V 22 
Y4V C31 C23 C 0 1 N N N N N N -24.097 -2.116 -2.668 8.248  0.246  0.539  C31 Y4V 23 
Y4V C32 C24 C 0 1 N N N N N N -23.370 -2.312 -1.302 7.031  1.060  0.094  C32 Y4V 24 
Y4V C33 C25 C 0 1 N N N N N N -23.463 -3.097 -3.694 8.465  -0.918 -0.430 C33 Y4V 25 
Y4V N03 N1  N 0 1 N N N N N N -21.760 -5.036 2.264  1.106  -0.042 -0.759 N03 Y4V 26 
Y4V N10 N2  N 0 1 N N N N N N -19.026 -5.321 4.739  -2.509 0.294  -0.278 N10 Y4V 27 
Y4V N15 N3  N 0 1 N N N N N N -15.703 -1.438 2.806  -3.235 3.317  1.804  N15 Y4V 28 
Y4V O01 O1  O 0 1 N N N N N N -20.776 -2.973 2.563  2.203  1.868  -1.038 O01 Y4V 29 
Y4V O18 O2  O 0 1 N N N N N N -16.992 -0.924 4.643  -1.702 1.698  1.389  O18 Y4V 30 
Y4V O20 O3  O 0 1 N N N N N N -15.846 -6.446 6.301  -4.984 -0.454 -1.606 O20 Y4V 31 
Y4V O21 O4  O 0 1 N N N N N N -19.105 -6.047 2.566  -1.112 -1.430 -0.287 O21 Y4V 32 
Y4V O22 O5  O 0 1 N N N N N N -21.934 -3.233 0.649  3.399  0.125  -0.362 O22 Y4V 33 
Y4V H1  H1  H 0 1 N N N N N N -21.586 -4.843 4.358  -0.210 1.581  -0.577 H1  Y4V 34 
Y4V H2  H2  H 0 1 N N N N N N -21.641 -7.638 3.047  0.505  1.318  -2.962 H2  Y4V 35 
Y4V H3  H3  H 0 1 N N N N N N -21.521 -7.323 4.812  -0.373 -0.229 -3.029 H3  Y4V 36 
Y4V H4  H4  H 0 1 N N N N N N -23.847 -6.445 3.007  -2.474 0.989  -2.391 H4  Y4V 37 
Y4V H5  H5  H 0 1 N N N N N N -25.035 -5.927 5.136  -2.496 3.441  -2.461 H5  Y4V 38 
Y4V H6  H6  H 0 1 N N N N N N -23.549 -6.339 6.056  -1.314 2.894  -1.248 H6  Y4V 39 
Y4V H7  H7  H 0 1 N N N N N N -23.551 -4.936 4.934  -0.756 3.471  -2.837 H7  Y4V 40 
Y4V H8  H8  H 0 1 N N N N N N -25.199 -8.192 4.170  -1.928 0.543  -4.768 H8  Y4V 41 
Y4V H9  H9  H 0 1 N N N N N N -23.836 -8.902 3.240  -2.787 2.092  -4.590 H9  Y4V 42 
Y4V H10 H10 H 0 1 N N N N N N -23.723 -8.752 5.026  -1.026 2.074  -4.848 H10 Y4V 43 
Y4V H11 H11 H 0 1 N N N N N N -17.111 -5.912 4.011  -3.124 -1.173 1.089  H11 Y4V 44 
Y4V H12 H12 H 0 1 N N N N N N -15.960 -3.983 5.342  -4.906 1.181  0.329  H12 Y4V 45 
Y4V H13 H13 H 0 1 N N N N N N -17.605 -3.403 5.773  -5.421 -0.155 1.385  H13 Y4V 46 
Y4V H14 H14 H 0 1 N N N N N N -18.135 -3.258 3.290  -3.488 0.365  2.915  H14 Y4V 47 
Y4V H15 H15 H 0 1 N N N N N N -14.455 -2.852 1.816  -5.302 3.548  1.451  H15 Y4V 48 
Y4V H16 H16 H 0 1 N N N N N N -16.025 -2.531 1.006  -4.721 4.201  3.012  H16 Y4V 49 
Y4V H17 H17 H 0 1 N N N N N N -16.651 -4.482 1.946  -5.923 1.711  2.783  H17 Y4V 50 
Y4V H18 H18 H 0 1 N N N N N N -15.344 -4.422 3.177  -4.682 2.073  4.028  H18 Y4V 51 
Y4V H19 H19 H 0 1 N N N N N N -17.609 -5.646 7.039  -3.554 -1.910 -1.282 H19 Y4V 52 
Y4V S1  S1  S 0 1 N Y N N N N -17.773 -7.241 6.122  -5.465 -2.453 0.078  S1  Y4V 53 
Y4V H21 H21 H 0 1 N N N N N N -20.098 -2.613 -0.169 4.420  1.806  0.334  H21 Y4V 54 
Y4V H22 H22 H 0 1 N N N N N N -21.103 -1.304 0.542  4.746  1.366  -1.360 H22 Y4V 55 
Y4V H23 H23 H 0 1 N N N N N N -21.544 -4.051 -2.061 5.126  -1.640 -0.885 H23 Y4V 56 
Y4V H24 H24 H 0 1 N N N N N N -20.211 -2.937 -2.518 6.180  -0.612 -1.884 H24 Y4V 57 
Y4V H25 H25 H 0 1 N N N N N N -21.500 -3.564 -4.540 7.380  -2.645 -1.126 H25 Y4V 58 
Y4V H26 H26 H 0 1 N N N N N N -20.667 -1.229 -4.434 6.103  -3.001 0.969  H26 Y4V 59 
Y4V H27 H27 H 0 1 N N N N N N -22.257 -1.295 -5.268 7.852  -2.942 1.290  H27 Y4V 60 
Y4V H28 H28 H 0 1 N N N N N N -22.143 0.632  -3.671 6.598  -1.588 2.945  H28 Y4V 61 
Y4V H29 H29 H 0 1 N N N N N N -20.606 -0.311 -1.973 5.397  0.445  2.187  H29 Y4V 62 
Y4V H30 H30 H 0 1 N N N N N N -22.174 0.104  -1.201 4.669  -1.023 1.493  H30 Y4V 63 
Y4V H31 H31 H 0 1 N N N N N N -24.218 0.040  -2.348 7.853  0.528  2.638  H31 Y4V 64 
Y4V H32 H32 H 0 1 N N N N N N -24.345 -0.460 -4.069 8.875  -0.881 2.264  H32 Y4V 65 
Y4V H33 H33 H 0 1 N N N N N N -25.176 -2.301 -2.565 9.131  0.885  0.543  H33 Y4V 66 
Y4V H34 H34 H 0 1 N N N N N N -23.805 -1.626 -0.560 7.202  1.449  -0.910 H34 Y4V 67 
Y4V H35 H35 H 0 1 N N N N N N -23.508 -3.350 -0.966 6.876  1.889  0.784  H35 Y4V 68 
Y4V H36 H36 H 0 1 N N N N N N -23.935 -2.945 -4.676 9.332  -1.498 -0.113 H36 Y4V 69 
Y4V H37 H37 H 0 1 N N N N N N -23.637 -4.130 -3.359 8.636  -0.529 -1.434 H37 Y4V 70 
Y4V H38 H38 H 0 1 N N N N N N -22.302 -5.634 1.673  1.143  -0.996 -0.585 H38 Y4V 71 
Y4V H39 H39 H 0 1 N N N N N N -19.547 -4.994 5.527  -2.681 1.216  -0.526 H39 Y4V 72 
Y4V H40 H40 H 0 1 N N N N N N -15.253 -0.554 2.678  -2.700 4.086  1.553  H40 Y4V 73 
Y4V H41 H41 H 0 1 N N N N N N -15.651 -6.950 7.082  -4.413 0.176  -2.068 H41 Y4V 74 
Y4V O2  O6  O 0 1 N Y N N N N ?       ?      ?      -5.904 -3.446 -0.839 O2  Y4V 75 
Y4V O3  O7  O 0 1 N Y N N N N ?       ?      ?      -4.632 -3.221 1.094  O3  Y4V 76 
Y4V O1  O8  O 0 1 N Y N N N N ?       ?      ?      -6.394 -1.722 0.867  O1  Y4V 77 
Y4V H20 H20 H 0 1 N Y N N N N ?       ?      ?      -5.136 -3.870 1.605  H20 Y4V 78 
# 
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 
Y4V C27 C26 SING N N 1  
Y4V C27 C28 SING N N 2  
Y4V C26 C33 SING N N 3  
Y4V C26 C25 SING N N 4  
Y4V C33 C31 SING N N 5  
Y4V C28 C30 SING N N 6  
Y4V C28 C29 SING N N 7  
Y4V C30 C31 SING N N 8  
Y4V C31 C32 SING N N 9  
Y4V C25 C24 SING N N 10 
Y4V C29 C24 SING N N 11 
Y4V C24 C32 SING N N 12 
Y4V C24 C23 SING N N 13 
Y4V C23 O22 SING N N 14 
Y4V O22 C02 SING N N 15 
Y4V C02 N03 SING N N 16 
Y4V C02 O01 DOUB N N 17 
Y4V C16 C17 SING N N 18 
Y4V C16 N15 SING N N 19 
Y4V N03 C04 SING N N 20 
Y4V O21 C09 DOUB N N 21 
Y4V C17 C13 SING N N 22 
Y4V N15 C14 SING N N 23 
Y4V C04 C09 SING N N 24 
Y4V C04 C05 SING N N 25 
Y4V C09 N10 SING N N 26 
Y4V C13 C14 SING N N 27 
Y4V C13 C12 SING N N 28 
Y4V C14 O18 DOUB N N 29 
Y4V C05 C06 SING N N 30 
Y4V C06 C08 SING N N 31 
Y4V C06 C07 SING N N 32 
Y4V N10 C11 SING N N 33 
Y4V C11 C12 SING N N 34 
Y4V C11 C19 SING N N 35 
Y4V C19 O20 SING N N 36 
Y4V C04 H1  SING N N 37 
Y4V C05 H2  SING N N 38 
Y4V C05 H3  SING N N 39 
Y4V C06 H4  SING N N 40 
Y4V C07 H5  SING N N 41 
Y4V C07 H6  SING N N 42 
Y4V C07 H7  SING N N 43 
Y4V C08 H8  SING N N 44 
Y4V C08 H9  SING N N 45 
Y4V C08 H10 SING N N 46 
Y4V C11 H11 SING N N 47 
Y4V C12 H12 SING N N 48 
Y4V C12 H13 SING N N 49 
Y4V C13 H14 SING N N 50 
Y4V C16 H15 SING N N 51 
Y4V C16 H16 SING N N 52 
Y4V C17 H17 SING N N 53 
Y4V C17 H18 SING N N 54 
Y4V C19 H19 SING N N 55 
Y4V C19 S1  SING N N 56 
Y4V C23 H21 SING N N 57 
Y4V C23 H22 SING N N 58 
Y4V C25 H23 SING N N 59 
Y4V C25 H24 SING N N 60 
Y4V C26 H25 SING N N 61 
Y4V C27 H26 SING N N 62 
Y4V C27 H27 SING N N 63 
Y4V C28 H28 SING N N 64 
Y4V C29 H29 SING N N 65 
Y4V C29 H30 SING N N 66 
Y4V C30 H31 SING N N 67 
Y4V C30 H32 SING N N 68 
Y4V C31 H33 SING N N 69 
Y4V C32 H34 SING N N 70 
Y4V C32 H35 SING N N 71 
Y4V C33 H36 SING N N 72 
Y4V C33 H37 SING N N 73 
Y4V N03 H38 SING N N 74 
Y4V N10 H39 SING N N 75 
Y4V N15 H40 SING N N 76 
Y4V O20 H41 SING N N 77 
Y4V S1  O2  DOUB N N 78 
Y4V S1  O3  SING N N 79 
Y4V S1  O1  DOUB N N 80 
Y4V O3  H20 SING N N 81 
# 
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 
Y4V SMILES           ACDLabs              12.01 "C(NC(C(NC(CC1C(=O)NCC1)CO)=O)CC(C)C)(=O)OCC24CC3CC(CC(C2)C3)C4"                                                                                                                                                                                    
Y4V InChI            InChI                1.03  "InChI=1S/C25H41N3O8S/c1-14(2)5-19(22(30)27-20(23(31)37(33,34)35)9-18-3-4-26-21(18)29)28-24(32)36-13-25-10-15-6-16(11-25)8-17(7-15)12-25/h14-20,23,31H,3-13H2,1-2H3,(H,26,29)(H,27,30)(H,28,32)(H,33,34,35)/t15-,16+,17-,18-,19-,20-,23+,25-/m0/s1" 
Y4V InChIKey         InChI                1.03  AFONNBAHWVWJGI-CLEZYGTASA-N                                                                                                                                                                                                                         
Y4V SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OCC12CC3CC(CC(C3)C1)C2)C(=O)N[C@@H](C[C@@H]4CCNC4=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                                        
Y4V SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OCC12CC3CC(CC(C3)C1)C2)C(=O)N[CH](C[CH]4CCNC4=O)[CH](O)[S](O)(=O)=O"                                                                                                                                                              
Y4V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCC23CC4CC(C2)CC(C4)C3"                                                                                                                                                         
Y4V SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC23CC4CC(C2)CC(C4)C3"                                                                                                                                                                            
# 
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 
Y4V "SYSTEMATIC NAME" ACDLabs              12.01 "N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]methoxy}carbonyl)-L-leucinamide"                      
Y4V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},2~{S})-2-[[(2~{S})-2-(1-adamantylmethoxycarbonylamino)-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y4V "Create component"   2021-02-03 RCSB 
Y4V "Other modification" 2021-02-09 RCSB 
Y4V "Modify name"        2021-02-09 RCSB 
Y4V "Initial release"    2021-02-17 RCSB 
Y4V "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y4V 
_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               C19 
_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      ? 
# 
