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 ? #