data_4WI
#
_chem_comp.id 4WI
_chem_comp.name "(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H34 F3 N5 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-07-15
_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 9I7
_chem_comp.formula_weight 501.542
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ?
_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 7RFS
_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
4WI C8 C1 C 0 1 N N N N N N 6.572 1.373 18.105 3.870 2.000 0.928 C8 4WI 1
4WI C3 C2 C 0 1 N N N N N N 7.852 -3.217 19.713 5.102 -1.303 -1.708 C3 4WI 2
4WI C1 C3 C 0 1 N N N N N N 9.193 -0.664 21.659 2.202 -0.741 -0.548 C1 4WI 3
4WI C13 C4 C 0 1 N N N N N N 10.255 2.169 22.026 -1.088 -0.017 0.086 C13 4WI 4
4WI C21 C5 C 0 1 N N N N N N 12.250 4.895 22.778 -4.722 0.366 -0.026 C21 4WI 5
4WI C6 C6 C 0 1 N N N N N N 5.620 0.469 20.076 5.910 3.171 0.385 C6 4WI 6
4WI C7 C7 C 0 1 N N N N N N 5.047 1.849 19.806 5.781 2.894 1.899 C7 4WI 7
4WI C10 C8 C 0 1 N N N N N N 11.164 0.893 24.031 -0.365 -2.281 -0.807 C10 4WI 8
4WI C5 C9 C 0 1 N N S N N N 6.931 0.492 19.282 4.853 2.207 -0.203 C5 4WI 9
4WI C9 C10 C 0 1 N N S N N N 10.609 -0.250 21.925 1.182 -1.094 0.504 C9 4WI 10
4WI C11 C11 C 0 1 N N S N N N 11.688 -0.488 24.080 0.315 -3.349 0.076 C11 4WI 11
4WI C12 C12 C 0 1 N N R N N N 11.354 -1.196 22.813 1.334 -2.569 0.933 C12 4WI 12
4WI C18 C13 C 0 1 N N N N N N 12.815 -1.019 23.214 0.096 -3.280 1.589 C18 4WI 13
4WI C19 C14 C 0 1 N N N N N N 13.636 -0.021 22.474 -1.037 -2.391 2.104 C19 4WI 14
4WI C20 C15 C 0 1 N N N N N N 13.552 -2.205 23.718 0.362 -4.547 2.405 C20 4WI 15
4WI C16 C16 C 0 1 N N N N N N 8.922 5.082 24.062 -1.750 1.983 -1.895 C16 4WI 16
4WI C17 C17 C 0 1 N N N N N N 7.919 2.927 23.533 -3.601 0.538 -2.748 C17 4WI 17
4WI C23 C18 C 0 1 N N N N N N 8.301 4.608 21.742 -1.239 -0.272 -2.843 C23 4WI 18
4WI C4 C19 C 0 1 N N N N N N 7.333 -0.901 18.827 5.501 0.879 -0.599 C4 4WI 19
4WI C2 C20 C 0 1 N N S N N N 7.746 -1.749 20.019 4.443 -0.044 -1.206 C2 4WI 20
4WI C14 C21 C 0 1 N N S N N N 10.252 3.427 22.860 -2.406 -0.077 -0.642 C14 4WI 21
4WI C22 C22 C 0 1 N N N N N N 13.138 5.636 21.809 -5.760 1.132 0.751 C22 4WI 22
4WI C15 C23 C 0 1 N N N N N N 8.851 3.997 23.015 -2.249 0.543 -2.032 C15 4WI 23
4WI N5 N1 N 0 1 N N N N N N 6.776 -3.940 19.630 4.757 -2.439 -1.231 N5 4WI 24
4WI N2 N2 N 0 1 N N N N N N 5.414 2.061 18.429 4.414 2.397 2.092 N2 4WI 25
4WI N3 N3 N 0 1 N N N N N N 10.544 1.003 22.693 -0.192 -1.013 -0.059 N3 4WI 26
4WI N1 N4 N 0 1 N N N N N N 9.055 -1.335 20.472 3.451 -0.387 -0.183 N1 4WI 27
4WI N4 N5 N 0 1 N N N N N N 11.163 4.306 22.150 -3.416 0.668 0.114 N4 4WI 28
4WI O1 O1 O 0 1 N N N N N N 7.211 1.469 17.073 2.753 1.546 0.803 O1 4WI 29
4WI O2 O2 O 0 1 N N N N N N 8.280 -0.420 22.434 1.900 -0.776 -1.722 O2 4WI 30
4WI O3 O3 O 0 1 N N N N N N 9.993 2.178 20.830 -0.834 0.928 0.803 O3 4WI 31
4WI O4 O4 O 0 1 N N N N N N 12.481 4.874 23.983 -5.061 -0.523 -0.779 O4 4WI 32
4WI F1 F1 F 0 1 N N N N N N 13.131 5.084 20.574 -5.689 2.488 0.414 F1 4WI 33
4WI F2 F2 F 0 1 N N N N N N 14.445 5.618 22.161 -7.033 0.641 0.440 F2 4WI 34
4WI F3 F3 F 0 1 N N N N N N 12.800 6.947 21.669 -5.524 0.980 2.122 F3 4WI 35
4WI H33 H1 H 0 1 N N N N N N 8.821 -3.670 19.562 5.865 -1.246 -2.470 H33 4WI 36
4WI H5 H3 H 0 1 N N N N N N 4.947 -0.320 19.709 5.663 4.207 0.156 H5 4WI 37
4WI H6 H4 H 0 1 N N N N N N 5.808 0.320 21.149 6.909 2.922 0.026 H6 4WI 38
4WI H7 H5 H 0 1 N N N N N N 5.502 2.606 20.462 6.504 2.138 2.207 H7 4WI 39
4WI H8 H6 H 0 1 N N N N N N 3.955 1.861 19.935 5.934 3.813 2.465 H8 4WI 40
4WI H11 H7 H 0 1 N N N N N N 11.979 1.623 24.144 0.128 -2.220 -1.777 H11 4WI 41
4WI H12 H8 H 0 1 N N N N N N 10.416 1.054 24.821 -1.423 -2.509 -0.932 H12 4WI 42
4WI H4 H9 H 0 1 N N N N N N 7.733 0.950 19.879 4.358 2.662 -1.061 H4 4WI 43
4WI H10 H10 H 0 1 N N N N N N 11.151 -0.102 20.979 1.280 -0.431 1.364 H10 4WI 44
4WI H13 H11 H 0 1 N N N N N N 11.501 -1.047 25.009 0.565 -4.303 -0.387 H13 4WI 45
4WI H14 H12 H 0 1 N N N N N N 10.946 -2.213 22.905 2.339 -2.933 1.145 H14 4WI 46
4WI H23 H13 H 0 1 N N N N N N 14.658 -0.013 22.880 -1.444 -1.807 1.278 H23 4WI 47
4WI H24 H14 H 0 1 N N N N N N 13.667 -0.290 21.408 -1.823 -3.014 2.530 H24 4WI 48
4WI H25 H15 H 0 1 N N N N N N 13.189 0.978 22.588 -0.652 -1.718 2.869 H25 4WI 49
4WI H26 H16 H 0 1 N N N N N N 12.856 -2.873 24.246 1.032 -4.313 3.232 H26 4WI 50
4WI H27 H17 H 0 1 N N N N N N 14.005 -2.742 22.872 -0.580 -4.931 2.798 H27 4WI 51
4WI H28 H18 H 0 1 N N N N N N 14.342 -1.879 24.410 0.823 -5.301 1.766 H28 4WI 52
4WI H17 H19 H 0 1 N N N N N N 9.319 4.663 24.998 -1.639 2.425 -2.885 H17 4WI 53
4WI H19 H20 H 0 1 N N N N N N 9.584 5.887 23.711 -2.470 2.563 -1.317 H19 4WI 54
4WI H18 H21 H 0 1 N N N N N N 7.915 5.486 24.240 -0.787 1.987 -1.385 H18 4WI 55
4WI H20 H22 H 0 1 N N N N N N 8.333 2.495 24.456 -3.957 -0.488 -2.846 H20 4WI 56
4WI H21 H23 H 0 1 N N N N N N 6.935 3.370 23.745 -4.321 1.118 -2.171 H21 4WI 57
4WI H22 H24 H 0 1 N N N N N N 7.810 2.137 22.775 -3.490 0.979 -3.739 H22 4WI 58
4WI H29 H25 H 0 1 N N N N N N 7.289 4.998 21.929 -1.563 -1.311 -2.887 H29 4WI 59
4WI H30 H26 H 0 1 N N N N N N 8.956 5.430 21.417 -1.175 0.132 -3.853 H30 4WI 60
4WI H31 H27 H 0 1 N N N N N N 8.258 3.840 20.956 -0.261 -0.216 -2.366 H31 4WI 61
4WI H2 H28 H 0 1 N N N N N N 6.480 -1.377 18.321 6.286 1.063 -1.333 H2 4WI 62
4WI H3 H29 H 0 1 N N N N N N 8.178 -0.824 18.127 5.932 0.407 0.284 H3 4WI 63
4WI H32 H30 H 0 1 N N N N N N 7.012 -1.605 20.825 3.950 0.463 -2.034 H32 4WI 64
4WI H15 H31 H 0 1 N N N N N N 10.656 3.198 23.857 -2.720 -1.116 -0.741 H15 4WI 65
4WI H36 H32 H 0 1 N Y N N N N 6.982 -4.896 19.422 5.182 -3.249 -1.555 H36 4WI 66
4WI H9 H35 H 0 1 N N N N N N 4.899 2.632 17.789 3.960 2.361 2.948 H9 4WI 67
4WI H1 H36 H 0 1 N N N N N N 9.862 -1.539 19.918 3.692 -0.359 0.756 H1 4WI 68
4WI H16 H37 H 0 1 N N N N N N 11.002 4.492 21.181 -3.145 1.379 0.715 H16 4WI 69
#
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
4WI O1 C8 DOUB N N 1
4WI C8 N2 SING N N 2
4WI C8 C5 SING N N 3
4WI N2 C7 SING N N 4
4WI C4 C5 SING N N 5
4WI C4 C2 SING N N 6
4WI C5 C6 SING N N 7
4WI N5 C3 DOUB N N 8
4WI C3 C2 SING N N 9
4WI C7 C6 SING N N 10
4WI C2 N1 SING N N 11
4WI N1 C1 SING N N 12
4WI F1 C22 SING N N 13
4WI O3 C13 DOUB N N 14
4WI C1 C9 SING N N 15
4WI C1 O2 DOUB N N 16
4WI F3 C22 SING N N 17
4WI C23 C15 SING N N 18
4WI C22 F2 SING N N 19
4WI C22 C21 SING N N 20
4WI C9 N3 SING N N 21
4WI C9 C12 SING N N 22
4WI C13 N3 SING N N 23
4WI C13 C14 SING N N 24
4WI N4 C21 SING N N 25
4WI N4 C14 SING N N 26
4WI C19 C18 SING N N 27
4WI N3 C10 SING N N 28
4WI C21 O4 DOUB N N 29
4WI C12 C18 SING N N 30
4WI C12 C11 SING N N 31
4WI C14 C15 SING N N 32
4WI C15 C17 SING N N 33
4WI C15 C16 SING N N 34
4WI C18 C20 SING N N 35
4WI C18 C11 SING N N 36
4WI C10 C11 SING N N 37
4WI C3 H33 SING N N 38
4WI C6 H5 SING N N 39
4WI C6 H6 SING N N 40
4WI C7 H7 SING N N 41
4WI C7 H8 SING N N 42
4WI C10 H11 SING N N 43
4WI C10 H12 SING N N 44
4WI C5 H4 SING N N 45
4WI C9 H10 SING N N 46
4WI C11 H13 SING N N 47
4WI C12 H14 SING N N 48
4WI C19 H23 SING N N 49
4WI C19 H24 SING N N 50
4WI C19 H25 SING N N 51
4WI C20 H26 SING N N 52
4WI C20 H27 SING N N 53
4WI C20 H28 SING N N 54
4WI C16 H17 SING N N 55
4WI C16 H19 SING N N 56
4WI C16 H18 SING N N 57
4WI C17 H20 SING N N 58
4WI C17 H21 SING N N 59
4WI C17 H22 SING N N 60
4WI C23 H29 SING N N 61
4WI C23 H30 SING N N 62
4WI C23 H31 SING N N 63
4WI C4 H2 SING N N 64
4WI C4 H3 SING N N 65
4WI C2 H32 SING N N 66
4WI C14 H15 SING N N 67
4WI N5 H36 SING N N 68
4WI N2 H9 SING N N 69
4WI N1 H1 SING N N 70
4WI N4 H16 SING N N 71
#
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
4WI SMILES ACDLabs 12.01 "CC1(C)C2C(C(=O)NC(C=N)CC3CCNC3=O)N(CC21)C(=O)C(NC(=O)C(F)(F)F)C(C)(C)C"
4WI InChI InChI 1.03 "InChI=1S/C23H34F3N5O4/c1-21(2,3)16(30-20(35)23(24,25)26)19(34)31-10-13-14(22(13,4)5)15(31)18(33)29-12(9-27)8-11-6-7-28-17(11)32/h9,11-16,27H,6-8,10H2,1-5H3,(H,28,32)(H,29,33)(H,30,35)/b27-9+/t11-,12-,13-,14-,15-,16+/m0/s1"
4WI InChIKey InChI 1.03 WDVIRQQKRMIXGS-XIFHJVQQSA-N
4WI SMILES_CANONICAL CACTVS 3.385 "CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C=N)C2(C)C"
4WI SMILES CACTVS 3.385 "CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCNC3=O)C=N)C2(C)C"
4WI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F"
4WI SMILES "OpenEye OEToolkits" 2.0.7 "CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C=N)C"
#
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
4WI "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide"
4WI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},2~{S},5~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
4WI "Create component" 2021-07-15 RCSB
4WI "Initial release" 2021-11-10 RCSB
4WI "Other modification" 2021-12-14 RCSB
4WI "Modify PCM" 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 4WI "PF-07321332, bound form" PDB ?
2 4WI "nirmatrelvir, bound form" PDB "drug name"
3 4WI "Paxlovid, bound form" PDB "drug brand name"
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 4WI CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C3 SG ? ?
2 4WI SER None "Covalent chemical modification" "Amino-acid side chain" "Any position" C3 OG ? ?
#