data_R8H
#
_chem_comp.id R8H
_chem_comp.name "(2~{R})-5-oxidanylidene-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino)butan-2-yl]-1-(phenylmethyl)pyrrolidine-2-carboxamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C28 H30 N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-18
_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 486.562
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code R8H
_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 7AEH
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_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
R8H N1 N1 N 0 1 N N N N N N 5.203 -1.189 25.196 1.952 -1.646 0.361 N1 R8H 1
R8H N3 N2 N 0 1 Y N N N N N 6.401 0.622 17.460 -6.315 -0.670 -0.679 N3 R8H 2
R8H C4 C1 C 0 1 Y N N N N N 5.539 -6.793 23.733 0.736 2.905 -2.284 C4 R8H 3
R8H C5 C2 C 0 1 Y N N N N N 4.775 -7.207 24.812 1.757 2.487 -3.116 C5 R8H 4
R8H C6 C3 C 0 1 Y N N N N N 5.160 -6.890 26.092 2.941 2.021 -2.576 C6 R8H 5
R8H C7 C4 C 0 1 Y N N N N N 6.309 -6.159 26.299 3.105 1.974 -1.204 C7 R8H 6
R8H C8 C5 C 0 1 Y N N N N N 7.082 -5.752 25.221 2.083 2.392 -0.372 C8 R8H 7
R8H C10 C6 C 0 1 N N R N N N 6.162 -1.442 24.119 1.146 -0.807 1.256 C10 R8H 8
R8H C13 C7 C 0 1 N N N N N N 4.869 0.112 25.337 1.866 -2.944 0.700 C13 R8H 9
R8H C15 C8 C 0 1 Y N N N N N 3.366 -2.754 25.810 4.180 -0.983 -0.335 C15 R8H 10
R8H C17 C9 C 0 1 Y N N N N N 0.969 -2.564 25.967 6.447 -1.752 -0.374 C17 R8H 11
R8H C20 C10 C 0 1 Y N N N N N 3.197 -3.909 25.059 4.550 0.065 0.487 C20 R8H 12
R8H C21 C11 C 0 1 N N N N N N 7.194 -3.103 19.865 -3.157 1.432 1.561 C21 R8H 13
R8H C22 C12 C 0 1 N N N N N N 7.626 -1.278 18.298 -4.596 -0.466 1.045 C22 R8H 14
R8H C24 C13 C 0 1 Y N N N N N 6.031 0.065 19.753 -4.539 -2.204 -0.747 C24 R8H 15
R8H C26 C14 C 0 1 Y N N N N N 4.810 1.851 18.762 -6.279 -2.298 -2.372 C26 R8H 16
R8H O3 O1 O 0 1 N N N N N N 6.037 -3.238 19.503 -3.260 1.153 2.737 O3 R8H 17
R8H N2 N3 N 0 1 N N N N N N 7.945 -2.063 19.483 -3.786 0.684 0.633 N2 R8H 18
R8H C23 C15 C 0 1 Y N N N N N 6.657 -0.141 18.533 -5.186 -1.127 -0.173 C23 R8H 19
R8H C27 C16 C 0 1 Y N N N N N 5.482 1.593 17.592 -6.869 -1.217 -1.744 C27 R8H 20
R8H C25 C17 C 0 1 Y N N N N N 5.091 1.075 19.851 -5.091 -2.806 -1.868 C25 R8H 21
R8H C C18 C 0 1 N N S N N N 7.862 -4.180 20.715 -2.325 2.614 1.137 C R8H 22
R8H O O2 O 0 1 N N N N N N 9.157 -3.737 21.065 -1.860 3.309 2.296 O R8H 23
R8H C1 C19 C 0 1 N N R N N N 7.023 -4.472 21.982 -1.126 2.128 0.320 C1 R8H 24
R8H C2 C20 C 0 1 N N N N N N 7.573 -5.681 22.750 -0.215 3.313 -0.004 C2 R8H 25
R8H C3 C21 C 0 1 Y N N N N N 6.710 -6.072 23.925 0.899 2.858 -0.912 C3 R8H 26
R8H N N4 N 0 1 N N N N N N 7.001 -3.318 22.874 -0.378 1.134 1.094 N R8H 27
R8H C9 C22 C 0 1 N N N N N N 5.910 -2.604 23.148 0.376 0.215 0.460 C9 R8H 28
R8H O1 O3 O 0 1 N N N N N N 4.830 -2.809 22.609 0.436 0.210 -0.752 O1 R8H 29
R8H O2 O4 O 0 1 N N N N N N 4.045 0.540 26.128 2.435 -3.850 0.128 O2 R8H 30
R8H C12 C23 C 0 1 N N N N N N 5.703 0.918 24.386 0.958 -3.110 1.898 C12 R8H 31
R8H C11 C24 C 0 1 N N N N N N 6.225 -0.098 23.380 0.175 -1.776 1.966 C11 R8H 32
R8H C14 C25 C 0 1 N N N N N N 4.748 -2.231 26.118 2.743 -1.136 -0.762 C14 R8H 33
R8H C19 C26 C 0 1 Y N N N N N 1.928 -4.385 24.765 5.868 0.205 0.878 C19 R8H 34
R8H C18 C27 C 0 1 Y N N N N N 0.815 -3.712 25.218 6.817 -0.703 0.447 C18 R8H 35
R8H C16 C28 C 0 1 Y N N N N N 2.236 -2.089 26.264 5.130 -1.888 -0.770 C16 R8H 36
R8H H1 H1 H 0 1 N N N N N N 5.220 -7.034 22.730 -0.188 3.273 -2.705 H1 R8H 37
R8H H2 H2 H 0 1 N N N N N N 3.875 -7.780 24.646 1.630 2.523 -4.188 H2 R8H 38
R8H H3 H3 H 0 1 N N N N N N 4.564 -7.213 26.933 3.739 1.693 -3.226 H3 R8H 39
R8H H4 H4 H 0 1 N N N N N N 6.609 -5.902 27.304 4.030 1.609 -0.783 H4 R8H 40
R8H H5 H5 H 0 1 N N N N N N 7.982 -5.180 25.394 2.210 2.355 0.700 H5 R8H 41
R8H H6 H6 H 0 1 N N N N N N 7.149 -1.608 24.575 1.786 -0.312 1.986 H6 R8H 42
R8H H7 H7 H 0 1 N N N N N N 0.098 -2.033 26.323 7.189 -2.460 -0.714 H7 R8H 43
R8H H8 H8 H 0 1 N N N N N N 4.064 -4.443 24.699 3.808 0.775 0.823 H8 R8H 44
R8H H9 H9 H 0 1 N N N N N N 7.187 -1.953 17.548 -3.967 -1.180 1.578 H9 R8H 45
R8H H10 H10 H 0 1 N N N N N N 8.562 -0.854 17.906 -5.398 -0.129 1.701 H10 R8H 46
R8H H11 H11 H 0 1 N N N N N N 6.272 -0.550 20.608 -3.615 -2.573 -0.328 H11 R8H 47
R8H H12 H12 H 0 1 N N N N N N 4.080 2.645 18.819 -6.737 -2.741 -3.243 H12 R8H 48
R8H H13 H13 H 0 1 N N N N N N 8.748 -1.818 20.026 -3.704 0.907 -0.307 H13 R8H 49
R8H H14 H14 H 0 1 N N N N N N 5.259 2.205 16.730 -7.795 -0.816 -2.130 H14 R8H 50
R8H H15 H15 H 0 1 N N N N N N 4.580 1.250 20.786 -4.608 -3.649 -2.338 H15 R8H 51
R8H H16 H16 H 0 1 N N N N N N 7.926 -5.104 20.122 -2.931 3.286 0.530 H16 R8H 52
R8H H17 H17 H 0 1 N N N N N N 9.586 -4.398 21.595 -1.312 2.772 2.885 H17 R8H 53
R8H H18 H18 H 0 1 N N N N N N 5.996 -4.704 21.665 -1.478 1.676 -0.608 H18 R8H 54
R8H H19 H19 H 0 1 N N N N N N 7.636 -6.536 22.061 -0.794 4.091 -0.502 H19 R8H 55
R8H H20 H20 H 0 1 N N N N N N 8.579 -5.434 23.120 0.208 3.710 0.919 H20 R8H 56
R8H H21 H21 H 0 1 N N N N N N 7.860 -3.045 23.308 -0.426 1.138 2.063 H21 R8H 57
R8H H22 H22 H 0 1 N N N N N N 6.536 1.404 24.915 0.271 -3.942 1.744 H22 R8H 58
R8H H23 H23 H 0 1 N N N N N N 5.091 1.682 23.885 1.545 -3.264 2.803 H23 R8H 59
R8H H24 H24 H 0 1 N N N N N N 7.260 0.138 23.091 0.011 -1.475 3.001 H24 R8H 60
R8H H25 H25 H 0 1 N N N N N N 5.589 -0.118 22.483 -0.770 -1.846 1.427 H25 R8H 61
R8H H26 H26 H 0 1 N N N N N N 5.456 -3.071 26.069 2.684 -1.835 -1.596 H26 R8H 62
R8H H27 H27 H 0 1 N N N N N N 4.743 -1.815 27.136 2.351 -0.167 -1.071 H27 R8H 63
R8H H28 H28 H 0 1 N N N N N N 1.812 -5.285 24.180 6.157 1.025 1.519 H28 R8H 64
R8H H29 H29 H 0 1 N N N N N N -0.173 -4.081 24.988 7.847 -0.594 0.753 H29 R8H 65
R8H H30 H30 H 0 1 N N N N N N 2.345 -1.192 26.855 4.842 -2.705 -1.416 H30 R8H 66
#
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
R8H N3 C27 DOUB Y N 1
R8H N3 C23 SING Y N 2
R8H C27 C26 SING Y N 3
R8H C22 C23 SING N N 4
R8H C22 N2 SING N N 5
R8H C23 C24 DOUB Y N 6
R8H C26 C25 DOUB Y N 7
R8H N2 C21 SING N N 8
R8H O3 C21 DOUB N N 9
R8H C24 C25 SING Y N 10
R8H C21 C SING N N 11
R8H C O SING N N 12
R8H C C1 SING N N 13
R8H C1 C2 SING N N 14
R8H C1 N SING N N 15
R8H O1 C9 DOUB N N 16
R8H C2 C3 SING N N 17
R8H N C9 SING N N 18
R8H C9 C10 SING N N 19
R8H C11 C10 SING N N 20
R8H C11 C12 SING N N 21
R8H C4 C3 DOUB Y N 22
R8H C4 C5 SING Y N 23
R8H C3 C8 SING Y N 24
R8H C10 N1 SING N N 25
R8H C12 C13 SING N N 26
R8H C19 C20 DOUB Y N 27
R8H C19 C18 SING Y N 28
R8H C5 C6 DOUB Y N 29
R8H C20 C15 SING Y N 30
R8H N1 C13 SING N N 31
R8H N1 C14 SING N N 32
R8H C18 C17 DOUB Y N 33
R8H C8 C7 DOUB Y N 34
R8H C13 O2 DOUB N N 35
R8H C15 C14 SING N N 36
R8H C15 C16 DOUB Y N 37
R8H C17 C16 SING Y N 38
R8H C6 C7 SING Y N 39
R8H C4 H1 SING N N 40
R8H C5 H2 SING N N 41
R8H C6 H3 SING N N 42
R8H C7 H4 SING N N 43
R8H C8 H5 SING N N 44
R8H C10 H6 SING N N 45
R8H C17 H7 SING N N 46
R8H C20 H8 SING N N 47
R8H C22 H9 SING N N 48
R8H C22 H10 SING N N 49
R8H C24 H11 SING N N 50
R8H C26 H12 SING N N 51
R8H N2 H13 SING N N 52
R8H C27 H14 SING N N 53
R8H C25 H15 SING N N 54
R8H C H16 SING N N 55
R8H O H17 SING N N 56
R8H C1 H18 SING N N 57
R8H C2 H19 SING N N 58
R8H C2 H20 SING N N 59
R8H N H21 SING N N 60
R8H C12 H22 SING N N 61
R8H C12 H23 SING N N 62
R8H C11 H24 SING N N 63
R8H C11 H25 SING N N 64
R8H C14 H26 SING N N 65
R8H C14 H27 SING N N 66
R8H C19 H28 SING N N 67
R8H C18 H29 SING N N 68
R8H C16 H30 SING N N 69
#
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
R8H InChI InChI 1.03 "InChI=1S/C28H30N4O4/c33-25-15-14-24(32(25)19-21-11-5-2-6-12-21)27(35)31-23(17-20-9-3-1-4-10-20)26(34)28(36)30-18-22-13-7-8-16-29-22/h1-13,16,23-24,26,34H,14-15,17-19H2,(H,30,36)(H,31,35)/t23-,24-,26+/m1/s1"
R8H InChIKey InChI 1.03 LGWQYJCCERJRJX-MZKUHISZSA-N
R8H SMILES_CANONICAL CACTVS 3.385 "O[C@@H]([C@@H](Cc1ccccc1)NC(=O)[C@H]2CCC(=O)N2Cc3ccccc3)C(=O)NCc4ccccn4"
R8H SMILES CACTVS 3.385 "O[CH]([CH](Cc1ccccc1)NC(=O)[CH]2CCC(=O)N2Cc3ccccc3)C(=O)NCc4ccccn4"
R8H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C[C@H]([C@@H](C(=O)NCc2ccccn2)O)NC(=O)[C@H]3CCC(=O)N3Cc4ccccc4"
R8H SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CC(C(C(=O)NCc2ccccn2)O)NC(=O)C3CCC(=O)N3Cc4ccccc4"
#
_pdbx_chem_comp_identifier.comp_id R8H
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "(2~{R})-5-oxidanylidene-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino)butan-2-yl]-1-(phenylmethyl)pyrrolidine-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
R8H "Create component" 2020-09-18 PDBE
R8H "Initial release" 2021-07-07 RCSB
R8H "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id R8H
_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 C
_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 ?
#