data_YVK # _chem_comp.id YVK _chem_comp.name "(6S)-6-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}-1-phenylpiperidin-2-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C30 H34 N4 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-23 _chem_comp.pdbx_modified_date 2024-02-23 _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 498.616 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YVK _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 8GA2 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 YVK C10 C1 C 0 1 N N N N N N -4.116 -9.766 -11.641 -0.770 3.135 -1.069 C10 YVK 1 YVK C15 C2 C 0 1 N N N N N N -3.191 -8.408 -14.166 1.058 3.354 1.210 C15 YVK 2 YVK C17 C3 C 0 1 Y N N N N N -7.286 -8.492 -11.538 -1.628 0.206 0.743 C17 YVK 3 YVK C20 C4 C 0 1 N N N N N N -10.070 -9.540 -13.788 -4.983 0.117 2.559 C20 YVK 4 YVK C21 C5 C 0 1 N N N N N N -10.789 -10.385 -12.876 -5.437 -1.224 1.978 C21 YVK 5 YVK C22 C6 C 0 1 N N N N N N -9.816 -11.276 -12.042 -4.833 -1.422 0.618 C22 YVK 6 YVK C24 C7 C 0 1 Y N N N N N -7.537 -11.641 -11.119 -3.285 -1.045 -1.099 C24 YVK 7 YVK C26 C8 C 0 1 Y N N N N N -5.611 -13.426 -10.938 -2.199 -2.583 -2.584 C26 YVK 8 YVK C28 C9 C 0 1 Y N N N N N -6.908 -12.666 -8.774 -2.909 -0.440 -3.389 C28 YVK 9 YVK C01 C10 C 0 1 N N N N N N -7.522 -3.037 -7.552 4.642 -1.482 -2.147 C01 YVK 10 YVK C02 C11 C 0 1 Y N N N N N -6.474 -3.649 -6.625 4.779 -2.010 -0.743 C02 YVK 11 YVK C03 C12 C 0 1 Y N N N N N -5.677 -4.739 -6.858 3.956 -1.748 0.316 C03 YVK 12 YVK C04 C13 C 0 1 Y N N N N N -5.650 -5.627 -8.097 2.743 -0.893 0.344 C04 YVK 13 YVK C05 C14 C 0 1 Y N N N N N -6.924 -6.238 -8.596 1.501 -1.462 0.587 C05 YVK 14 YVK C06 C15 C 0 1 Y N N N N N -6.883 -7.159 -9.860 0.364 -0.654 0.613 C06 YVK 15 YVK C07 C16 C 0 1 Y N N N N N -5.686 -7.427 -10.496 0.489 0.729 0.395 C07 YVK 16 YVK C09 C17 C 0 1 N N N N N N -4.978 -8.799 -12.475 -1.171 2.651 0.326 C09 YVK 17 YVK C11 C18 C 0 1 N N N N N N -2.772 -10.132 -12.273 0.743 2.994 -1.243 C11 YVK 18 YVK C12 C19 C 0 1 N N N N N N -2.588 -9.766 -13.749 1.458 3.838 -0.185 C12 YVK 19 YVK C14 C20 C 0 1 N N N N N N -0.690 -11.087 -14.055 3.448 4.674 -1.228 C14 YVK 20 YVK C16 C21 C 0 1 N N N N N N -4.096 -7.746 -13.129 -0.456 3.494 1.383 C16 YVK 21 YVK C18 C22 C 0 1 N N S N N N -8.012 -9.405 -12.561 -3.120 0.326 0.923 C18 YVK 22 YVK C19 C23 C 0 1 N N N N N N -9.150 -8.657 -13.077 -3.460 0.220 2.410 C19 YVK 23 YVK C25 C24 C 0 1 Y N N N N N -6.477 -12.498 -11.794 -2.684 -2.276 -1.328 C25 YVK 24 YVK C27 C25 C 0 1 Y N N N N N -5.823 -13.506 -9.429 -2.312 -1.667 -3.613 C27 YVK 25 YVK C29 C26 C 0 1 Y N N N N N -7.773 -11.736 -9.618 -3.395 -0.126 -2.135 C29 YVK 26 YVK C32 C27 C 0 1 Y N N N N N -4.337 -6.796 -9.978 1.738 1.286 0.153 C32 YVK 27 YVK C33 C28 C 0 1 Y N N N N N -4.366 -5.907 -8.783 2.856 0.484 0.128 C33 YVK 28 YVK C34 C29 C 0 1 Y N N N N N -4.874 -4.935 -5.759 4.535 -2.489 1.384 C34 YVK 29 YVK C35 C30 C 0 1 N N N N N N -3.829 -6.054 -5.547 4.036 -2.568 2.804 C35 YVK 30 YVK N08 N1 N 0 1 Y N N N N N -5.951 -8.225 -11.532 -0.789 1.245 0.483 N08 YVK 31 YVK N23 N2 N 0 1 N N N N N N -8.393 -10.773 -11.898 -3.782 -0.733 0.171 N23 YVK 32 YVK N31 N3 N 0 1 Y N N N N N -7.854 -7.803 -10.509 -0.956 -0.904 0.819 N31 YVK 33 YVK N36 N4 N 0 1 Y N N N N N -5.173 -3.989 -4.861 5.581 -3.083 0.891 N36 YVK 34 YVK O13 O1 O 0 1 N N N N N N -1.218 -9.792 -14.104 2.872 3.707 -0.347 O13 YVK 35 YVK O30 O2 O 0 1 N N N N N N -10.141 -12.281 -11.523 -5.327 -2.254 -0.114 O30 YVK 36 YVK O37 O3 O 0 1 Y N N N N N -6.164 -3.181 -5.415 5.729 -2.836 -0.283 O37 YVK 37 YVK H1 H1 H 0 1 N N N N N N -3.919 -9.296 -10.666 -1.280 2.534 -1.822 H1 YVK 38 YVK H2 H2 H 0 1 N N N N N N -4.688 -10.693 -11.492 -1.054 4.181 -1.186 H2 YVK 39 YVK H3 H3 H 0 1 N N N N N N -2.360 -7.719 -14.380 1.342 2.308 1.327 H3 YVK 40 YVK H4 H4 H 0 1 N N N N N N -3.782 -8.566 -15.080 1.567 3.955 1.963 H4 YVK 41 YVK H5 H5 H 0 1 N N N N N N -10.789 -8.929 -14.353 -5.460 0.933 2.016 H5 YVK 42 YVK H6 H6 H 0 1 N N N N N N -9.497 -10.170 -14.484 -5.252 0.171 3.614 H6 YVK 43 YVK H7 H7 H 0 1 N N N N N N -11.375 -9.755 -12.190 -5.117 -2.031 2.637 H7 YVK 44 YVK H8 H8 H 0 1 N N N N N N -11.468 -11.034 -13.448 -6.524 -1.234 1.897 H8 YVK 45 YVK H9 H9 H 0 1 N N N N N N -4.845 -14.028 -11.405 -1.732 -3.541 -2.762 H9 YVK 46 YVK H10 H10 H 0 1 N N N N N N -7.067 -12.728 -7.708 -2.995 0.274 -4.195 H10 YVK 47 YVK H11 H11 H 0 1 N N N N N N -7.974 -2.159 -7.067 5.450 -1.876 -2.764 H11 YVK 48 YVK H12 H12 H 0 1 N N N N N N -7.044 -2.729 -8.494 3.683 -1.795 -2.561 H12 YVK 49 YVK H13 H13 H 0 1 N N N N N N -8.304 -3.782 -7.764 4.693 -0.393 -2.132 H13 YVK 50 YVK H14 H14 H 0 1 N N N N N N -7.858 -6.045 -8.090 1.416 -2.526 0.754 H14 YVK 51 YVK H15 H15 H 0 1 N N N N N N -5.503 -9.369 -13.256 -2.249 2.751 0.450 H15 YVK 52 YVK H16 H16 H 0 1 N N N N N N -2.645 -11.221 -12.180 1.027 1.949 -1.126 H16 YVK 53 YVK H17 H17 H 0 1 N N N N N N -1.984 -9.621 -11.701 1.029 3.339 -2.237 H17 YVK 54 YVK H18 H18 H 0 1 N N N N N N -3.110 -10.537 -14.335 1.174 4.884 -0.302 H18 YVK 55 YVK H19 H19 H 0 1 N N N N N N 0.373 -11.061 -14.337 3.000 4.577 -2.217 H19 YVK 56 YVK H20 H20 H 0 1 N N N N N N -0.789 -11.485 -13.034 3.260 5.675 -0.841 H20 YVK 57 YVK H21 H21 H 0 1 N N N N N N -1.239 -11.734 -14.755 4.523 4.507 -1.298 H21 YVK 58 YVK H22 H22 H 0 1 N N N N N N -3.477 -7.258 -12.361 -0.741 3.150 2.377 H22 YVK 59 YVK H23 H23 H 0 1 N N N N N N -4.729 -6.994 -13.622 -0.740 4.540 1.266 H23 YVK 60 YVK H24 H24 H 0 1 N N N N N N -7.313 -9.614 -13.385 -3.451 1.295 0.549 H24 YVK 61 YVK H25 H25 H 0 1 N N N N N N -8.788 -7.881 -13.768 -3.100 1.107 2.932 H25 YVK 62 YVK H26 H26 H 0 1 N N N N N N -9.681 -8.183 -12.238 -2.991 -0.670 2.830 H26 YVK 63 YVK H27 H27 H 0 1 N N N N N N -6.337 -12.452 -12.864 -2.596 -2.992 -0.524 H27 YVK 64 YVK H28 H28 H 0 1 N N N N N N -5.205 -14.157 -8.829 -1.932 -1.910 -4.595 H28 YVK 65 YVK H29 H29 H 0 1 N N N N N N -8.550 -11.147 -9.153 -3.862 0.832 -1.960 H29 YVK 66 YVK H30 H30 H 0 1 N N N N N N -3.405 -7.005 -10.482 1.832 2.349 -0.015 H30 YVK 67 YVK H31 H31 H 0 1 N N N N N N -3.451 -5.466 -8.416 3.826 0.920 -0.060 H31 YVK 68 YVK H32 H32 H 0 1 N N N N N N -3.376 -5.949 -4.550 3.336 -3.399 2.897 H32 YVK 69 YVK H33 H33 H 0 1 N N N N N N -4.321 -7.035 -5.624 4.878 -2.725 3.477 H33 YVK 70 YVK H34 H34 H 0 1 N N N N N N -3.046 -5.975 -6.316 3.531 -1.637 3.064 H34 YVK 71 # 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 YVK C15 C12 SING N N 1 YVK C15 C16 SING N N 2 YVK O13 C14 SING N N 3 YVK O13 C12 SING N N 4 YVK C20 C19 SING N N 5 YVK C20 C21 SING N N 6 YVK C12 C11 SING N N 7 YVK C16 C09 SING N N 8 YVK C19 C18 SING N N 9 YVK C21 C22 SING N N 10 YVK C18 N23 SING N N 11 YVK C18 C17 SING N N 12 YVK C09 C10 SING N N 13 YVK C09 N08 SING N N 14 YVK C11 C10 SING N N 15 YVK C22 N23 SING N N 16 YVK C22 O30 DOUB N N 17 YVK N23 C24 SING N N 18 YVK C25 C24 DOUB Y N 19 YVK C25 C26 SING Y N 20 YVK C17 N08 SING Y N 21 YVK C17 N31 DOUB Y N 22 YVK N08 C07 SING Y N 23 YVK C24 C29 SING Y N 24 YVK C26 C27 DOUB Y N 25 YVK N31 C06 SING Y N 26 YVK C07 C32 DOUB Y N 27 YVK C07 C06 SING Y N 28 YVK C32 C33 SING Y N 29 YVK C06 C05 DOUB Y N 30 YVK C29 C28 DOUB Y N 31 YVK C27 C28 SING Y N 32 YVK C33 C04 DOUB Y N 33 YVK C05 C04 SING Y N 34 YVK C04 C03 SING N N 35 YVK C01 C02 SING N N 36 YVK C03 C02 DOUB Y N 37 YVK C03 C34 SING Y N 38 YVK C02 O37 SING Y N 39 YVK C34 C35 SING N N 40 YVK C34 N36 DOUB Y N 41 YVK O37 N36 SING Y N 42 YVK C10 H1 SING N N 43 YVK C10 H2 SING N N 44 YVK C15 H3 SING N N 45 YVK C15 H4 SING N N 46 YVK C20 H5 SING N N 47 YVK C20 H6 SING N N 48 YVK C21 H7 SING N N 49 YVK C21 H8 SING N N 50 YVK C26 H9 SING N N 51 YVK C28 H10 SING N N 52 YVK C01 H11 SING N N 53 YVK C01 H12 SING N N 54 YVK C01 H13 SING N N 55 YVK C05 H14 SING N N 56 YVK C09 H15 SING N N 57 YVK C11 H16 SING N N 58 YVK C11 H17 SING N N 59 YVK C12 H18 SING N N 60 YVK C14 H19 SING N N 61 YVK C14 H20 SING N N 62 YVK C14 H21 SING N N 63 YVK C16 H22 SING N N 64 YVK C16 H23 SING N N 65 YVK C18 H24 SING N N 66 YVK C19 H25 SING N N 67 YVK C19 H26 SING N N 68 YVK C25 H27 SING N N 69 YVK C27 H28 SING N N 70 YVK C29 H29 SING N N 71 YVK C32 H30 SING N N 72 YVK C33 H31 SING N N 73 YVK C35 H32 SING N N 74 YVK C35 H33 SING N N 75 YVK C35 H34 SING N N 76 # 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 YVK SMILES ACDLabs 12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3c3ccccc3)n(C3CCC(OC)CC3)c2cc1" YVK InChI InChI 1.06 "InChI=1S/C30H34N4O3/c1-19-29(20(2)37-32-19)21-12-17-26-25(18-21)31-30(34(26)23-13-15-24(36-3)16-14-23)27-10-7-11-28(35)33(27)22-8-5-4-6-9-22/h4-6,8-9,12,17-18,23-24,27H,7,10-11,13-16H2,1-3H3/t23-,24+,27-/m0/s1" YVK InChIKey InChI 1.06 YQBUUWAEHZBNID-XFAFFCHDSA-N YVK SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1CC[C@@H](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[C@@H]5CCCC(=O)N5c6ccccc6" YVK SMILES CACTVS 3.385 "CO[CH]1CC[CH](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[CH]5CCCC(=O)N5c6ccccc6" YVK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)[C@@H]5CCCC(=O)N5c6ccccc6" YVK SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6ccccc6" # 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 YVK "SYSTEMATIC NAME" ACDLabs 12.01 "(6S)-6-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}-1-phenylpiperidin-2-one" YVK "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(6~{S})-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(4-methoxycyclohexyl)benzimidazol-2-yl]-1-phenyl-piperidin-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YVK "Create component" 2023-02-23 RCSB YVK "Initial release" 2024-02-28 RCSB #