data_YP5 # _chem_comp.id YP5 _chem_comp.name "(2-{[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]amino}pyrimidin-5-yl)[(4s,6S)-6-hydroxy-6-methyl-1-azaspiro[3.3]heptan-1-yl]methanone" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H23 Cl N4 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-19 _chem_comp.pdbx_modified_date 2024-12-13 _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 398.886 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YP5 _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 7G3N _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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 YP5 C11 C1 C 0 1 Y N N N N N -14.257 9.550 48.071 -2.082 -0.308 -0.156 C11 YP5 1 YP5 C16 C2 C 0 1 Y N N N N N -13.130 8.941 47.551 -1.017 0.369 -0.765 C16 YP5 2 YP5 C18 C3 C 0 1 N N R N N N -13.288 5.486 45.393 2.830 -0.932 -0.422 C18 YP5 3 YP5 C19 C4 C 0 1 N N N N N N -12.816 6.189 44.071 4.023 -1.874 -0.691 C19 YP5 4 YP5 C20 C5 C 0 1 Y N N N N N -12.106 5.027 43.380 5.256 -1.022 -0.483 C20 YP5 5 YP5 C21 C6 C 0 1 Y N N N N N -11.158 5.050 42.406 6.566 -1.228 -0.881 C21 YP5 6 YP5 C22 C7 C 0 1 Y N N N N N -10.623 3.819 41.931 7.541 -0.298 -0.573 C22 YP5 7 YP5 C23 C8 C 0 1 Y N N N N N -11.063 2.703 42.509 7.207 0.843 0.134 C23 YP5 8 YP5 C24 C9 C 0 1 Y N N N N N -12.027 2.625 43.469 5.899 1.050 0.531 C24 YP5 9 YP5 C25 C10 C 0 1 Y N N N N N -12.519 3.847 43.950 4.922 0.118 0.224 C25 YP5 10 YP5 C26 C11 C 0 1 N N N N N N -13.571 4.051 45.009 3.441 0.110 0.539 C26 YP5 11 YP5 C28 C12 C 0 1 N N N N N N -13.115 13.950 49.369 -6.679 0.492 1.116 C28 YP5 12 YP5 C1 C13 C 0 1 N N N N N N -14.578 15.809 50.675 -8.142 2.202 -0.120 C1 YP5 13 YP5 C2 C14 C 0 1 N N N N N N -14.421 14.331 50.213 -6.788 1.493 -0.048 C2 YP5 14 YP5 O3 O1 O 0 1 N N N N N N -15.649 13.925 49.577 -5.685 2.397 -0.130 O3 YP5 15 YP5 C4 C15 C 0 1 N N N N N N -13.913 13.223 51.294 -6.672 0.289 -1.000 C4 YP5 16 YP5 C5 C16 C 0 1 N N N N N N -12.899 12.619 50.225 -5.952 -0.434 0.141 C5 YP5 17 YP5 C6 C17 C 0 1 N N N N N N -11.492 12.043 50.691 -6.019 -1.955 0.286 C6 YP5 18 YP5 C7 C18 C 0 1 N N N N N N -11.646 10.907 49.620 -4.603 -1.849 0.886 C7 YP5 19 YP5 N8 N1 N 0 1 N N N N N N -13.104 11.283 49.529 -4.493 -0.567 0.160 N8 YP5 20 YP5 C9 C19 C 0 1 N N N N N N -14.195 10.828 48.826 -3.468 0.178 -0.298 C9 YP5 21 YP5 O10 O2 O 0 1 N N N N N N -15.216 11.479 48.801 -3.685 1.250 -0.829 O10 YP5 22 YP5 C12 C20 C 0 1 Y N N N N N -15.467 8.937 47.863 -1.797 -1.461 0.588 C12 YP5 23 YP5 N13 N2 N 0 1 Y N N N N N -15.615 7.788 47.160 -0.545 -1.865 0.687 N13 YP5 24 YP5 C14 C21 C 0 1 Y N N N N N -14.386 7.252 46.701 0.436 -1.197 0.094 C14 YP5 25 YP5 N15 N3 N 0 1 Y N N N N N -13.161 7.821 46.907 0.207 -0.101 -0.618 N15 YP5 26 YP5 N17 N4 N 0 1 N N N N N N -14.465 6.116 46.000 1.731 -1.654 0.223 N17 YP5 27 YP5 CL27 CL1 CL 0 0 N N N N N N -10.434 1.174 41.833 8.429 2.013 0.522 CL27 YP5 28 YP5 H40 H1 H 0 1 N N N N N N -12.175 9.426 47.690 -1.195 1.261 -1.347 H40 YP5 29 YP5 H42 H2 H 0 1 N N N N N N -12.452 5.505 46.108 2.495 -0.458 -1.345 H42 YP5 30 YP5 H44 H3 H 0 1 N N N N N N -13.668 6.555 43.479 4.014 -2.706 0.013 H44 YP5 31 YP5 H43 H4 H 0 1 N N N N N N -12.127 7.022 44.277 3.988 -2.245 -1.716 H43 YP5 32 YP5 H45 H5 H 0 1 N N N N N N -10.815 5.989 41.998 6.827 -2.118 -1.433 H45 YP5 33 YP5 H46 H6 H 0 1 N N N N N N -9.892 3.792 41.136 8.562 -0.462 -0.885 H46 YP5 34 YP5 H47 H7 H 0 1 N N N N N N -12.391 1.677 43.838 5.639 1.940 1.084 H47 YP5 35 YP5 H48 H8 H 0 1 N N N N N N -13.432 3.367 45.859 3.010 1.094 0.355 H48 YP5 36 YP5 H49 H9 H 0 1 N N N N N N -14.586 3.930 44.603 3.277 -0.188 1.574 H49 YP5 37 YP5 H51 H10 H 0 1 N N N N N N -13.315 13.764 48.303 -6.052 0.841 1.937 H51 YP5 38 YP5 H50 H11 H 0 1 N N N N N N -12.296 14.678 49.467 -7.641 0.105 1.453 H50 YP5 39 YP5 H31 H12 H 0 1 N N N N N N -13.651 16.141 51.164 -8.294 2.593 -1.126 H31 YP5 40 YP5 H29 H13 H 0 1 N N N N N N -14.780 16.446 49.802 -8.936 1.493 0.117 H29 YP5 41 YP5 H30 H14 H 0 1 N N N N N N -15.415 15.884 51.385 -8.162 3.023 0.596 H30 YP5 42 YP5 H32 H15 H 0 1 N N N N N N -15.564 13.032 49.265 -5.742 3.144 0.482 H32 YP5 43 YP5 H33 H16 H 0 1 N N N N N N -13.424 13.655 52.180 -7.631 -0.157 -1.261 H33 YP5 44 YP5 H34 H17 H 0 1 N N N N N N -14.696 12.520 51.614 -6.039 0.476 -1.868 H34 YP5 45 YP5 H36 H18 H 0 1 N N N N N N -10.643 12.720 50.516 -6.773 -2.297 0.995 H36 YP5 46 YP5 H35 H19 H 0 1 N N N N N N -11.469 11.687 51.731 -6.056 -2.486 -0.665 H35 YP5 47 YP5 H38 H20 H 0 1 N N N N N N -11.072 11.067 48.695 -4.593 -1.742 1.970 H38 YP5 48 YP5 H37 H21 H 0 1 N N N N N N -11.457 9.891 49.998 -3.917 -2.616 0.527 H37 YP5 49 YP5 H39 H22 H 0 1 N N N N N N -16.350 9.396 48.283 -2.591 -2.010 1.073 H39 YP5 50 YP5 H41 H23 H 0 1 N N N N N N -14.858 5.435 46.617 1.914 -2.453 0.741 H41 YP5 51 # 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 YP5 C1 C2 SING N N 1 YP5 C2 O3 SING N N 2 YP5 C2 C4 SING N N 3 YP5 C2 C28 SING N N 4 YP5 C4 C5 SING N N 5 YP5 C5 C6 SING N N 6 YP5 C5 N8 SING N N 7 YP5 C5 C28 SING N N 8 YP5 C6 C7 SING N N 9 YP5 C7 N8 SING N N 10 YP5 N8 C9 SING N N 11 YP5 C9 O10 DOUB N N 12 YP5 C9 C11 SING N N 13 YP5 C11 C12 DOUB Y N 14 YP5 C11 C16 SING Y N 15 YP5 C12 N13 SING Y N 16 YP5 N13 C14 DOUB Y N 17 YP5 C14 N15 SING Y N 18 YP5 C14 N17 SING N N 19 YP5 N15 C16 DOUB Y N 20 YP5 N17 C18 SING N N 21 YP5 C18 C19 SING N N 22 YP5 C18 C26 SING N N 23 YP5 C19 C20 SING N N 24 YP5 C20 C21 DOUB Y N 25 YP5 C20 C25 SING Y N 26 YP5 C21 C22 SING Y N 27 YP5 C22 C23 DOUB Y N 28 YP5 C23 C24 SING Y N 29 YP5 C23 CL27 SING N N 30 YP5 C24 C25 DOUB Y N 31 YP5 C25 C26 SING N N 32 YP5 C16 H40 SING N N 33 YP5 C18 H42 SING N N 34 YP5 C19 H44 SING N N 35 YP5 C19 H43 SING N N 36 YP5 C21 H45 SING N N 37 YP5 C22 H46 SING N N 38 YP5 C24 H47 SING N N 39 YP5 C26 H48 SING N N 40 YP5 C26 H49 SING N N 41 YP5 C28 H51 SING N N 42 YP5 C28 H50 SING N N 43 YP5 C1 H31 SING N N 44 YP5 C1 H29 SING N N 45 YP5 C1 H30 SING N N 46 YP5 O3 H32 SING N N 47 YP5 C4 H33 SING N N 48 YP5 C4 H34 SING N N 49 YP5 C6 H36 SING N N 50 YP5 C6 H35 SING N N 51 YP5 C7 H38 SING N N 52 YP5 C7 H37 SING N N 53 YP5 C12 H39 SING N N 54 YP5 N17 H41 SING N N 55 # 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 YP5 SMILES ACDLabs 12.01 "O=C(c1cnc(NC2Cc3ccc(Cl)cc3C2)nc1)N1CCC21CC(C)(O)C2" YP5 InChI InChI 1.06 "InChI=1S/C21H23ClN4O2/c1-20(28)11-21(12-20)4-5-26(21)18(27)15-9-23-19(24-10-15)25-17-7-13-2-3-16(22)6-14(13)8-17/h2-3,6,9-10,17,28H,4-5,7-8,11-12H2,1H3,(H,23,24,25)/t17-,20-,21+/m0/s1" YP5 InChIKey InChI 1.06 FMXQAKFCTVPOGB-DZFGPLHGSA-N YP5 SMILES_CANONICAL CACTVS 3.385 "C[C@@]1(O)C[C@@]2(CCN2C(=O)c3cnc(N[C@@H]4Cc5ccc(Cl)cc5C4)nc3)C1" YP5 SMILES CACTVS 3.385 "C[C]1(O)C[C]2(CCN2C(=O)c3cnc(N[CH]4Cc5ccc(Cl)cc5C4)nc3)C1" YP5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1(CC2(C1)CCN2C(=O)c3cnc(nc3)N[C@@H]4Cc5ccc(cc5C4)Cl)O" YP5 SMILES "OpenEye OEToolkits" 2.0.7 "CC1(CC2(C1)CCN2C(=O)c3cnc(nc3)NC4Cc5ccc(cc5C4)Cl)O" # 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 YP5 "SYSTEMATIC NAME" ACDLabs 12.01 "(2-{[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]amino}pyrimidin-5-yl)[(4s,6S)-6-hydroxy-6-methyl-1-azaspiro[3.3]heptan-1-yl]methanone" YP5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[2-[[(2~{R})-5-chloranyl-2,3-dihydro-1~{H}-inden-2-yl]amino]pyrimidin-5-yl]-(6-methyl-6-oxidanyl-1-azaspiro[3.3]heptan-1-yl)methanone" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YP5 "Create component" 2023-06-19 RCSB YP5 "Initial release" 2024-12-18 RCSB #