data_Y9V # _chem_comp.id Y9V _chem_comp.name "N-[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]-5-(3-methyl-1,2,4-oxadiazol-5-yl)pyrimidin-2-amine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H14 Cl N5 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-12 _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 327.768 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y9V _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 7G3W _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 Y9V C10 C1 C 0 1 Y N N N N N -12.477 4.205 44.212 -3.806 -0.485 -0.211 C10 Y9V 1 Y9V C11 C2 C 0 1 Y N N N N N -11.994 3.070 43.783 -5.136 -0.553 -0.589 C11 Y9V 2 Y9V C15 C3 C 0 1 Y N N N N N -11.104 5.401 42.718 -4.311 1.383 1.199 C15 Y9V 3 Y9V C16 C4 C 0 1 Y N N N N N -12.065 5.402 43.687 -3.393 0.484 0.684 C16 Y9V 4 Y9V C17 C5 C 0 1 N N N N N N -12.729 6.548 44.313 -1.906 0.350 0.934 C17 Y9V 5 Y9V C18 C6 C 0 1 Y N N N N N -13.893 11.062 49.128 4.972 0.266 -0.134 C18 Y9V 6 Y9V C21 C7 C 0 1 Y N N N N N -14.142 12.933 50.342 7.088 0.383 -0.032 C21 Y9V 7 Y9V C23 C8 C 0 1 N N N N N N -14.808 14.023 51.069 8.540 0.060 0.212 C23 Y9V 8 Y9V C1 C9 C 0 1 Y N N N N N -12.892 9.243 47.840 2.522 0.651 -0.464 C1 Y9V 9 Y9V C2 C10 C 0 1 Y N N N N N -13.983 9.872 48.323 3.567 -0.177 -0.039 C2 Y9V 10 Y9V C3 C11 C 0 1 Y N N N N N -15.286 9.336 47.992 3.246 -1.439 0.478 C3 Y9V 11 Y9V N4 N1 N 0 1 Y N N N N N -15.529 8.270 47.342 1.977 -1.799 0.545 N4 Y9V 12 Y9V C5 C12 C 0 1 Y N N N N N -14.319 7.646 46.844 1.016 -0.984 0.132 C5 Y9V 13 Y9V N6 N2 N 0 1 Y N N N N N -13.021 8.095 47.138 1.279 0.217 -0.363 N6 Y9V 14 Y9V N7 N3 N 0 1 N N N N N N -14.411 6.523 46.127 -0.298 -1.400 0.221 N7 Y9V 15 Y9V C8 C13 C 0 1 N N R N N N -13.266 5.836 45.639 -1.378 -0.517 -0.229 C8 Y9V 16 Y9V C9 C14 C 0 1 N N N N N N -13.491 4.380 45.289 -2.623 -1.333 -0.628 C9 Y9V 17 Y9V C12 C15 C 0 1 Y N N N N N -11.003 3.101 42.759 -6.052 0.346 -0.074 C12 Y9V 18 Y9V CL13 CL1 CL 0 0 N N N N N N -10.338 1.587 42.117 -7.719 0.257 -0.551 CL13 Y9V 19 Y9V C14 C16 C 0 1 Y N N N N N -10.582 4.210 42.235 -5.638 1.315 0.821 C14 Y9V 20 Y9V O19 O1 O 0 1 Y N N N N N -12.662 11.576 49.468 5.411 1.443 -0.608 O19 Y9V 21 Y9V N20 N4 N 0 1 Y N N N N N -12.809 12.773 50.210 6.621 1.486 -0.539 N20 Y9V 22 Y9V N22 N5 N 0 1 Y N N N N N -14.867 11.818 49.625 6.043 -0.416 0.235 N22 Y9V 23 Y9V H30 H1 H 0 1 N N N N N N -12.337 2.132 44.194 -5.459 -1.310 -1.288 H30 Y9V 24 Y9V H32 H2 H 0 1 N N N N N N -10.745 6.340 42.322 -3.989 2.140 1.899 H32 Y9V 25 Y9V H34 H3 H 0 1 N N N N N N -13.550 6.938 43.693 -1.430 1.331 0.921 H34 Y9V 26 Y9V H33 H4 H 0 1 N N N N N N -12.023 7.361 44.539 -1.726 -0.145 1.888 H33 Y9V 27 Y9V H36 H5 H 0 1 N N N N N N -14.050 14.697 51.495 8.958 -0.422 -0.672 H36 Y9V 28 Y9V H37 H6 H 0 1 N N N N N N -15.452 14.586 50.377 9.087 0.980 0.417 H37 Y9V 29 Y9V H35 H7 H 0 1 N N N N N N -15.421 13.602 51.880 8.624 -0.611 1.066 H35 Y9V 30 Y9V H24 H8 H 0 1 N N N N N N -11.911 9.659 48.015 2.728 1.633 -0.865 H24 Y9V 31 Y9V H25 H9 H 0 1 N N N N N N -16.142 9.900 48.333 4.024 -2.107 0.816 H25 Y9V 32 Y9V H26 H10 H 0 1 N N N N N N -14.906 5.868 46.698 -0.507 -2.276 0.581 H26 Y9V 33 Y9V H27 H11 H 0 1 N N N N N N -12.461 5.889 46.386 -1.044 0.110 -1.056 H27 Y9V 34 Y9V H28 H12 H 0 1 N N N N N N -13.292 3.720 46.146 -2.636 -2.286 -0.099 H28 Y9V 35 Y9V H29 H13 H 0 1 N N N N N N -14.512 4.203 44.919 -2.638 -1.498 -1.706 H29 Y9V 36 Y9V H31 H14 H 0 1 N N N N N N -9.846 4.206 41.445 -6.352 2.018 1.225 H31 Y9V 37 # 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 Y9V C1 C2 DOUB Y N 1 Y9V C1 N6 SING Y N 2 Y9V C2 C3 SING Y N 3 Y9V C2 C18 SING N N 4 Y9V C3 N4 DOUB Y N 5 Y9V N4 C5 SING Y N 6 Y9V C5 N6 DOUB Y N 7 Y9V C5 N7 SING N N 8 Y9V N7 C8 SING N N 9 Y9V C8 C9 SING N N 10 Y9V C8 C17 SING N N 11 Y9V C9 C10 SING N N 12 Y9V C10 C11 DOUB Y N 13 Y9V C10 C16 SING Y N 14 Y9V C11 C12 SING Y N 15 Y9V C12 CL13 SING N N 16 Y9V C12 C14 DOUB Y N 17 Y9V C14 C15 SING Y N 18 Y9V C15 C16 DOUB Y N 19 Y9V C16 C17 SING N N 20 Y9V C18 O19 SING Y N 21 Y9V C18 N22 DOUB Y N 22 Y9V O19 N20 SING Y N 23 Y9V N20 C21 DOUB Y N 24 Y9V C21 N22 SING Y N 25 Y9V C21 C23 SING N N 26 Y9V C11 H30 SING N N 27 Y9V C15 H32 SING N N 28 Y9V C17 H34 SING N N 29 Y9V C17 H33 SING N N 30 Y9V C23 H36 SING N N 31 Y9V C23 H37 SING N N 32 Y9V C23 H35 SING N N 33 Y9V C1 H24 SING N N 34 Y9V C3 H25 SING N N 35 Y9V N7 H26 SING N N 36 Y9V C8 H27 SING N N 37 Y9V C9 H28 SING N N 38 Y9V C9 H29 SING N N 39 Y9V C14 H31 SING N N 40 # 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 Y9V SMILES ACDLabs 12.01 "Cc1nc(on1)c1cnc(NC2Cc3ccc(Cl)cc3C2)nc1" Y9V InChI InChI 1.06 "InChI=1S/C16H14ClN5O/c1-9-20-15(23-22-9)12-7-18-16(19-8-12)21-14-5-10-2-3-13(17)4-11(10)6-14/h2-4,7-8,14H,5-6H2,1H3,(H,18,19,21)" Y9V InChIKey InChI 1.06 JJQCQNKADMBVHU-UHFFFAOYSA-N Y9V SMILES_CANONICAL CACTVS 3.385 "Cc1noc(n1)c2cnc(N[C@@H]3Cc4ccc(Cl)cc4C3)nc2" Y9V SMILES CACTVS 3.385 "Cc1noc(n1)c2cnc(N[CH]3Cc4ccc(Cl)cc4C3)nc2" Y9V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1nc(on1)c2cnc(nc2)N[C@@H]3Cc4ccc(cc4C3)Cl" Y9V SMILES "OpenEye OEToolkits" 2.0.7 "Cc1nc(on1)c2cnc(nc2)NC3Cc4ccc(cc4C3)Cl" # 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 Y9V "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]-5-(3-methyl-1,2,4-oxadiazol-5-yl)pyrimidin-2-amine" Y9V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[(2~{R})-5-chloranyl-2,3-dihydro-1~{H}-inden-2-yl]-5-(3-methyl-1,2,4-oxadiazol-5-yl)pyrimidin-2-amine" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y9V "Create component" 2023-06-12 RCSB Y9V "Initial release" 2024-12-18 RCSB #