data_ZUK # _chem_comp.id ZUK _chem_comp.name 5-pyrimidin-2-yl-D-norvaline _chem_comp.type "D-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C9 H13 N3 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-07-31 _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 195.218 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZUK _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 2KMJ _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 ZUK C C C 0 1 N N N Y N Y 3.382 5.319 6.266 3.943 -0.172 -0.068 C ZUK 1 ZUK N N N 0 1 N N N Y Y N 3.887 3.119 7.232 2.460 1.586 -0.851 N ZUK 2 ZUK O O O 0 1 N N N Y N Y 2.263 5.071 5.810 4.638 0.705 0.387 O ZUK 3 ZUK CA CA C 0 1 N N R Y N N 3.917 4.555 7.473 2.559 0.147 -0.571 CA ZUK 4 ZUK CB CB C 0 1 N N N N N N 3.101 4.910 8.721 1.528 -0.238 0.492 CB ZUK 5 ZUK CD CD C 0 1 N N N N N N 4.374 3.519 10.407 -0.913 -0.415 0.997 CD ZUK 6 ZUK CE CE C 0 1 Y N N N N N 3.460 2.907 11.435 -2.301 -0.210 0.448 CE ZUK 7 ZUK CG CG C 0 1 N N N N N N 3.905 4.913 10.018 0.118 -0.030 -0.066 CG ZUK 8 ZUK CT CT C 0 1 Y N N N N N 1.673 1.733 13.436 -4.765 0.153 -0.525 CT ZUK 9 ZUK CH1 CH1 C 0 1 Y N N N N N 2.510 2.894 13.741 -4.114 -1.062 -0.676 CH1 ZUK 10 ZUK CH2 CH2 C 0 1 Y N N N N N 1.769 1.182 12.081 -4.109 1.173 0.146 CH2 ZUK 11 ZUK OXT OXT O 0 1 N Y N Y N Y 4.182 6.263 5.768 4.405 -1.431 -0.131 OXT ZUK 12 ZUK NZ1 NZ1 N 0 1 Y N N N N N 3.383 3.441 12.710 -2.895 -1.204 -0.181 NZ1 ZUK 13 ZUK NZ2 NZ2 N 0 1 Y N N N N N 2.676 1.805 11.120 -2.891 0.957 0.614 NZ2 ZUK 14 ZUK H HN H 0 1 N N N Y Y N 4.241 2.638 8.034 1.562 1.816 -1.250 HN ZUK 15 ZUK HA HA H 0 1 N N N Y N N 4.964 4.849 7.638 2.365 -0.414 -1.485 HA ZUK 16 ZUK HT HT H 0 1 N N N N N N 1.015 1.302 14.176 -5.758 0.301 -0.922 HT ZUK 17 ZUK HB HB H 0 1 N N N N N N 2.298 4.165 8.823 1.660 -1.285 0.764 HB ZUK 18 ZUK HD HD H 0 1 N N N N N N 4.381 2.882 9.511 -0.775 0.210 1.880 HD ZUK 19 ZUK HG HG H 0 1 N N N N N N 3.268 5.306 10.824 -0.014 1.017 -0.338 HG ZUK 20 ZUK HBA HBA H 0 1 N N N N N N 2.687 5.919 8.578 1.665 0.387 1.374 HBA ZUK 21 ZUK HDA HDA H 0 1 N N N N N N 5.388 3.588 10.827 -0.780 -1.462 1.269 HDA ZUK 22 ZUK HGA HGA H 0 1 N N N N N N 4.788 5.554 9.881 -0.019 -0.655 -0.948 HGA ZUK 23 ZUK HH1 HH1 H 0 1 N N N N N N 2.481 3.342 14.723 -4.594 -1.879 -1.193 HH1 ZUK 24 ZUK HH2 HH2 H 0 1 N N N N N N 1.176 0.325 11.796 -4.585 2.133 0.282 HH2 ZUK 25 ZUK H2 HNA H 0 1 N Y N Y Y N 2.945 2.830 7.059 2.635 2.129 -0.019 HNA ZUK 26 ZUK HXT HXT H 0 1 N Y N Y N Y 3.753 6.688 5.034 5.299 -1.587 0.204 HXT ZUK 27 # 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 ZUK C CA SING N N 1 ZUK N H SING N N 2 ZUK N CA SING N N 3 ZUK N H2 SING N N 4 ZUK O C DOUB N N 5 ZUK CA HA SING N N 6 ZUK CA CB SING N N 7 ZUK CB HBA SING N N 8 ZUK CB CG SING N N 9 ZUK CD HDA SING N N 10 ZUK CD CE SING N N 11 ZUK CE NZ1 SING Y N 12 ZUK CG CD SING N N 13 ZUK CG HGA SING N N 14 ZUK CT CH1 SING Y N 15 ZUK CT HT SING N N 16 ZUK CH1 HH1 SING N N 17 ZUK CH2 CT DOUB Y N 18 ZUK OXT C SING N N 19 ZUK OXT HXT SING N N 20 ZUK NZ1 CH1 DOUB Y N 21 ZUK NZ2 CE DOUB Y N 22 ZUK NZ2 CH2 SING Y N 23 ZUK HB CB SING N N 24 ZUK HD CD SING N N 25 ZUK HG CG SING N N 26 ZUK HH2 CH2 SING N N 27 # 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 ZUK SMILES ACDLabs 11.02 "O=C(O)C(N)CCCc1ncccn1" ZUK SMILES_CANONICAL CACTVS 3.352 "N[C@H](CCCc1ncccn1)C(O)=O" ZUK SMILES CACTVS 3.352 "N[CH](CCCc1ncccn1)C(O)=O" ZUK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1cnc(nc1)CCC[C@H](C(=O)O)N" ZUK SMILES "OpenEye OEToolkits" 1.7.0 "c1cnc(nc1)CCCC(C(=O)O)N" ZUK InChI InChI 1.03 "InChI=1S/C9H13N3O2/c10-7(9(13)14)3-1-4-8-11-5-2-6-12-8/h2,5-7H,1,3-4,10H2,(H,13,14)/t7-/m1/s1" ZUK InChIKey InChI 1.03 UREVLRRGQRTHIJ-SSDOTTSWSA-N # 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 ZUK "SYSTEMATIC NAME" ACDLabs 11.02 5-pyrimidin-2-yl-D-norvaline ZUK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(2R)-2-azanyl-5-pyrimidin-2-yl-pentanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ZUK "Create component" 2009-07-31 RCSB ZUK "Modify descriptor" 2011-06-04 RCSB ZUK "Modify backbone" 2023-11-03 PDBE ZUK "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id ZUK _pdbx_chem_comp_pcm.modified_residue_id ? _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Non-standard residue" _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 ? _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 ? #