data_PYD # _chem_comp.id PYD _chem_comp.name 2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C6 H9 N3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-09-13 _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 123.156 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PYD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4THI _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 PYD "N1'" "N1'" N 0 1 Y N N N N N 14.689 27.263 5.358 1.233 0.000 1.135 "N1'" PYD 1 PYD "C2'" "C2'" C 0 1 Y N N N N N 14.884 27.868 4.158 -0.028 0.000 1.514 "C2'" PYD 2 PYD CM2 CM2 C 0 1 N N N N N N 14.275 29.185 3.979 -0.351 0.001 2.986 CM2 PYD 3 PYD "N3'" "N3'" N 0 1 Y N N N N N 15.585 27.312 3.189 -1.015 -0.004 0.642 "N3'" PYD 4 PYD "C4'" "C4'" C 0 1 Y N N N N N 16.121 26.057 3.408 -0.767 0.001 -0.664 "C4'" PYD 5 PYD "N4'" "N4'" N 0 1 N N N N N N 16.802 25.536 2.428 -1.807 0.001 -1.578 "N4'" PYD 6 PYD "C5'" "C5'" C 0 1 Y N N N N N 15.929 25.362 4.653 0.559 0.000 -1.099 "C5'" PYD 7 PYD "C6'" "C6'" C 0 1 Y N N N N N 15.206 26.016 5.595 1.561 -0.000 -0.148 "C6'" PYD 8 PYD "C7'" "C7'" C 0 1 N N N N N N 16.506 23.977 4.906 0.890 -0.000 -2.569 "C7'" PYD 9 PYD HM21 1HM2 H 0 0 N N N N N N 14.435 29.681 2.993 -0.429 1.028 3.341 HM21 PYD 10 PYD HM22 2HM2 H 0 0 N N N N N N 13.182 29.123 4.193 -1.299 -0.512 3.150 HM22 PYD 11 PYD HM23 3HM2 H 0 0 N N N N N N 14.606 29.864 4.798 0.439 -0.513 3.532 HM23 PYD 12 PYD HN41 1HN4 H 0 0 N N N N N N 17.197 24.609 2.589 -2.726 0.001 -1.268 HN41 PYD 13 PYD HN42 2HN4 H 0 0 N N N N N N 17.540 26.179 2.143 -1.617 0.000 -2.530 HN42 PYD 14 PYD "HC6'" "HC6'" H 0 0 N N N N N N 15.035 25.526 6.568 2.599 -0.000 -0.447 "HC6'" PYD 15 PYD HC71 1HC7 H 0 0 N N N N N N 16.357 23.438 5.870 0.969 -1.028 -2.923 HC71 PYD 16 PYD HC72 2HC7 H 0 0 N N N N N N 16.152 23.308 4.086 0.102 0.513 -3.119 HC72 PYD 17 PYD HC73 3HC7 H 0 0 N N N N N N 17.602 24.026 4.711 1.838 0.512 -2.729 HC73 PYD 18 # 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 PYD "N1'" "C2'" DOUB Y N 1 PYD "N1'" "C6'" SING Y N 2 PYD "C2'" CM2 SING N N 3 PYD "C2'" "N3'" SING Y N 4 PYD CM2 HM21 SING N N 5 PYD CM2 HM22 SING N N 6 PYD CM2 HM23 SING N N 7 PYD "N3'" "C4'" DOUB Y N 8 PYD "C4'" "N4'" SING N N 9 PYD "C4'" "C5'" SING Y N 10 PYD "N4'" HN41 SING N N 11 PYD "N4'" HN42 SING N N 12 PYD "C5'" "C6'" DOUB Y N 13 PYD "C5'" "C7'" SING N N 14 PYD "C6'" "HC6'" SING N N 15 PYD "C7'" HC71 SING N N 16 PYD "C7'" HC72 SING N N 17 PYD "C7'" HC73 SING N N 18 # 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 PYD SMILES ACDLabs 10.04 "n1c(N)c(cnc1C)C" PYD SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(C)c(N)n1" PYD SMILES CACTVS 3.341 "Cc1ncc(C)c(N)n1" PYD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1cnc(nc1N)C" PYD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1cnc(nc1N)C" PYD InChI InChI 1.03 "InChI=1S/C6H9N3/c1-4-3-8-5(2)9-6(4)7/h3H,1-2H3,(H2,7,8,9)" PYD InChIKey InChI 1.03 UXKNAXNFIYFMIB-UHFFFAOYSA-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 PYD "SYSTEMATIC NAME" ACDLabs 10.04 2,5-dimethylpyrimidin-4-amine PYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2,5-dimethylpyrimidin-4-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 PYD "Create component" 1999-09-13 RCSB PYD "Modify descriptor" 2011-06-04 RCSB PYD "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id PYD _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 "C6'" _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 ? #