data_5ZE
#
_chem_comp.id 5ZE
_chem_comp.name 4,6-dimethylpyrimidin-2-amine
_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 2013-07-30
_chem_comp.pdbx_modified_date 2014-02-21
_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 5ZE
_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 4LLX
_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
5ZE C1 C1 C 0 1 N N N N N N 5.693 11.082 44.763 2.511 1.395 0.001 C1 5ZE 1
5ZE C2 C2 C 0 1 Y N N N N N 4.891 12.203 44.130 1.192 0.667 0.001 C2 5ZE 2
5ZE C3 C3 C 0 1 Y N N N N N 4.785 12.337 42.729 0.000 1.375 0.001 C3 5ZE 3
5ZE C4 C4 C 0 1 Y N N N N N 4.016 13.394 42.212 -1.191 0.667 0.000 C4 5ZE 4
5ZE C5 C5 C 0 1 N N N N N N 3.839 13.613 40.722 -2.511 1.395 -0.001 C5 5ZE 5
5ZE N6 N6 N 0 1 Y N N N N N 3.417 14.264 43.066 -1.156 -0.655 0.001 N6 5ZE 6
5ZE C7 C7 C 0 1 Y N N N N N 3.537 14.119 44.409 -0.000 -1.302 0.001 C7 5ZE 7
5ZE N8 N8 N 0 1 N N N N N N 2.916 14.990 45.213 -0.000 -2.686 0.001 N8 5ZE 8
5ZE N9 N9 N 0 1 Y N N N N N 4.253 13.091 44.940 1.156 -0.655 -0.004 N9 5ZE 9
5ZE H1 H1 H 0 1 N N N N N N 5.634 11.161 45.859 2.827 1.574 -1.027 H1 5ZE 10
5ZE H2 H2 H 0 1 N N N N N N 5.283 10.112 44.443 2.401 2.348 0.518 H2 5ZE 11
5ZE H3 H3 H 0 1 N N N N N N 6.744 11.159 44.446 3.260 0.789 0.511 H3 5ZE 12
5ZE H4 H4 H 0 1 N N N N N N 5.284 11.643 42.069 0.000 2.455 0.001 H4 5ZE 13
5ZE H5 H5 H 0 1 N N N N N N 3.212 14.501 40.553 -2.829 1.570 -1.029 H5 5ZE 14
5ZE H6 H6 H 0 1 N N N N N N 4.823 13.765 40.254 -3.259 0.791 0.513 H6 5ZE 15
5ZE H7 H7 H 0 1 N N N N N N 3.354 12.732 40.277 -2.400 2.350 0.513 H7 5ZE 16
5ZE H8 H8 H 0 1 N N N N N N 2.424 15.662 44.660 -0.840 -3.171 0.000 H8 5ZE 17
5ZE H9 H9 H 0 1 N N N N N N 2.269 14.501 45.798 0.840 -3.171 0.001 H9 5ZE 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
5ZE C5 C4 SING N N 1
5ZE C4 C3 DOUB Y N 2
5ZE C4 N6 SING Y N 3
5ZE C3 C2 SING Y N 4
5ZE N6 C7 DOUB Y N 5
5ZE C2 C1 SING N N 6
5ZE C2 N9 DOUB Y N 7
5ZE C7 N9 SING Y N 8
5ZE C7 N8 SING N N 9
5ZE C1 H1 SING N N 10
5ZE C1 H2 SING N N 11
5ZE C1 H3 SING N N 12
5ZE C3 H4 SING N N 13
5ZE C5 H5 SING N N 14
5ZE C5 H6 SING N N 15
5ZE C5 H7 SING N N 16
5ZE N8 H8 SING N N 17
5ZE N8 H9 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
5ZE SMILES ACDLabs 12.01 n1c(cc(nc1N)C)C
5ZE InChI InChI 1.03 InChI=1S/C6H9N3/c1-4-3-5(2)9-6(7)8-4/h3H,1-2H3,(H2,7,8,9)
5ZE InChIKey InChI 1.03 IDQNBVFPZMCDDN-UHFFFAOYSA-N
5ZE SMILES_CANONICAL CACTVS 3.385 Cc1cc(C)nc(N)n1
5ZE SMILES CACTVS 3.385 Cc1cc(C)nc(N)n1
5ZE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 Cc1cc(nc(n1)N)C
5ZE SMILES "OpenEye OEToolkits" 1.7.6 Cc1cc(nc(n1)N)C
#
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
5ZE "SYSTEMATIC NAME" ACDLabs 12.01 4,6-dimethylpyrimidin-2-amine
5ZE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 4,6-dimethylpyrimidin-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
5ZE 'Create component' 2013-07-30 RCSB
5ZE 'Initial release' 2014-02-26 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
5ZE C1 C 8.196 -1.785 1
5ZE C2 C 6.897 -1.035 2
5ZE C3 C 5.598 -1.785 3
5ZE C4 C 4.299 -1.035 4
5ZE C5 C 3.000 -1.785 5
5ZE N6 N 4.299 0.465 6
5ZE C7 C 5.598 1.215 7
5ZE N8 N 5.598 2.715 8
5ZE N9 N 6.897 0.465 9
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
5ZE C5 C4 SINGLE NONE 1
5ZE C4 C3 SINGLE NONE 2
5ZE C4 N6 DOUBLE NONE 3
5ZE C3 C2 DOUBLE NONE 4
5ZE N6 C7 SINGLE NONE 5
5ZE C2 C1 SINGLE NONE 6
5ZE C2 N9 SINGLE NONE 7
5ZE C7 N9 DOUBLE NONE 8
5ZE C7 N8 SINGLE NONE 9
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
5ZE MurckoScaffold S1 scaffold c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
5ZE pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
5ZE C2 S1 1
5ZE C3 S1 1
5ZE C4 S1 1
5ZE N6 S1 1
5ZE C7 S1 1
5ZE N9 S1 1
5ZE C3 F1 1
5ZE C4 F1 1
5ZE N6 F1 1
5ZE C7 F1 1
5ZE N9 F1 1
5ZE C2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5ZE
_pdbe_chem_comp_rdkit_properties.exactmw 123.080
_pdbe_chem_comp_rdkit_properties.amw 123.159
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 66.701
_pdbe_chem_comp_rdkit_properties.tpsa 51.800
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.186
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.562
_pdbe_chem_comp_rdkit_properties.chi0v 4.342
_pdbe_chem_comp_rdkit_properties.chi1v 2.118
_pdbe_chem_comp_rdkit_properties.chi2v 0.660
_pdbe_chem_comp_rdkit_properties.chi3v 0.660
_pdbe_chem_comp_rdkit_properties.chi4v 0.393
_pdbe_chem_comp_rdkit_properties.chi0n 13.342
_pdbe_chem_comp_rdkit_properties.chi1n 6.512
_pdbe_chem_comp_rdkit_properties.chi2n 0.660
_pdbe_chem_comp_rdkit_properties.chi3n 0.660
_pdbe_chem_comp_rdkit_properties.chi4n 0.393
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.120
_pdbe_chem_comp_rdkit_properties.kappa1 1.309
_pdbe_chem_comp_rdkit_properties.kappa2 2.009
_pdbe_chem_comp_rdkit_properties.kappa3 1.384
_pdbe_chem_comp_rdkit_properties.Phi 0.292
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
5ZE UniChem ChEMBL CHEMBL4546836
5ZE UniChem PDBe 5ZE
5ZE UniChem ChEBI 181699
5ZE UniChem ZINC ZINC000000163774
5ZE UniChem fdasrs 4S48MI253M
5ZE UniChem SureChEMBL SCHEMBL151114
5ZE UniChem 'PubChem TPHARMA' 14867236
5ZE UniChem ACTor 767-15-7
5ZE UniChem BindingDb 50532276
5ZE UniChem 'EPA CompTox Dashboard' DTXSID8052510
5ZE UniChem ChemicalBook CB7234640
5ZE UniChem Nikkaji J96E
5ZE UniChem eMolecules 476793
5ZE UniChem PubChem 13021
5ZE UniChem Mcule MCULE-4633571562
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
5ZE C1 2.484 -1.071 0.491 ETKDGv3 1
5ZE C2 1.093 -0.593 0.223 ETKDGv3 2
5ZE C3 0.848 0.705 -0.006 ETKDGv3 3
5ZE C4 -0.543 1.129 -0.265 ETKDGv3 4
5ZE C5 -0.863 2.571 -0.489 ETKDGv3 5
5ZE N6 -1.499 0.245 -0.243 ETKDGv3 6
5ZE C7 -1.220 -1.143 0.002 ETKDGv3 7
5ZE N8 -2.283 -2.093 0.008 ETKDGv3 8
5ZE N9 0.003 -1.531 0.221 ETKDGv3 9
5ZE H1 2.493 -2.173 0.627 ETKDGv3 10
5ZE H2 2.875 -0.595 1.415 ETKDGv3 11
5ZE H3 3.145 -0.813 -0.364 ETKDGv3 12
5ZE H4 1.651 1.433 -0.004 ETKDGv3 13
5ZE H5 -1.864 2.682 -0.958 ETKDGv3 14
5ZE H6 -0.106 3.029 -1.160 ETKDGv3 15
5ZE H7 -0.859 3.106 0.484 ETKDGv3 16
5ZE H8 -3.265 -1.784 -0.167 ETKDGv3 17
5ZE H9 -2.091 -3.104 0.186 ETKDGv3 18
#