data_DU7
#
_chem_comp.id DU7
_chem_comp.name 4-chloro-6-methylpyrimidin-2-amine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H6 Cl N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-11-06
_chem_comp.pdbx_modified_date 2018-11-02
_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 143.574
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DU7
_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 6BJ7
_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
DU7 C4 C1 C 0 1 Y N N N N N -3.461 28.214 54.688 -1.047 -1.177 -0.002 C4 DU7 1
DU7 C3 C2 C 0 1 Y N N N N N -1.310 27.757 55.012 0.908 0.038 -0.001 C3 DU7 2
DU7 C2 C3 C 0 1 Y N N N N N -1.409 26.484 54.580 0.166 1.210 -0.004 C2 DU7 3
DU7 C1 C4 C 0 1 Y N N N N N -2.616 26.111 54.178 -1.217 1.118 -0.001 C1 DU7 4
DU7 CL CL1 CL 0 0 N N N N N N 0.185 28.260 55.571 2.643 0.096 0.001 CL DU7 5
DU7 N N1 N 0 1 Y N N N N N -2.248 28.654 55.095 0.276 -1.126 0.000 N DU7 6
DU7 N1 N2 N 0 1 N N N N N N -4.539 29.129 54.758 -1.675 -2.411 0.001 N1 DU7 7
DU7 N2 N3 N 0 1 Y N N N N N -3.603 26.955 54.228 -1.785 -0.076 0.001 N2 DU7 8
DU7 C C5 C 0 1 N N N N N N -2.840 24.698 53.653 -2.064 2.365 0.002 C DU7 9
DU7 H3 H1 H 0 1 N N N N N N -0.563 25.813 54.563 0.655 2.173 -0.005 H3 DU7 10
DU7 H5 H2 H 0 1 N N N N N N -5.372 28.690 54.422 -1.147 -3.224 0.003 H5 DU7 11
DU7 H4 H3 H 0 1 N N N N N N -4.672 29.415 55.707 -2.644 -2.462 -0.001 H4 DU7 12
DU7 H2 H4 H 0 1 N N N N N N -3.894 24.576 53.364 -2.265 2.665 1.031 H2 DU7 13
DU7 H1 H5 H 0 1 N N N N N N -2.198 24.527 52.776 -1.533 3.166 -0.513 H1 DU7 14
DU7 H H6 H 0 1 N N N N N N -2.589 23.971 54.439 -3.006 2.166 -0.509 H DU7 15
#
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
DU7 C C1 SING N N 1
DU7 C1 N2 DOUB Y N 2
DU7 C1 C2 SING Y N 3
DU7 N2 C4 SING Y N 4
DU7 C2 C3 DOUB Y N 5
DU7 C4 N1 SING N N 6
DU7 C4 N DOUB Y N 7
DU7 C3 N SING Y N 8
DU7 C3 CL SING N N 9
DU7 C2 H3 SING N N 10
DU7 N1 H5 SING N N 11
DU7 N1 H4 SING N N 12
DU7 C H2 SING N N 13
DU7 C H1 SING N N 14
DU7 C H SING N N 15
#
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
DU7 SMILES ACDLabs 12.01 c1(N)nc(Cl)cc(n1)C
DU7 InChI InChI 1.03 InChI=1S/C5H6ClN3/c1-3-2-4(6)9-5(7)8-3/h2H,1H3,(H2,7,8,9)
DU7 InChIKey InChI 1.03 NPTGVVKPLWFPPX-UHFFFAOYSA-N
DU7 SMILES_CANONICAL CACTVS 3.385 Cc1cc(Cl)nc(N)n1
DU7 SMILES CACTVS 3.385 Cc1cc(Cl)nc(N)n1
DU7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 Cc1cc(nc(n1)N)Cl
DU7 SMILES "OpenEye OEToolkits" 2.0.6 Cc1cc(nc(n1)N)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
DU7 "SYSTEMATIC NAME" ACDLabs 12.01 4-chloro-6-methylpyrimidin-2-amine
DU7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 4-chloranyl-6-methyl-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
DU7 'Create component' 2017-11-06 RCSB
DU7 'Initial release' 2018-11-07 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
DU7 C4 C 4.299 -1.035 1
DU7 C3 C 5.598 1.215 2
DU7 C2 C 6.897 0.465 3
DU7 C1 C 6.897 -1.035 4
DU7 CL Cl 5.598 2.715 5
DU7 N N 4.299 0.465 6
DU7 N1 N 3.000 -1.785 7
DU7 N2 N 5.598 -1.785 8
DU7 C C 8.196 -1.785 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
DU7 C C1 SINGLE NONE 1
DU7 C1 N2 SINGLE NONE 2
DU7 C1 C2 DOUBLE NONE 3
DU7 N2 C4 DOUBLE NONE 4
DU7 C2 C3 SINGLE NONE 5
DU7 C4 N1 SINGLE NONE 6
DU7 C4 N SINGLE NONE 7
DU7 C3 N DOUBLE NONE 8
DU7 C3 CL 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
DU7 MurckoScaffold S1 scaffold c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
DU7 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
DU7 C4 S1 1
DU7 C3 S1 1
DU7 C2 S1 1
DU7 C1 S1 1
DU7 N S1 1
DU7 N2 S1 1
DU7 C2 F1 1
DU7 C1 F1 1
DU7 N2 F1 1
DU7 C4 F1 1
DU7 N F1 1
DU7 C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DU7
_pdbe_chem_comp_rdkit_properties.exactmw 143.025
_pdbe_chem_comp_rdkit_properties.amw 143.577
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_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 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_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 66.425
_pdbe_chem_comp_rdkit_properties.tpsa 51.800
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.585
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.101
_pdbe_chem_comp_rdkit_properties.chi0v 4.976
_pdbe_chem_comp_rdkit_properties.chi1v 2.435
_pdbe_chem_comp_rdkit_properties.chi2v 0.811
_pdbe_chem_comp_rdkit_properties.chi3v 0.811
_pdbe_chem_comp_rdkit_properties.chi4v 0.531
_pdbe_chem_comp_rdkit_properties.chi0n 10.220
_pdbe_chem_comp_rdkit_properties.chi1n 4.951
_pdbe_chem_comp_rdkit_properties.chi2n 0.632
_pdbe_chem_comp_rdkit_properties.chi3n 0.632
_pdbe_chem_comp_rdkit_properties.chi4n 0.366
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.830
_pdbe_chem_comp_rdkit_properties.kappa1 2.092
_pdbe_chem_comp_rdkit_properties.kappa2 2.188
_pdbe_chem_comp_rdkit_properties.kappa3 1.536
_pdbe_chem_comp_rdkit_properties.Phi 0.508
#
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
DU7 UniChem ChEBI 58960
DU7 UniChem ZINC ZINC000000039463
DU7 UniChem eMolecules 479622
DU7 UniChem fdasrs 8ZBB1FM476
DU7 UniChem Nikkaji J616E
DU7 UniChem BindingDb 47756
DU7 UniChem 'EPA CompTox Dashboard' DTXSID5022229
DU7 UniChem ChemicalBook CB2458081
DU7 UniChem CCDC ACMPYR
DU7 UniChem ACTor 5600-21-5
DU7 UniChem SureChEMBL SCHEMBL150686
DU7 UniChem 'PubChem TPHARMA' 16659433
DU7 UniChem PubChem 21810
DU7 UniChem Mcule MCULE-1686570214
#
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
DU7 C4 1.472 -0.353 0.145 ETKDGv3 1
DU7 C3 0.446 1.779 0.421 ETKDGv3 2
DU7 C2 -0.853 1.159 0.106 ETKDGv3 3
DU7 C1 -0.888 -0.154 -0.161 ETKDGv3 4
DU7 CL 0.542 3.491 0.777 ETKDGv3 5
DU7 N 1.525 1.054 0.434 ETKDGv3 6
DU7 N1 2.667 -1.130 0.165 ETKDGv3 7
DU7 N2 0.332 -0.917 -0.134 ETKDGv3 8
DU7 C -2.181 -0.833 -0.486 ETKDGv3 9
DU7 H3 -1.756 1.757 0.093 ETKDGv3 10
DU7 H5 2.639 -2.153 -0.043 ETKDGv3 11
DU7 H4 3.582 -0.681 0.389 ETKDGv3 12
DU7 H2 -2.629 -0.377 -1.394 ETKDGv3 13
DU7 H1 -2.887 -0.728 0.365 ETKDGv3 14
DU7 H -2.011 -1.913 -0.677 ETKDGv3 15
#