data_PW7
#
_chem_comp.id PW7
_chem_comp.name 4-(trifluoromethyl)pyrimidin-2-amine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H4 F3 N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-08-27
_chem_comp.pdbx_modified_date 2019-12-20
_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 163.101
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PW7
_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 5QTL
_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
PW7 N1 N1 N 0 1 N N N N N N -4.500 -0.275 2.487 -2.964 1.496 0.000 N1 PW7 1
PW7 C4 C1 C 0 1 Y N N N N N -2.113 2.570 4.210 -0.237 -1.513 0.000 C4 PW7 2
PW7 N N2 N 0 1 Y N N N N N -3.853 1.954 2.542 -0.743 0.767 -0.005 N PW7 3
PW7 C C2 C 0 1 N N N N N N -3.092 4.298 2.700 1.637 0.158 0.000 C PW7 4
PW7 C1 C3 C 0 1 Y N N N N N -3.016 2.847 3.171 0.171 -0.189 -0.002 C1 PW7 5
PW7 C2 C4 C 0 1 Y N N N N N -3.750 0.693 3.079 -2.034 0.470 0.004 C2 PW7 6
PW7 C3 C5 C 0 1 Y N N N N N -2.124 1.252 4.636 -1.595 -1.789 -0.002 C3 PW7 7
PW7 F F1 F 0 1 N N N N N N -2.291 4.530 1.708 2.221 -0.280 -1.193 F PW7 8
PW7 F1 F2 F 0 1 N N N N N N -2.755 5.191 3.635 1.789 1.544 0.113 F1 PW7 9
PW7 F2 F3 F 0 1 N N N N N N -4.302 4.680 2.321 2.263 -0.469 1.083 F2 PW7 10
PW7 N2 N3 N 0 1 Y N N N N N -2.910 0.335 4.125 -2.457 -0.785 0.001 N2 PW7 11
PW7 H1 H1 H 0 1 N N N N N N -5.019 0.121 1.729 -2.667 2.419 -0.009 H1 PW7 12
PW7 H2 H2 H 0 1 N N N N N N -3.900 -0.995 2.139 -3.912 1.291 0.003 H2 PW7 13
PW7 H3 H3 H 0 1 N N N N N N -1.466 3.320 4.640 0.488 -2.314 -0.002 H3 PW7 14
PW7 H4 H4 H 0 1 N N N N N N -1.451 0.965 5.430 -1.946 -2.810 -0.005 H4 PW7 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
PW7 F C SING N N 1
PW7 F2 C SING N N 2
PW7 N1 C2 SING N N 3
PW7 N C2 DOUB Y N 4
PW7 N C1 SING Y N 5
PW7 C C1 SING N N 6
PW7 C F1 SING N N 7
PW7 C2 N2 SING Y N 8
PW7 C1 C4 DOUB Y N 9
PW7 N2 C3 DOUB Y N 10
PW7 C4 C3 SING Y N 11
PW7 N1 H1 SING N N 12
PW7 N1 H2 SING N N 13
PW7 C4 H3 SING N N 14
PW7 C3 H4 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
PW7 SMILES ACDLabs 12.01 Nc1nc(ccn1)C(F)(F)F
PW7 InChI InChI 1.03 InChI=1S/C5H4F3N3/c6-5(7,8)3-1-2-10-4(9)11-3/h1-2H,(H2,9,10,11)
PW7 InChIKey InChI 1.03 NKOTXYPTXKUCDL-UHFFFAOYSA-N
PW7 SMILES_CANONICAL CACTVS 3.385 Nc1nccc(n1)C(F)(F)F
PW7 SMILES CACTVS 3.385 Nc1nccc(n1)C(F)(F)F
PW7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1cnc(nc1C(F)(F)F)N
PW7 SMILES "OpenEye OEToolkits" 2.0.6 c1cnc(nc1C(F)(F)F)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
PW7 "SYSTEMATIC NAME" ACDLabs 12.01 4-(trifluoromethyl)pyrimidin-2-amine
PW7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 4-(trifluoromethyl)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
PW7 'Create component' 2019-08-27 RCSB
PW7 'Initial release' 2019-12-25 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
PW7 N1 N 9.495 -0.851 1
PW7 C4 C 5.598 1.399 2
PW7 N N 6.897 -0.851 3
PW7 C C 4.299 -0.851 4
PW7 C1 C 5.598 -0.101 5
PW7 C2 C 8.196 -0.101 6
PW7 C3 C 6.897 2.150 7
PW7 F F 3.000 -1.601 8
PW7 F1 F 5.049 -2.150 9
PW7 F2 F 3.549 0.449 10
PW7 N2 N 8.196 1.399 11
#
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
PW7 F C SINGLE NONE 1
PW7 F2 C SINGLE NONE 2
PW7 N1 C2 SINGLE NONE 3
PW7 N C2 DOUBLE NONE 4
PW7 N C1 SINGLE NONE 5
PW7 C C1 SINGLE NONE 6
PW7 C F1 SINGLE NONE 7
PW7 C2 N2 SINGLE NONE 8
PW7 C1 C4 DOUBLE NONE 9
PW7 N2 C3 DOUBLE NONE 10
PW7 C4 C3 SINGLE NONE 11
#
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
PW7 MurckoScaffold S1 scaffold c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
PW7 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
PW7 C4 S1 1
PW7 N S1 1
PW7 C1 S1 1
PW7 C2 S1 1
PW7 C3 S1 1
PW7 N2 S1 1
PW7 C4 F1 1
PW7 C1 F1 1
PW7 N F1 1
PW7 C2 F1 1
PW7 N2 F1 1
PW7 C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PW7
_pdbe_chem_comp_rdkit_properties.exactmw 163.036
_pdbe_chem_comp_rdkit_properties.amw 163.102
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 65.808
_pdbe_chem_comp_rdkit_properties.tpsa 51.800
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.642
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.356
_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 0.418
_pdbe_chem_comp_rdkit_properties.chi0n 8.976
_pdbe_chem_comp_rdkit_properties.chi1n 4.329
_pdbe_chem_comp_rdkit_properties.chi2n 0.811
_pdbe_chem_comp_rdkit_properties.chi3n 0.811
_pdbe_chem_comp_rdkit_properties.chi4n 0.418
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.330
_pdbe_chem_comp_rdkit_properties.kappa1 3.890
_pdbe_chem_comp_rdkit_properties.kappa2 2.370
_pdbe_chem_comp_rdkit_properties.kappa3 1.792
_pdbe_chem_comp_rdkit_properties.Phi 0.838
#
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
PW7 UniChem PDBe PW7
PW7 UniChem ZINC ZINC000001023366
PW7 UniChem 'EPA CompTox Dashboard' DTXSID80344318
PW7 UniChem ChemicalBook CB8397302
PW7 UniChem eMolecules 861131
PW7 UniChem SureChEMBL SCHEMBL345262
PW7 UniChem 'PubChem TPHARMA' 15586162
PW7 UniChem PubChem 595915
PW7 UniChem Mcule MCULE-9954972855
PW7 UniChem ACTor 16075-42-6
PW7 UniChem Nikkaji J101.492G
#
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
PW7 N1 -2.672 -1.069 0.365 ETKDGv3 1
PW7 C4 0.850 1.200 0.096 ETKDGv3 2
PW7 N -0.369 -0.857 -0.124 ETKDGv3 3
PW7 C 2.112 -0.776 -0.688 ETKDGv3 4
PW7 C1 0.853 -0.103 -0.226 ETKDGv3 5
PW7 C2 -1.476 -0.299 0.274 ETKDGv3 6
PW7 C3 -0.411 1.814 0.544 ETKDGv3 7
PW7 F 2.576 -0.161 -1.838 ETKDGv3 8
PW7 F1 3.079 -0.687 0.298 ETKDGv3 9
PW7 F2 1.872 -2.111 -0.961 ETKDGv3 10
PW7 N2 -1.492 1.096 0.621 ETKDGv3 11
PW7 H1 -3.561 -0.624 0.684 ETKDGv3 12
PW7 H2 -2.671 -2.083 0.115 ETKDGv3 13
PW7 H3 1.751 1.798 0.031 ETKDGv3 14
PW7 H4 -0.440 2.862 0.809 ETKDGv3 15
#