data_VQB
#
_chem_comp.id VQB
_chem_comp.name 4-chloro-6-(pyrrolidin-1-yl)pyrimidin-5-amine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H11 Cl N4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-02
_chem_comp.pdbx_modified_date 2022-10-28
_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 198.653
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VQB
_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 7FKS
_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
VQB N1 N1 N 0 1 Y N N N N N 0.767 12.866 -35.560 1.952 -1.513 -0.261 N1 VQB 1
VQB C7 C1 C 0 1 N N N N N N -3.458 15.343 -34.612 -2.718 -0.798 0.609 C7 VQB 2
VQB N2 N2 N 0 1 N N N N N N -2.625 12.638 -34.392 0.684 1.808 0.460 N2 VQB 3
VQB C1 C2 C 0 1 Y N N N N N -1.161 14.623 -34.756 -0.420 -0.360 0.303 C1 VQB 4
VQB C5 C3 C 0 1 N N N N N N -2.998 17.708 -34.239 -3.538 1.174 -0.536 C5 VQB 5
VQB C6 C4 C 0 1 N N N N N N -4.059 16.618 -34.020 -3.787 -0.353 -0.412 C6 VQB 6
VQB N3 N3 N 0 1 N N N N N N -2.075 15.531 -34.213 -1.649 0.217 0.592 N3 VQB 7
VQB C4 C5 C 0 1 N N N N N N -1.712 16.952 -34.461 -1.996 1.251 -0.406 C4 VQB 8
VQB C3 C6 C 0 1 Y N N N N N -0.408 12.460 -35.174 1.941 -0.202 -0.056 C3 VQB 9
VQB C2 C7 C 0 1 Y N N N N N -1.473 13.234 -34.760 0.739 0.426 0.237 C2 VQB 10
VQB CL CL1 CL 0 0 N N N N N N -0.701 10.825 -35.152 3.412 0.715 -0.152 CL VQB 11
VQB C C8 C 0 1 Y N N N N N 0.929 14.168 -35.536 0.843 -2.220 -0.190 C VQB 12
VQB N N4 N 0 1 Y N N N N N -0.004 15.061 -35.134 -0.322 -1.667 0.084 N VQB 13
VQB H1 H1 H 0 1 N N N N N N -3.569 15.305 -35.706 -3.158 -0.856 1.604 H1 VQB 14
VQB H2 H2 H 0 1 N N N N N N -3.895 14.437 -34.167 -2.313 -1.768 0.322 H2 VQB 15
VQB H3 H3 H 0 1 N N N N N N -3.290 13.335 -34.122 1.494 2.340 0.410 H3 VQB 16
VQB H4 H4 H 0 1 N N N N N N -2.988 12.111 -35.161 -0.164 2.233 0.663 H4 VQB 17
VQB H5 H5 H 0 1 N N N N N N -2.919 18.356 -33.354 -3.867 1.546 -1.506 H5 VQB 18
VQB H6 H6 H 0 1 N N N N N N -3.246 18.319 -35.120 -4.026 1.716 0.274 H6 VQB 19
VQB H7 H7 H 0 1 N N N N N N -4.993 16.880 -34.539 -3.632 -0.847 -1.372 H7 VQB 20
VQB H8 H8 H 0 1 N N N N N N -4.260 16.486 -32.947 -4.789 -0.550 -0.032 H8 VQB 21
VQB H9 H9 H 0 1 N N N N N N -1.352 17.088 -35.492 -1.523 1.029 -1.363 H9 VQB 22
VQB H10 H10 H 0 1 N N N N N N -0.937 17.285 -33.755 -1.694 2.237 -0.053 H10 VQB 23
VQB H11 H11 H 0 1 N N N N N N 1.882 14.557 -35.863 0.889 -3.285 -0.363 H11 VQB 24
#
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
VQB N1 C DOUB Y N 1
VQB N1 C3 SING Y N 2
VQB C N SING Y N 3
VQB C3 CL SING N N 4
VQB C3 C2 DOUB Y N 5
VQB N C1 DOUB Y N 6
VQB C2 C1 SING Y N 7
VQB C2 N2 SING N N 8
VQB C1 N3 SING N N 9
VQB C7 N3 SING N N 10
VQB C7 C6 SING N N 11
VQB C4 C5 SING N N 12
VQB C4 N3 SING N N 13
VQB C5 C6 SING N N 14
VQB C7 H1 SING N N 15
VQB C7 H2 SING N N 16
VQB N2 H3 SING N N 17
VQB N2 H4 SING N N 18
VQB C5 H5 SING N N 19
VQB C5 H6 SING N N 20
VQB C6 H7 SING N N 21
VQB C6 H8 SING N N 22
VQB C4 H9 SING N N 23
VQB C4 H10 SING N N 24
VQB C H11 SING N N 25
#
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
VQB SMILES ACDLabs 12.01 Nc1c(ncnc1Cl)N1CCCC1
VQB InChI InChI 1.06 InChI=1S/C8H11ClN4/c9-7-6(10)8(12-5-11-7)13-3-1-2-4-13/h5H,1-4,10H2
VQB InChIKey InChI 1.06 HGBSHFZMWYKLPY-UHFFFAOYSA-N
VQB SMILES_CANONICAL CACTVS 3.385 Nc1c(Cl)ncnc1N2CCCC2
VQB SMILES CACTVS 3.385 Nc1c(Cl)ncnc1N2CCCC2
VQB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1nc(c(c(n1)Cl)N)N2CCCC2
VQB SMILES "OpenEye OEToolkits" 2.0.7 c1nc(c(c(n1)Cl)N)N2CCCC2
#
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
VQB "SYSTEMATIC NAME" ACDLabs 12.01 4-chloro-6-(pyrrolidin-1-yl)pyrimidin-5-amine
VQB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 4-chloranyl-6-pyrrolidin-1-yl-pyrimidin-5-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
VQB 'Create component' 2022-09-02 RCSB
VQB 'Initial release' 2022-11-02 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
VQB N1 N 6.404 -3.404 1
VQB C7 C 7.617 1.978 2
VQB N2 N 3.805 -0.404 3
VQB C1 C 6.404 -0.404 4
VQB C5 C 5.654 3.404 5
VQB C6 C 7.154 3.404 6
VQB N3 N 6.404 1.096 7
VQB C4 C 5.190 1.978 8
VQB C3 C 5.104 -2.654 9
VQB C2 C 5.104 -1.154 10
VQB CL Cl 3.805 -3.404 11
VQB C C 7.702 -2.654 12
VQB N N 7.702 -1.154 13
#
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
VQB N1 C DOUBLE NONE 1
VQB N1 C3 SINGLE NONE 2
VQB C N SINGLE NONE 3
VQB C3 CL SINGLE NONE 4
VQB C3 C2 DOUBLE NONE 5
VQB N C1 DOUBLE NONE 6
VQB C2 C1 SINGLE NONE 7
VQB C2 N2 SINGLE NONE 8
VQB C1 N3 SINGLE NONE 9
VQB C7 N3 SINGLE NONE 10
VQB C7 C6 SINGLE NONE 11
VQB C4 C5 SINGLE NONE 12
VQB C4 N3 SINGLE NONE 13
VQB C5 C6 SINGLE NONE 14
#
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
VQB MurckoScaffold S1 scaffold c1cc(N2CCCC2)ncn1 InChI=1S/C8H11N3/c1-2-6-11(5-1)8-3-4-9-7-10-8/h3-4,7H,1-2,5-6H2 WZRAVWCMDRGDQR-UHFFFAOYSA-N
VQB 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
VQB N1 S1 1
VQB C7 S1 1
VQB C1 S1 1
VQB C5 S1 1
VQB C6 S1 1
VQB N3 S1 1
VQB C4 S1 1
VQB C3 S1 1
VQB C2 S1 1
VQB C S1 1
VQB N S1 1
VQB C2 F1 1
VQB C3 F1 1
VQB N1 F1 1
VQB C F1 1
VQB N F1 1
VQB C1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VQB
_pdbe_chem_comp_rdkit_properties.exactmw 198.067
_pdbe_chem_comp_rdkit_properties.amw 198.657
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 97.298
_pdbe_chem_comp_rdkit_properties.tpsa 55.040
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.551
_pdbe_chem_comp_rdkit_properties.CrippenMR 51.253
_pdbe_chem_comp_rdkit_properties.chi0v 6.923
_pdbe_chem_comp_rdkit_properties.chi1v 3.606
_pdbe_chem_comp_rdkit_properties.chi2v 1.585
_pdbe_chem_comp_rdkit_properties.chi3v 1.585
_pdbe_chem_comp_rdkit_properties.chi4v 0.894
_pdbe_chem_comp_rdkit_properties.chi0n 17.167
_pdbe_chem_comp_rdkit_properties.chi1n 8.622
_pdbe_chem_comp_rdkit_properties.chi2n 1.321
_pdbe_chem_comp_rdkit_properties.chi3n 1.321
_pdbe_chem_comp_rdkit_properties.chi4n 0.772
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.030
_pdbe_chem_comp_rdkit_properties.kappa1 2.507
_pdbe_chem_comp_rdkit_properties.kappa2 3.377
_pdbe_chem_comp_rdkit_properties.kappa3 1.536
_pdbe_chem_comp_rdkit_properties.Phi 0.651
#
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
VQB UniChem ChEMBL CHEMBL1905991
VQB UniChem PDBe VQB
VQB UniChem ZINC ZINC000000802036
VQB UniChem ACTor 626217-76-3
VQB UniChem 'EPA CompTox Dashboard' DTXSID90360165
VQB UniChem eMolecules 1483452
VQB UniChem PubChem 1085196
VQB UniChem Mcule MCULE-3345745545
#
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
VQB N1 3.502 1.385 0.062 ETKDGv3 1
VQB C7 -1.245 -0.098 1.185 ETKDGv3 2
VQB N2 1.660 -1.762 0.901 ETKDGv3 3
VQB C1 0.899 0.472 -0.030 ETKDGv3 4
VQB C5 -2.741 0.024 -0.728 ETKDGv3 5
VQB C6 -2.658 -0.430 0.728 ETKDGv3 6
VQB N3 -0.474 0.061 -0.034 ETKDGv3 7
VQB C4 -1.303 0.108 -1.225 ETKDGv3 8
VQB C3 3.223 0.066 0.558 ETKDGv3 9
VQB C2 1.963 -0.415 0.511 ETKDGv3 10
VQB CL 4.570 -0.888 1.163 ETKDGv3 11
VQB C 2.562 2.132 -0.436 ETKDGv3 12
VQB N 1.211 1.655 -0.476 ETKDGv3 13
VQB H1 -1.238 0.855 1.757 ETKDGv3 14
VQB H2 -0.836 -0.913 1.817 ETKDGv3 15
VQB H3 0.739 -2.191 0.663 ETKDGv3 16
VQB H4 2.359 -2.373 1.377 ETKDGv3 17
VQB H5 -3.340 -0.686 -1.339 ETKDGv3 18
VQB H6 -3.212 1.031 -0.776 ETKDGv3 19
VQB H7 -2.818 -1.529 0.782 ETKDGv3 20
VQB H8 -3.419 0.082 1.357 ETKDGv3 21
VQB H9 -1.139 1.055 -1.784 ETKDGv3 22
VQB H10 -1.061 -0.760 -1.877 ETKDGv3 23
VQB H11 2.797 3.120 -0.807 ETKDGv3 24
#