data_QRO
#
_chem_comp.id QRO
_chem_comp.name "5-[2-(3,4-difluorophenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H10 F2 N2 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-11-29
_chem_comp.pdbx_modified_date 2013-11-29
_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 296.226
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code QRO
_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 3W2J
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
QRO OAA OAA O 0 1 N N N N N N -6.077 -15.792 14.200 0.551 2.080 0.310 OAA QRO 1
QRO CAN CAN C 0 1 N N N N N N -5.255 -14.840 14.269 1.760 2.064 0.196 CAN QRO 2
QRO OAD OAD O 0 1 N N N N N N -4.028 -14.839 14.394 2.446 3.222 0.140 OAD QRO 3
QRO CAR CAR C 0 1 N N N N N N -5.889 -13.468 14.196 2.480 0.771 0.126 CAR QRO 4
QRO NAL NAL N 0 1 N N N N N N -5.436 -12.574 15.208 3.835 0.743 -0.127 NAL QRO 5
QRO CAT CAT C 0 1 N N N N N N -5.801 -11.260 15.181 4.506 -0.419 -0.195 CAT QRO 6
QRO OAB OAB O 0 1 N N N N N N -5.431 -10.506 16.121 5.701 -0.400 -0.419 OAB QRO 7
QRO NAM NAM N 0 1 N N N N N N -6.638 -10.828 14.216 3.892 -1.602 -0.020 NAM QRO 8
QRO CAU CAU C 0 1 N N N N N N -7.135 -11.659 13.212 2.567 -1.654 0.231 CAU QRO 9
QRO OAC OAC O 0 1 N N N N N N -7.831 -11.123 12.357 2.008 -2.723 0.389 OAC QRO 10
QRO CAS CAS C 0 1 N N N N N N -6.678 -12.980 13.168 1.813 -0.397 0.315 CAS QRO 11
QRO CAK CAK C 0 1 N N N N N N -7.047 -13.880 12.035 0.332 -0.403 0.594 CAK QRO 12
QRO CAJ CAJ C 0 1 N N N N N N -6.389 -13.444 10.729 -0.435 -0.517 -0.725 CAJ QRO 13
QRO CAO CAO C 0 1 Y N N N N N -5.061 -13.451 10.796 -1.916 -0.523 -0.446 CAO QRO 14
QRO CAI CAI C 0 1 Y N N N N N -4.327 -12.274 10.981 -2.616 0.669 -0.409 CAI QRO 15
QRO CAQ CAQ C 0 1 Y N N N N N -2.920 -12.310 11.105 -3.976 0.664 -0.153 CAQ QRO 16
QRO FAF FAF F 0 1 N N N N N N -2.228 -11.203 11.372 -4.661 1.827 -0.117 FAF QRO 17
QRO CAP CAP C 0 1 Y N N N N N -2.205 -13.452 11.033 -4.635 -0.537 0.065 CAP QRO 18
QRO FAE FAE F 0 1 N N N N N N -0.791 -13.434 11.118 -5.963 -0.544 0.314 FAE QRO 19
QRO CAH CAH C 0 1 Y N N N N N -2.891 -14.646 10.815 -3.931 -1.728 0.026 CAH QRO 20
QRO CAG CAG C 0 1 Y N N N N N -4.297 -14.645 10.678 -2.574 -1.720 -0.234 CAG QRO 21
QRO H1 H1 H 0 1 N N N N N N -3.713 -15.734 14.440 1.933 4.039 0.194 H1 QRO 22
QRO H2 H2 H 0 1 N N N N N N -6.915 -9.867 14.220 4.404 -2.424 -0.076 H2 QRO 23
QRO H4 H4 H 0 1 N N N N N N -8.139 -13.862 11.907 0.086 -1.252 1.232 H4 QRO 24
QRO H5 H5 H 0 1 N N N N N N -6.723 -14.904 12.273 0.053 0.522 1.098 H5 QRO 25
QRO H6 H6 H 0 1 N N N N N N -6.724 -12.424 10.490 -0.189 0.332 -1.363 H6 QRO 26
QRO H7 H7 H 0 1 N N N N N N -6.705 -14.131 9.930 -0.156 -1.442 -1.229 H7 QRO 27
QRO H8 H8 H 0 1 N N N N N N -4.842 -11.326 11.030 -2.102 1.603 -0.578 H8 QRO 28
QRO H9 H9 H 0 1 N N N N N N -2.345 -15.576 10.751 -4.443 -2.663 0.196 H9 QRO 29
QRO H10 H10 H 0 1 N N N N N N -4.806 -15.576 10.478 -2.026 -2.650 -0.268 H10 QRO 30
QRO H11 H11 H 0 1 N N N N N N -4.847 -12.912 15.942 4.313 1.577 -0.259 H11 QRO 31
#
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
QRO CAG CAO DOUB Y N 1
QRO CAG CAH SING Y N 2
QRO CAJ CAO SING N N 3
QRO CAJ CAK SING N N 4
QRO CAO CAI SING Y N 5
QRO CAH CAP DOUB Y N 6
QRO CAI CAQ DOUB Y N 7
QRO CAP CAQ SING Y N 8
QRO CAP FAE SING N N 9
QRO CAQ FAF SING N N 10
QRO CAK CAS SING N N 11
QRO OAC CAU DOUB N N 12
QRO CAS CAU SING N N 13
QRO CAS CAR DOUB N N 14
QRO CAU NAM SING N N 15
QRO CAR CAN SING N N 16
QRO CAR NAL SING N N 17
QRO OAA CAN DOUB N N 18
QRO NAM CAT SING N N 19
QRO CAN OAD SING N N 20
QRO CAT NAL SING N N 21
QRO CAT OAB DOUB N N 22
QRO OAD H1 SING N N 23
QRO NAM H2 SING N N 24
QRO CAK H4 SING N N 25
QRO CAK H5 SING N N 26
QRO CAJ H6 SING N N 27
QRO CAJ H7 SING N N 28
QRO CAI H8 SING N N 29
QRO CAH H9 SING N N 30
QRO CAG H10 SING N N 31
QRO NAL H11 SING N N 32
#
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
QRO SMILES ACDLabs 12.01 O=C1NC(C(=O)O)=C(C(=O)N1)CCc2ccc(F)c(F)c2
QRO InChI InChI 1.03 InChI=1S/C13H10F2N2O4/c14-8-4-2-6(5-9(8)15)1-3-7-10(12(19)20)16-13(21)17-11(7)18/h2,4-5H,1,3H2,(H,19,20)(H2,16,17,18,21)
QRO InChIKey InChI 1.03 KTXYBNZQKHWXBC-UHFFFAOYSA-N
QRO SMILES_CANONICAL CACTVS 3.370 OC(=O)C1=C(CCc2ccc(F)c(F)c2)C(=O)NC(=O)N1
QRO SMILES CACTVS 3.370 OC(=O)C1=C(CCc2ccc(F)c(F)c2)C(=O)NC(=O)N1
QRO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cc(c(cc1CCC2=C(NC(=O)NC2=O)C(=O)O)F)F
QRO SMILES "OpenEye OEToolkits" 1.7.6 c1cc(c(cc1CCC2=C(NC(=O)NC2=O)C(=O)O)F)F
#
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
QRO "SYSTEMATIC NAME" ACDLabs 12.01 "5-[2-(3,4-difluorophenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid"
QRO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-[2-[3,4-bis(fluoranyl)phenyl]ethyl]-2,4-bis(oxidanylidene)-1H-pyrimidine-6-carboxylic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
QRO 'Create component' 2012-11-29 PDBJ
QRO 'Initial release' 2013-12-04 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
QRO OAA O 8.196 -5.018 1
QRO CAN C 8.196 -3.518 2
QRO OAD O 6.897 -2.768 3
QRO CAR C 9.495 -2.768 4
QRO NAL N 10.794 -3.518 5
QRO CAT C 12.093 -2.768 6
QRO OAB O 13.392 -3.518 7
QRO NAM N 12.093 -1.268 8
QRO CAU C 10.794 -0.517 9
QRO OAC O 10.794 0.983 10
QRO CAS C 9.495 -1.268 11
QRO CAK C 8.196 -0.517 12
QRO CAJ C 8.196 0.983 13
QRO CAO C 6.897 1.732 14
QRO CAI C 6.897 3.232 15
QRO CAQ C 5.598 3.982 16
QRO FAF F 5.598 5.482 17
QRO CAP C 4.299 3.232 18
QRO FAE F 3.000 3.982 19
QRO CAH C 4.299 1.732 20
QRO CAG C 5.598 0.983 21
#
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
QRO CAG CAO SINGLE NONE 1
QRO CAG CAH DOUBLE NONE 2
QRO CAJ CAO SINGLE NONE 3
QRO CAJ CAK SINGLE NONE 4
QRO CAO CAI DOUBLE NONE 5
QRO CAH CAP SINGLE NONE 6
QRO CAI CAQ SINGLE NONE 7
QRO CAP CAQ DOUBLE NONE 8
QRO CAP FAE SINGLE NONE 9
QRO CAQ FAF SINGLE NONE 10
QRO CAK CAS SINGLE NONE 11
QRO OAC CAU DOUBLE NONE 12
QRO CAS CAU SINGLE NONE 13
QRO CAS CAR DOUBLE NONE 14
QRO CAU NAM SINGLE NONE 15
QRO CAR CAN SINGLE NONE 16
QRO CAR NAL SINGLE NONE 17
QRO OAA CAN DOUBLE NONE 18
QRO NAM CAT SINGLE NONE 19
QRO CAN OAD SINGLE NONE 20
QRO CAT NAL SINGLE NONE 21
QRO CAT OAB DOUBLE NONE 22
#
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
QRO MurckoScaffold S1 scaffold 'O=c1[nH]cc(CCc2ccccc2)c(=O)[nH]1' InChI=1S/C12H12N2O2/c15-11-10(8-13-12(16)14-11)7-6-9-4-2-1-3-5-9/h1-5,8H,6-7H2,(H2,13,14,15,16) JIXBEKSHVUECRD-UHFFFAOYSA-N
QRO phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
QRO pyrimidine F2 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
QRO CAR S1 1
QRO NAL S1 1
QRO CAT S1 1
QRO OAB S1 1
QRO NAM S1 1
QRO CAU S1 1
QRO OAC S1 1
QRO CAS S1 1
QRO CAK S1 1
QRO CAJ S1 1
QRO CAO S1 1
QRO CAI S1 1
QRO CAQ S1 1
QRO CAP S1 1
QRO CAH S1 1
QRO CAG S1 1
QRO CAO F1 1
QRO CAG F1 1
QRO CAH F1 1
QRO CAP F1 1
QRO CAQ F1 1
QRO CAI F1 1
QRO CAS F2 1
QRO CAU F2 1
QRO NAM F2 1
QRO CAT F2 1
QRO NAL F2 1
QRO CAR F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id QRO
_pdbe_chem_comp_rdkit_properties.exactmw 296.061
_pdbe_chem_comp_rdkit_properties.amw 296.229
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.154
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 129.885
_pdbe_chem_comp_rdkit_properties.tpsa 103.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.460
_pdbe_chem_comp_rdkit_properties.CrippenMR 67.827
_pdbe_chem_comp_rdkit_properties.chi0v 9.783
_pdbe_chem_comp_rdkit_properties.chi1v 5.089
_pdbe_chem_comp_rdkit_properties.chi2v 2.086
_pdbe_chem_comp_rdkit_properties.chi3v 2.086
_pdbe_chem_comp_rdkit_properties.chi4v 1.237
_pdbe_chem_comp_rdkit_properties.chi0n 19.783
_pdbe_chem_comp_rdkit_properties.chi1n 9.892
_pdbe_chem_comp_rdkit_properties.chi2n 2.086
_pdbe_chem_comp_rdkit_properties.chi3n 2.086
_pdbe_chem_comp_rdkit_properties.chi4n 1.237
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.770
_pdbe_chem_comp_rdkit_properties.kappa1 6.334
_pdbe_chem_comp_rdkit_properties.kappa2 5.695
_pdbe_chem_comp_rdkit_properties.kappa3 3.220
_pdbe_chem_comp_rdkit_properties.Phi 1.718
#
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
QRO UniChem ChEMBL CHEMBL3991402
QRO UniChem PDBe QRO
QRO UniChem ZINC ZINC000095920675
QRO UniChem PubChem 72187565
QRO UniChem BindingDb 50211961
#
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
QRO OAA -3.048 0.399 -2.357 ETKDGv3 1
QRO CAN -2.825 0.698 -1.153 ETKDGv3 2
QRO OAD -3.250 1.933 -0.673 ETKDGv3 3
QRO CAR -2.179 -0.297 -0.264 ETKDGv3 4
QRO NAL -2.530 -1.678 -0.478 ETKDGv3 5
QRO CAT -1.957 -2.726 0.302 ETKDGv3 6
QRO OAB -2.285 -3.925 0.098 ETKDGv3 7
QRO NAM -1.010 -2.404 1.313 ETKDGv3 8
QRO CAU -0.647 -1.039 1.517 ETKDGv3 9
QRO OAC 0.212 -0.761 2.397 ETKDGv3 10
QRO CAS -1.266 0.040 0.693 ETKDGv3 11
QRO CAK -0.751 1.461 0.879 ETKDGv3 12
QRO CAJ 0.189 1.897 -0.255 ETKDGv3 13
QRO CAO 1.419 1.028 -0.321 ETKDGv3 14
QRO CAI 1.481 -0.014 -1.171 ETKDGv3 15
QRO CAQ 2.668 -0.895 -1.185 ETKDGv3 16
QRO FAF 2.720 -1.939 -2.049 ETKDGv3 17
QRO CAP 3.684 -0.664 -0.343 ETKDGv3 18
QRO FAE 4.774 -1.471 -0.350 ETKDGv3 19
QRO CAH 3.618 0.471 0.600 ETKDGv3 20
QRO CAG 2.546 1.273 0.612 ETKDGv3 21
QRO H1 -3.706 2.600 -1.283 ETKDGv3 22
QRO H2 -0.578 -3.159 1.891 ETKDGv3 23
QRO H4 -0.208 1.562 1.843 ETKDGv3 24
QRO H5 -1.589 2.178 0.974 ETKDGv3 25
QRO H6 -0.347 1.891 -1.228 ETKDGv3 26
QRO H7 0.501 2.949 -0.074 ETKDGv3 27
QRO H8 0.659 -0.229 -1.843 ETKDGv3 28
QRO H9 4.438 0.652 1.283 ETKDGv3 29
QRO H10 2.502 2.099 1.311 ETKDGv3 30
QRO H11 -3.233 -1.930 -1.209 ETKDGv3 31
#