data_LRO
#
_chem_comp.id LRO
_chem_comp.name "5-[2-(4-methylphenyl)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 "C14 H14 N2 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-11-27
_chem_comp.pdbx_modified_date 2013-11-22
_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 274.272
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LRO
_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 3W1U
_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
LRO OAB OAB O 0 1 N N N N N N 5.028 17.295 14.551 -2.273 -3.196 0.111 OAB LRO 1
LRO CAN CAN C 0 1 N N N N N N 6.244 17.203 14.528 -1.515 -2.086 0.179 CAN LRO 2
LRO OAE OAE O 0 1 N N N N N N 6.951 18.207 14.492 -0.310 -2.179 0.289 OAE LRO 3
LRO CAQ CAQ C 0 1 N N N N N N 6.778 15.850 14.534 -2.152 -0.748 0.120 CAQ LRO 4
LRO NAL NAL N 0 1 N N N N N N 6.277 15.056 15.569 -3.503 -0.632 -0.128 NAL LRO 5
LRO CAS CAS C 0 1 N N N N N N 6.685 13.672 15.630 -4.098 0.571 -0.185 CAS LRO 6
LRO OAC OAC O 0 1 N N N N N N 6.235 12.934 16.504 -5.292 0.630 -0.407 OAC LRO 7
LRO NAM NAM N 0 1 N N N N N N 7.581 13.185 14.654 -3.409 1.711 -0.004 NAM LRO 8
LRO CAT CAT C 0 1 N N N N N N 8.081 14.005 13.614 -2.083 1.676 0.244 CAT LRO 9
LRO OAD OAD O 0 1 N N N N N N 8.877 13.506 12.775 -1.457 2.706 0.409 OAD LRO 10
LRO CAR CAR C 0 1 N N N N N N 7.672 15.379 13.581 -1.411 0.373 0.316 CAR LRO 11
LRO CAK CAK C 0 1 N N N N N N 8.147 16.218 12.562 0.068 0.283 0.590 CAK LRO 12
LRO CAJ CAJ C 0 1 N N N N N N 7.653 15.767 11.161 0.837 0.357 -0.730 CAJ LRO 13
LRO CAP CAP C 0 1 Y N N N N N 6.249 16.012 10.987 2.317 0.266 -0.456 CAP LRO 14
LRO CAH CAH C 0 1 Y N N N N N 5.363 14.907 11.146 2.940 -0.967 -0.429 CAH LRO 15
LRO CAF CAF C 0 1 Y N N N N N 3.938 14.928 11.013 4.297 -1.050 -0.177 CAF LRO 16
LRO CAO CAO C 0 1 Y N N N N N 3.354 16.152 10.697 5.030 0.100 0.048 CAO LRO 17
LRO CAA CAA C 0 1 N N N N N N 1.882 16.151 10.600 6.509 0.009 0.323 CAA LRO 18
LRO CAG CAG C 0 1 Y N N N N N 4.223 17.300 10.585 4.406 1.334 0.020 CAG LRO 19
LRO CAI CAI C 0 1 Y N N N N N 5.659 17.259 10.700 3.051 1.417 -0.237 CAI LRO 20
LRO H1 H1 H 0 1 N N N N N N 4.779 18.212 14.536 -1.813 -4.046 0.154 H1 LRO 21
LRO H2 H2 H 0 1 N N N N N N 7.872 12.229 14.699 -3.868 2.564 -0.052 H2 LRO 22
LRO H4 H4 H 0 1 N N N N N N 9.247 16.203 12.573 0.370 1.110 1.233 H4 LRO 23
LRO H5 H5 H 0 1 N N N N N N 7.793 17.242 12.751 0.289 -0.662 1.086 H5 LRO 24
LRO H6 H6 H 0 1 N N N N N N 7.844 14.690 11.046 0.536 -0.470 -1.373 H6 LRO 25
LRO H7 H7 H 0 1 N N N N N N 8.209 16.322 10.391 0.617 1.302 -1.226 H7 LRO 26
LRO H8 H8 H 0 1 N N N N N N 5.813 13.956 11.392 2.368 -1.866 -0.605 H8 LRO 27
LRO H9 H9 H 0 1 N N N N N N 3.344 14.037 11.151 4.784 -2.014 -0.156 H9 LRO 28
LRO H10 H10 H 0 1 N N N N N N 1.583 15.952 9.560 7.057 0.062 -0.617 H10 LRO 29
LRO H11 H11 H 0 1 N N N N N N 1.472 15.368 11.255 6.810 0.836 0.966 H11 LRO 30
LRO H12 H12 H 0 1 N N N N N N 1.493 17.132 10.912 6.729 -0.936 0.819 H12 LRO 31
LRO H13 H13 H 0 1 N N N N N N 3.763 18.260 10.402 4.979 2.232 0.196 H13 LRO 32
LRO H14 H14 H 0 1 N N N N N N 6.259 18.148 10.571 2.564 2.381 -0.259 H14 LRO 33
LRO H15 H15 H 0 1 N N N N N N 5.652 15.437 16.250 -4.033 -1.433 -0.264 H15 LRO 34
#
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
LRO CAG CAO DOUB Y N 1
LRO CAG CAI SING Y N 2
LRO CAA CAO SING N N 3
LRO CAO CAF SING Y N 4
LRO CAI CAP DOUB Y N 5
LRO CAP CAH SING Y N 6
LRO CAP CAJ SING N N 7
LRO CAF CAH DOUB Y N 8
LRO CAJ CAK SING N N 9
LRO CAK CAR SING N N 10
LRO OAD CAT DOUB N N 11
LRO CAR CAT SING N N 12
LRO CAR CAQ DOUB N N 13
LRO CAT NAM SING N N 14
LRO OAE CAN DOUB N N 15
LRO CAN CAQ SING N N 16
LRO CAN OAB SING N N 17
LRO CAQ NAL SING N N 18
LRO NAM CAS SING N N 19
LRO NAL CAS SING N N 20
LRO CAS OAC DOUB N N 21
LRO OAB H1 SING N N 22
LRO NAM H2 SING N N 23
LRO CAK H4 SING N N 24
LRO CAK H5 SING N N 25
LRO CAJ H6 SING N N 26
LRO CAJ H7 SING N N 27
LRO CAH H8 SING N N 28
LRO CAF H9 SING N N 29
LRO CAA H10 SING N N 30
LRO CAA H11 SING N N 31
LRO CAA H12 SING N N 32
LRO CAG H13 SING N N 33
LRO CAI H14 SING N N 34
LRO NAL H15 SING N N 35
#
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
LRO SMILES ACDLabs 12.01 O=C1NC(C(=O)O)=C(C(=O)N1)CCc2ccc(cc2)C
LRO InChI InChI 1.03 InChI=1S/C14H14N2O4/c1-8-2-4-9(5-3-8)6-7-10-11(13(18)19)15-14(20)16-12(10)17/h2-5H,6-7H2,1H3,(H,18,19)(H2,15,16,17,20)
LRO InChIKey InChI 1.03 BBNOPYKTLSUCSO-UHFFFAOYSA-N
LRO SMILES_CANONICAL CACTVS 3.370 Cc1ccc(CCC2=C(NC(=O)NC2=O)C(O)=O)cc1
LRO SMILES CACTVS 3.370 Cc1ccc(CCC2=C(NC(=O)NC2=O)C(O)=O)cc1
LRO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 Cc1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O
LRO SMILES "OpenEye OEToolkits" 1.7.6 Cc1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O
#
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
LRO "SYSTEMATIC NAME" ACDLabs 12.01 "5-[2-(4-methylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid"
LRO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-[2-(4-methylphenyl)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
LRO 'Create component' 2012-11-27 PDBJ
LRO 'Initial release' 2013-11-27 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
LRO OAB O 6.897 -2.018 1
LRO CAN C 8.196 -2.768 2
LRO OAE O 8.196 -4.268 3
LRO CAQ C 9.495 -2.018 4
LRO NAL N 10.794 -2.768 5
LRO CAS C 12.093 -2.018 6
LRO OAC O 13.392 -2.768 7
LRO NAM N 12.093 -0.517 8
LRO CAT C 10.794 0.233 9
LRO OAD O 10.794 1.732 10
LRO CAR C 9.495 -0.517 11
LRO CAK C 8.196 0.233 12
LRO CAJ C 8.196 1.732 13
LRO CAP C 6.897 2.482 14
LRO CAH C 5.598 1.732 15
LRO CAF C 4.299 2.482 16
LRO CAO C 4.299 3.982 17
LRO CAA C 3.000 4.732 18
LRO CAG C 5.598 4.732 19
LRO CAI C 6.897 3.982 20
#
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
LRO CAG CAO SINGLE NONE 1
LRO CAG CAI DOUBLE NONE 2
LRO CAA CAO SINGLE NONE 3
LRO CAO CAF DOUBLE NONE 4
LRO CAI CAP SINGLE NONE 5
LRO CAP CAH DOUBLE NONE 6
LRO CAP CAJ SINGLE NONE 7
LRO CAF CAH SINGLE NONE 8
LRO CAJ CAK SINGLE NONE 9
LRO CAK CAR SINGLE NONE 10
LRO OAD CAT DOUBLE NONE 11
LRO CAR CAT SINGLE NONE 12
LRO CAR CAQ DOUBLE NONE 13
LRO CAT NAM SINGLE NONE 14
LRO OAE CAN DOUBLE NONE 15
LRO CAN CAQ SINGLE NONE 16
LRO CAN OAB SINGLE NONE 17
LRO CAQ NAL SINGLE NONE 18
LRO NAM CAS SINGLE NONE 19
LRO NAL CAS SINGLE NONE 20
LRO CAS OAC DOUBLE NONE 21
#
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
LRO 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
LRO phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
LRO 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
LRO CAQ S1 1
LRO NAL S1 1
LRO CAS S1 1
LRO OAC S1 1
LRO NAM S1 1
LRO CAT S1 1
LRO OAD S1 1
LRO CAR S1 1
LRO CAK S1 1
LRO CAJ S1 1
LRO CAP S1 1
LRO CAH S1 1
LRO CAF S1 1
LRO CAO S1 1
LRO CAG S1 1
LRO CAI S1 1
LRO CAP F1 1
LRO CAI F1 1
LRO CAG F1 1
LRO CAO F1 1
LRO CAF F1 1
LRO CAH F1 1
LRO CAR F2 1
LRO CAT F2 1
LRO NAM F2 1
LRO CAS F2 1
LRO NAL F2 1
LRO CAQ F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LRO
_pdbe_chem_comp_rdkit_properties.exactmw 274.095
_pdbe_chem_comp_rdkit_properties.amw 274.276
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.214
_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 133.539
_pdbe_chem_comp_rdkit_properties.tpsa 103.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.436
_pdbe_chem_comp_rdkit_properties.CrippenMR 72.382
_pdbe_chem_comp_rdkit_properties.chi0v 9.527
_pdbe_chem_comp_rdkit_properties.chi1v 4.961
_pdbe_chem_comp_rdkit_properties.chi2v 1.986
_pdbe_chem_comp_rdkit_properties.chi3v 1.986
_pdbe_chem_comp_rdkit_properties.chi4v 1.181
_pdbe_chem_comp_rdkit_properties.chi0n 23.527
_pdbe_chem_comp_rdkit_properties.chi1n 11.764
_pdbe_chem_comp_rdkit_properties.chi2n 1.986
_pdbe_chem_comp_rdkit_properties.chi3n 1.986
_pdbe_chem_comp_rdkit_properties.chi4n 1.181
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.630
_pdbe_chem_comp_rdkit_properties.kappa1 4.442
_pdbe_chem_comp_rdkit_properties.kappa2 5.561
_pdbe_chem_comp_rdkit_properties.kappa3 3.029
_pdbe_chem_comp_rdkit_properties.Phi 1.235
#
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
LRO UniChem ChEMBL CHEMBL3991051
LRO UniChem PDBe LRO
LRO UniChem ZINC ZINC000095921127
LRO UniChem PubChem 71819697
LRO UniChem BindingDb 50211954
#
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
LRO OAB -3.307 3.015 -1.033 ETKDGv3 1
LRO CAN -2.497 1.884 -0.989 ETKDGv3 2
LRO OAE -1.335 1.941 -1.474 ETKDGv3 3
LRO CAQ -3.042 0.619 -0.438 ETKDGv3 4
LRO NAL -4.453 0.388 -0.623 ETKDGv3 5
LRO CAS -5.082 -0.809 -0.163 ETKDGv3 6
LRO OAC -6.315 -0.989 -0.344 ETKDGv3 7
LRO NAM -4.301 -1.797 0.498 ETKDGv3 8
LRO CAT -2.907 -1.562 0.700 ETKDGv3 9
LRO OAD -2.214 -2.442 1.278 ETKDGv3 10
LRO CAR -2.282 -0.295 0.232 ETKDGv3 11
LRO CAK -0.811 -0.080 0.541 ETKDGv3 12
LRO CAJ 0.075 -0.751 -0.515 ETKDGv3 13
LRO CAP 1.528 -0.479 -0.236 ETKDGv3 14
LRO CAH 2.236 -1.288 0.572 ETKDGv3 15
LRO CAF 3.653 -0.991 0.869 ETKDGv3 16
LRO CAO 4.237 0.108 0.361 ETKDGv3 17
LRO CAA 5.683 0.394 0.633 ETKDGv3 18
LRO CAG 3.456 1.003 -0.527 ETKDGv3 19
LRO CAI 2.175 0.729 -0.803 ETKDGv3 20
LRO H1 -2.966 3.884 -1.425 ETKDGv3 21
LRO H2 -4.742 -2.683 0.833 ETKDGv3 22
LRO H4 -0.568 0.999 0.636 ETKDGv3 23
LRO H5 -0.577 -0.515 1.537 ETKDGv3 24
LRO H6 -0.182 -0.375 -1.528 ETKDGv3 25
LRO H7 -0.112 -1.848 -0.521 ETKDGv3 26
LRO H8 1.779 -2.164 1.015 ETKDGv3 27
LRO H9 4.211 -1.669 1.503 ETKDGv3 28
LRO H10 5.911 1.466 0.453 ETKDGv3 29
LRO H11 6.315 -0.225 -0.038 ETKDGv3 30
LRO H12 5.935 0.161 1.689 ETKDGv3 31
LRO H13 3.918 1.884 -0.953 ETKDGv3 32
LRO H14 1.612 1.394 -1.447 ETKDGv3 33
LRO H15 -5.035 1.093 -1.128 ETKDGv3 34
#