data_3LD
#
_chem_comp.id 3LD
_chem_comp.name 3-hydroxy-6-(2-phenylethyl)pyridazin-4(1H)-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H12 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-01-24
_chem_comp.pdbx_modified_date 2013-05-24
_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 216.236
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3LD
_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 3W4K
_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
3LD C4 C4 C 0 1 Y N N N N N 25.751 65.434 16.142 3.290 1.207 0.279 C4 3LD 1
3LD C5 C5 C 0 1 Y N N N N N 27.054 65.377 18.164 3.389 -1.182 0.160 C5 3LD 2
3LD C6 C6 C 0 1 Y N N N N N 26.928 65.188 16.807 2.661 -0.022 0.349 C6 3LD 3
3LD C7 C7 C 0 1 N N N N N N 30.064 66.910 16.933 -1.792 1.004 -0.327 C7 3LD 4
3LD C8 C8 C 0 1 N N N N N N 29.336 66.924 15.822 -1.068 -0.139 -0.410 C8 3LD 5
3LD C10 C10 C 0 1 N N N N N N 29.965 69.383 16.464 -3.779 -0.399 0.106 C10 3LD 6
3LD C1 C1 C 0 1 Y N N N N N 24.832 66.073 18.292 5.374 0.116 -0.166 C1 3LD 7
3LD C2 C2 C 0 1 Y N N N N N 24.723 65.886 16.924 4.646 1.276 0.022 C2 3LD 8
3LD C3 C3 C 0 1 Y N N N N N 26.014 65.818 18.941 4.745 -1.113 -0.098 C3 3LD 9
3LD C9 C9 C 0 1 N N N N N N 30.438 68.256 17.328 -3.175 0.925 -0.064 C9 3LD 10
3LD C11 C11 C 0 1 N N N N N N 28.120 64.700 16.069 1.183 -0.098 0.630 C11 3LD 11
3LD C12 C12 C 0 1 N N N N N N 28.834 65.692 15.159 0.410 -0.064 -0.691 C12 3LD 12
3LD N13 N13 N 0 1 N N N N N N 29.275 69.322 15.405 -3.018 -1.461 0.019 N13 3LD 13
3LD N14 N14 N 0 1 N N N N N N 28.966 68.040 15.111 -1.651 -1.339 -0.244 N14 3LD 14
3LD O15 O15 O 0 1 N N N N N N 31.133 68.528 18.294 -3.854 1.938 0.021 O15 3LD 15
3LD O16 O16 O 0 1 N N N N N N 30.352 70.572 16.917 -5.107 -0.522 0.361 O16 3LD 16
3LD H1 H1 H 0 1 N N N N N N 25.645 65.282 15.078 2.720 2.114 0.422 H1 3LD 17
3LD H2 H2 H 0 1 N N N N N N 28.005 65.171 18.633 2.898 -2.142 0.214 H2 3LD 18
3LD H3 H3 H 0 1 N N N N N N 30.341 66.016 17.471 -1.314 1.964 -0.457 H3 3LD 19
3LD H4 H4 H 0 1 N N N N N N 23.978 66.423 18.854 6.434 0.170 -0.368 H4 3LD 20
3LD H5 H5 H 0 1 N N N N N N 23.778 66.108 16.450 5.137 2.237 -0.032 H5 3LD 21
3LD H6 H6 H 0 1 N N N N N N 26.119 65.957 20.007 5.314 -2.019 -0.246 H6 3LD 22
3LD H7 H7 H 0 1 N N N N N N 27.799 63.852 15.446 0.960 -1.025 1.157 H7 3LD 23
3LD H8 H8 H 0 1 N N N N N N 28.850 64.351 16.814 0.886 0.751 1.246 H8 3LD 24
3LD H9 H9 H 0 1 N N N N N N 28.130 65.995 14.370 0.707 -0.912 -1.307 H9 3LD 25
3LD H10 H10 H 0 1 N N N N N N 29.694 65.177 14.705 0.633 0.864 -1.218 H10 3LD 26
3LD H11 H11 H 0 1 N N N N N N 28.412 67.888 14.293 -1.108 -2.141 -0.304 H11 3LD 27
3LD H12 H12 H 0 1 N N N N N N 30.872 70.458 17.704 -5.406 -1.437 0.456 H12 3LD 28
#
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
3LD N14 N13 SING N N 1
3LD N14 C8 SING N N 2
3LD C12 C8 SING N N 3
3LD C12 C11 SING N N 4
3LD N13 C10 DOUB N N 5
3LD C8 C7 DOUB N N 6
3LD C11 C6 SING N N 7
3LD C4 C6 DOUB Y N 8
3LD C4 C2 SING Y N 9
3LD C10 O16 SING N N 10
3LD C10 C9 SING N N 11
3LD C6 C5 SING Y N 12
3LD C2 C1 DOUB Y N 13
3LD C7 C9 SING N N 14
3LD C9 O15 DOUB N N 15
3LD C5 C3 DOUB Y N 16
3LD C1 C3 SING Y N 17
3LD C4 H1 SING N N 18
3LD C5 H2 SING N N 19
3LD C7 H3 SING N N 20
3LD C1 H4 SING N N 21
3LD C2 H5 SING N N 22
3LD C3 H6 SING N N 23
3LD C11 H7 SING N N 24
3LD C11 H8 SING N N 25
3LD C12 H9 SING N N 26
3LD C12 H10 SING N N 27
3LD N14 H11 SING N N 28
3LD O16 H12 SING N N 29
#
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
3LD SMILES ACDLabs 12.01 O=C1C=C(NN=C1O)CCc2ccccc2
3LD InChI InChI 1.03 InChI=1S/C12H12N2O2/c15-11-8-10(13-14-12(11)16)7-6-9-4-2-1-3-5-9/h1-5,8H,6-7H2,(H,13,15)(H,14,16)
3LD InChIKey InChI 1.03 LQVOQKJUHJKVFE-UHFFFAOYSA-N
3LD SMILES_CANONICAL CACTVS 3.370 OC1=NNC(=CC1=O)CCc2ccccc2
3LD SMILES CACTVS 3.370 OC1=NNC(=CC1=O)CCc2ccccc2
3LD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1ccc(cc1)CCC2=CC(=O)C(=NN2)O
3LD SMILES "OpenEye OEToolkits" 1.7.6 c1ccc(cc1)CCC2=CC(=O)C(=NN2)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
3LD "SYSTEMATIC NAME" ACDLabs 12.01 3-hydroxy-6-(2-phenylethyl)pyridazin-4(1H)-one
3LD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 3-oxidanyl-6-(2-phenylethyl)-1H-pyridazin-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3LD 'Create component' 2013-01-24 PDBJ
3LD 'Initial release' 2013-05-29 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
3LD C4 C 4.299 -0.375 1
3LD C5 C 5.598 -2.625 2
3LD C6 C 5.598 -1.125 3
3LD C7 C 9.495 1.125 4
3LD C8 C 9.495 -0.375 5
3LD C10 C 12.093 1.125 6
3LD C1 C 3.000 -2.625 7
3LD C2 C 3.000 -1.125 8
3LD C3 C 4.299 -3.375 9
3LD C9 C 10.794 1.875 10
3LD C11 C 6.897 -0.375 11
3LD C12 C 8.196 -1.125 12
3LD N13 N 12.093 -0.375 13
3LD N14 N 10.794 -1.125 14
3LD O15 O 10.794 3.375 15
3LD O16 O 13.392 1.875 16
#
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
3LD N14 N13 SINGLE NONE 1
3LD N14 C8 SINGLE NONE 2
3LD C12 C8 SINGLE NONE 3
3LD C12 C11 SINGLE NONE 4
3LD N13 C10 DOUBLE NONE 5
3LD C8 C7 DOUBLE NONE 6
3LD C11 C6 SINGLE NONE 7
3LD C4 C6 DOUBLE NONE 8
3LD C4 C2 SINGLE NONE 9
3LD C10 O16 SINGLE NONE 10
3LD C10 C9 SINGLE NONE 11
3LD C6 C5 SINGLE NONE 12
3LD C2 C1 DOUBLE NONE 13
3LD C7 C9 SINGLE NONE 14
3LD C9 O15 DOUBLE NONE 15
3LD C5 C3 DOUBLE NONE 16
3LD C1 C3 SINGLE NONE 17
#
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
3LD MurckoScaffold S1 scaffold 'O=c1cn[nH]c(CCc2ccccc2)c1' InChI=1S/C12H12N2O/c15-12-8-11(14-13-9-12)7-6-10-4-2-1-3-5-10/h1-5,8-9H,6-7H2,(H,14,15) XEIDHUYFSSNRFN-UHFFFAOYSA-N
3LD phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
3LD pyridazine F2 fragment c1ccnnc1 InChI=1S/C4H4N2/c1-2-4-6-5-3-1/h1-4H PBMFSQRYOILNGV-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
3LD C4 S1 1
3LD C5 S1 1
3LD C6 S1 1
3LD C7 S1 1
3LD C8 S1 1
3LD C10 S1 1
3LD C1 S1 1
3LD C2 S1 1
3LD C3 S1 1
3LD C9 S1 1
3LD C11 S1 1
3LD C12 S1 1
3LD N13 S1 1
3LD N14 S1 1
3LD O15 S1 1
3LD C4 F1 1
3LD C6 F1 1
3LD C5 F1 1
3LD C3 F1 1
3LD C1 F1 1
3LD C2 F1 1
3LD C7 F2 1
3LD C8 F2 1
3LD N14 F2 1
3LD N13 F2 1
3LD C10 F2 1
3LD C9 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 3LD
_pdbe_chem_comp_rdkit_properties.exactmw 216.090
_pdbe_chem_comp_rdkit_properties.amw 216.240
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_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 109.586
_pdbe_chem_comp_rdkit_properties.tpsa 65.980
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.589
_pdbe_chem_comp_rdkit_properties.CrippenMR 59.339
_pdbe_chem_comp_rdkit_properties.chi0v 7.711
_pdbe_chem_comp_rdkit_properties.chi1v 4.055
_pdbe_chem_comp_rdkit_properties.chi2v 1.473
_pdbe_chem_comp_rdkit_properties.chi3v 1.473
_pdbe_chem_comp_rdkit_properties.chi4v 0.817
_pdbe_chem_comp_rdkit_properties.chi0n 19.711
_pdbe_chem_comp_rdkit_properties.chi1n 9.911
_pdbe_chem_comp_rdkit_properties.chi2n 1.473
_pdbe_chem_comp_rdkit_properties.chi3n 1.473
_pdbe_chem_comp_rdkit_properties.chi4n 0.817
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.100
_pdbe_chem_comp_rdkit_properties.kappa1 3.197
_pdbe_chem_comp_rdkit_properties.kappa2 4.613
_pdbe_chem_comp_rdkit_properties.kappa3 2.475
_pdbe_chem_comp_rdkit_properties.Phi 0.922
#
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
3LD UniChem ChEMBL CHEMBL2338786
3LD UniChem PDBe 3LD
3LD UniChem ZINC ZINC000095590337
3LD UniChem SureChEMBL SCHEMBL14719095
3LD UniChem PubChem 71270198
3LD UniChem BindingDb 50431078
3LD UniChem BRENDA 89728
3LD UniChem BindingDb 347075
3LD UniChem SureChEMBL SCHEMBL16231620
3LD UniChem 'PubChem TPHARMA' 163490808
#
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
3LD C4 2.531 1.439 0.377 ETKDGv3 1
3LD C5 2.717 -0.993 0.521 ETKDGv3 2
3LD C6 1.913 0.255 0.540 ETKDGv3 3
3LD C7 -2.498 1.057 -0.559 ETKDGv3 4
3LD C8 -1.737 -0.044 -0.564 ETKDGv3 5
3LD C10 -4.529 -0.411 -0.206 ETKDGv3 6
3LD C1 4.718 0.368 0.205 ETKDGv3 7
3LD C2 3.998 1.497 0.210 ETKDGv3 8
3LD C3 4.045 -0.938 0.365 ETKDGv3 9
3LD C9 -3.951 0.929 -0.385 ETKDGv3 10
3LD C11 0.416 0.180 0.675 ETKDGv3 11
3LD C12 -0.242 0.053 -0.701 ETKDGv3 12
3LD N13 -3.749 -1.451 -0.203 ETKDGv3 13
3LD N14 -2.356 -1.329 -0.369 ETKDGv3 14
3LD O15 -4.686 1.952 -0.386 ETKDGv3 15
3LD O16 -5.903 -0.565 -0.041 ETKDGv3 16
3LD H1 1.963 2.362 0.363 ETKDGv3 17
3LD H2 2.230 -1.954 0.632 ETKDGv3 18
3LD H3 -2.056 2.040 -0.678 ETKDGv3 19
3LD H4 5.792 0.409 0.080 ETKDGv3 20
3LD H5 4.489 2.454 0.088 ETKDGv3 21
3LD H6 4.630 -1.849 0.352 ETKDGv3 22
3LD H7 0.145 -0.699 1.301 ETKDGv3 23
3LD H8 0.034 1.087 1.194 ETKDGv3 24
3LD H9 0.030 0.928 -1.333 ETKDGv3 25
3LD H10 0.137 -0.858 -1.214 ETKDGv3 26
3LD H11 -1.768 -2.192 -0.347 ETKDGv3 27
3LD H12 -6.314 -1.483 0.084 ETKDGv3 28
#