data_YBV
#
_chem_comp.id YBV
_chem_comp.name 5-(azetidin-3-ylamino)-4-chloranyl-2-methyl-pyridazin-3-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H11 Cl N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-02-17
_chem_comp.pdbx_modified_date 2022-08-05
_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 214.652
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YBV
_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 7LRO
_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
YBV C11 C1 C 0 1 N N N N N N -7.555 12.445 -27.813 0.151 -1.599 -0.153 C11 YBV 1
YBV C14 C2 C 0 1 N N N N N N -3.928 12.490 -29.101 3.822 -1.622 0.077 C14 YBV 2
YBV C02 C3 C 0 1 N N N N N N -5.905 11.225 -29.949 2.222 0.209 0.038 C02 YBV 3
YBV C03 C4 C 0 1 N N N N N N -7.340 10.906 -29.822 0.905 0.688 -0.023 C03 YBV 4
YBV C05 C5 C 0 1 N N N N N N -8.160 11.492 -28.780 -0.135 -0.218 -0.119 C05 YBV 5
YBV C07 C6 C 0 1 N N N N N N -10.406 11.974 -27.803 -2.542 -0.741 -0.282 C07 YBV 6
YBV C08 C7 C 0 1 N N N N N N -11.632 12.486 -28.444 -3.378 -0.870 1.003 C08 YBV 7
YBV C10 C8 C 0 1 N N N N N N -11.228 11.162 -26.899 -3.814 -0.168 -0.934 C10 YBV 8
YBV N06 N1 N 0 1 N N N N N N -9.565 11.164 -28.671 -1.446 0.226 -0.181 N06 YBV 9
YBV N09 N2 N 0 1 N N N N N N -12.411 11.929 -27.321 -4.233 0.197 0.437 N09 YBV 10
YBV N12 N3 N 0 1 N N N N N N -6.131 12.769 -27.934 1.383 -2.020 -0.090 N12 YBV 11
YBV N13 N4 N 0 1 N N N N N N -5.330 12.166 -28.986 2.449 -1.118 0.008 N13 YBV 12
YBV O01 O1 O 0 1 N N N N N N -5.232 10.754 -30.817 3.157 0.991 0.122 O01 YBV 13
YBV CL04 CL1 CL 0 0 N N N N N N -8.066 9.777 -30.951 0.586 2.395 0.014 CL04 YBV 14
YBV H1 H1 H 0 1 N N N N N N -8.155 12.891 -27.034 -0.656 -2.313 -0.228 H1 YBV 15
YBV H2 H2 H 0 1 N N N N N N -3.650 13.203 -28.311 4.099 -1.782 1.119 H2 YBV 16
YBV H3 H3 H 0 1 N N N N N N -3.330 11.573 -28.994 3.891 -2.565 -0.465 H3 YBV 17
YBV H4 H4 H 0 1 N N N N N N -3.735 12.940 -30.086 4.499 -0.895 -0.371 H4 YBV 18
YBV H6 H6 H 0 1 N N N N N N -9.845 12.760 -27.276 -2.228 -1.697 -0.699 H6 YBV 19
YBV H7 H7 H 0 1 N N N N N N -11.677 13.582 -28.528 -3.884 -1.830 1.104 H7 YBV 20
YBV H8 H8 H 0 1 N N N N N N -11.857 12.034 -29.421 -2.845 -0.572 1.906 H8 YBV 21
YBV H9 H9 H 0 1 N N N N N N -11.265 10.094 -27.158 -3.628 0.690 -1.580 H9 YBV 22
YBV H10 H10 H 0 1 N N N N N N -10.974 11.272 -25.835 -4.445 -0.924 -1.402 H10 YBV 23
YBV H11 H11 H 0 1 N N N N N N -9.952 11.219 -29.591 -1.637 1.176 -0.157 H11 YBV 24
YBV H12 H12 H 0 1 N N N N N N -12.717 12.610 -26.656 -5.210 -0.007 0.582 H12 YBV 25
#
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
YBV CL04 C03 SING N N 1
YBV O01 C02 DOUB N N 2
YBV C02 C03 SING N N 3
YBV C02 N13 SING N N 4
YBV C03 C05 DOUB N N 5
YBV C14 N13 SING N N 6
YBV N13 N12 SING N N 7
YBV C05 N06 SING N N 8
YBV C05 C11 SING N N 9
YBV N06 C07 SING N N 10
YBV C08 C07 SING N N 11
YBV C08 N09 SING N N 12
YBV N12 C11 DOUB N N 13
YBV C07 C10 SING N N 14
YBV N09 C10 SING N N 15
YBV C11 H1 SING N N 16
YBV C14 H2 SING N N 17
YBV C14 H3 SING N N 18
YBV C14 H4 SING N N 19
YBV C07 H6 SING N N 20
YBV C08 H7 SING N N 21
YBV C08 H8 SING N N 22
YBV C10 H9 SING N N 23
YBV C10 H10 SING N N 24
YBV N06 H11 SING N N 25
YBV N09 H12 SING N N 26
#
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
YBV InChI InChI 1.03 InChI=1S/C8H11ClN4O/c1-13-8(14)7(9)6(4-11-13)12-5-2-10-3-5/h4-5,10,12H,2-3H2,1H3
YBV InChIKey InChI 1.03 GZHCENKGUMJQPY-UHFFFAOYSA-N
YBV SMILES_CANONICAL CACTVS 3.385 CN1N=CC(=C(Cl)C1=O)NC2CNC2
YBV SMILES CACTVS 3.385 CN1N=CC(=C(Cl)C1=O)NC2CNC2
YBV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CN1C(=O)C(=C(C=N1)NC2CNC2)Cl
YBV SMILES "OpenEye OEToolkits" 2.0.7 CN1C(=O)C(=C(C=N1)NC2CNC2)Cl
#
_pdbx_chem_comp_identifier.comp_id YBV
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier 5-(azetidin-3-ylamino)-4-chloranyl-2-methyl-pyridazin-3-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
YBV 'Create component' 2021-02-17 RCSB
YBV 'Initial release' 2022-08-10 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
YBV C11 C 6.897 -0.388 1
YBV C14 C 5.598 -4.138 2
YBV C02 C 4.299 -1.888 3
YBV C03 C 4.299 -0.388 4
YBV C05 C 5.598 0.362 5
YBV C07 C 6.897 2.612 6
YBV C08 C 7.285 4.061 7
YBV C10 C 8.346 2.224 8
YBV N06 N 5.598 1.862 9
YBV N09 N 8.734 3.673 10
YBV N12 N 6.897 -1.888 11
YBV N13 N 5.598 -2.638 12
YBV O01 O 3.000 -2.638 13
YBV CL04 Cl 3.000 0.362 14
#
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
YBV CL04 C03 SINGLE NONE 1
YBV O01 C02 DOUBLE NONE 2
YBV C02 C03 SINGLE NONE 3
YBV C02 N13 SINGLE NONE 4
YBV C03 C05 DOUBLE NONE 5
YBV C14 N13 SINGLE NONE 6
YBV N13 N12 SINGLE NONE 7
YBV C05 N06 SINGLE NONE 8
YBV C05 C11 SINGLE NONE 9
YBV N06 C07 SINGLE NONE 10
YBV C08 C07 SINGLE NONE 11
YBV C08 N09 SINGLE NONE 12
YBV N12 C11 DOUBLE NONE 13
YBV C07 C10 SINGLE NONE 14
YBV N09 C10 SINGLE NONE 15
#
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
YBV MurckoScaffold S1 scaffold 'O=c1cc(NC2CNC2)cn[nH]1' InChI=1S/C7H10N4O/c12-7-1-5(4-9-11-7)10-6-2-8-3-6/h1,4,6,8H,2-3H2,(H2,10,11,12) SRDKDOMCYVOSEZ-UHFFFAOYSA-N
YBV pyridazine F1 fragment c1ccnnc1 InChI=1S/C4H4N2/c1-2-4-6-5-3-1/h1-4H PBMFSQRYOILNGV-UHFFFAOYSA-N
YBV Z1270443752 F2 fragment 'CNc1cn[nH]c(=O)c1.Cl' 'InChI=1S/C5H7N3O.ClH/c1-6-4-2-5(9)8-7-3-4;/h2-3H,1H3,(H2,6,8,9);1H' CQYGJBICWUHTRC-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
YBV C11 S1 1
YBV C02 S1 1
YBV C03 S1 1
YBV C05 S1 1
YBV C07 S1 1
YBV C08 S1 1
YBV C10 S1 1
YBV N06 S1 1
YBV N09 S1 1
YBV N12 S1 1
YBV N13 S1 1
YBV O01 S1 1
YBV C03 F1 1
YBV C02 F1 1
YBV N13 F1 1
YBV N12 F1 1
YBV C11 F1 1
YBV C05 F1 1
YBV CL04 F2 1
YBV C07 F2 1
YBV N06 F2 1
YBV C05 F2 1
YBV C11 F2 1
YBV N12 F2 1
YBV N13 F2 1
YBV C02 F2 1
YBV O01 F2 1
YBV C03 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YBV
_pdbe_chem_comp_rdkit_properties.exactmw 214.062
_pdbe_chem_comp_rdkit_properties.amw 214.656
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 101.638
_pdbe_chem_comp_rdkit_properties.tpsa 58.950
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.337
_pdbe_chem_comp_rdkit_properties.CrippenMR 54.052
_pdbe_chem_comp_rdkit_properties.chi0v 7.331
_pdbe_chem_comp_rdkit_properties.chi1v 3.786
_pdbe_chem_comp_rdkit_properties.chi2v 1.732
_pdbe_chem_comp_rdkit_properties.chi3v 1.732
_pdbe_chem_comp_rdkit_properties.chi4v 0.892
_pdbe_chem_comp_rdkit_properties.chi0n 17.575
_pdbe_chem_comp_rdkit_properties.chi1n 8.803
_pdbe_chem_comp_rdkit_properties.chi2n 1.391
_pdbe_chem_comp_rdkit_properties.chi3n 1.391
_pdbe_chem_comp_rdkit_properties.chi4n 0.728
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.070
_pdbe_chem_comp_rdkit_properties.kappa1 2.961
_pdbe_chem_comp_rdkit_properties.kappa2 3.588
_pdbe_chem_comp_rdkit_properties.kappa3 1.603
_pdbe_chem_comp_rdkit_properties.Phi 0.759
#
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
YBV UniChem ChEMBL CHEMBL4853420
YBV UniChem PDBe YBV
YBV UniChem SureChEMBL SCHEMBL17916627
YBV UniChem PubChem 114445962
#
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
YBV C11 1.064 -1.169 0.963 ETKDGv3 1
YBV C14 4.512 0.098 0.740 ETKDGv3 2
YBV C02 2.480 0.624 -0.656 ETKDGv3 3
YBV C03 1.051 0.396 -0.921 ETKDGv3 4
YBV C05 0.368 -0.451 -0.128 ETKDGv3 5
YBV C07 -2.025 0.339 -0.152 ETKDGv3 6
YBV C08 -3.310 0.072 -0.914 ETKDGv3 7
YBV C10 -2.872 0.120 1.089 ETKDGv3 8
YBV N06 -1.025 -0.714 -0.343 ETKDGv3 9
YBV N09 -4.087 -0.131 0.311 ETKDGv3 10
YBV N12 2.327 -0.972 1.202 ETKDGv3 11
YBV N13 3.095 -0.074 0.437 ETKDGv3 12
YBV O01 3.149 1.414 -1.377 ETKDGv3 13
YBV CL04 0.301 1.172 -2.315 ETKDGv3 14
YBV H1 0.513 -1.867 1.580 ETKDGv3 15
YBV H2 5.125 -0.282 -0.104 ETKDGv3 16
YBV H3 4.735 1.174 0.904 ETKDGv3 17
YBV H4 4.782 -0.463 1.660 ETKDGv3 18
YBV H6 -1.641 1.377 -0.256 ETKDGv3 19
YBV H7 -3.654 0.961 -1.491 ETKDGv3 20
YBV H8 -3.284 -0.856 -1.526 ETKDGv3 21
YBV H9 -2.952 1.037 1.716 ETKDGv3 22
YBV H10 -2.583 -0.780 1.675 ETKDGv3 23
YBV H11 -1.338 -1.710 -0.278 ETKDGv3 24
YBV H12 -4.733 0.684 0.433 ETKDGv3 25
#