data_LL1
#
_chem_comp.id LL1
_chem_comp.name 3-pyridin-4-yl-1H-indazole
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H9 N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-07-04
_chem_comp.pdbx_modified_date 2011-06-04
_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 195.220
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LL1
_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 3DNE
_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
LL1 C4 C4 C 0 1 Y N N N N N 8.177 10.453 3.588 1.148 -0.115 0.029 C4 LL1 1
LL1 C5 C5 C 0 1 Y N N N N N 8.490 10.906 4.898 1.371 -1.481 0.215 C5 LL1 2
LL1 C6 C6 C 0 1 Y N N N N N 9.832 11.148 5.300 2.649 -1.954 0.290 C6 LL1 3
LL1 C1 C1 C 0 1 Y N N N N N 10.884 10.975 4.363 3.731 -1.088 0.183 C1 LL1 4
LL1 C2 C2 C 0 1 Y N N N N N 10.577 10.505 3.031 3.538 0.252 0.001 C2 LL1 5
LL1 C3 C3 C 0 1 Y N N N N N 9.246 10.278 2.640 2.244 0.761 -0.079 C3 LL1 6
LL1 N11 N11 N 0 1 Y N N N N N 8.675 9.922 1.452 1.731 2.022 -0.253 N11 LL1 7
LL1 N12 N12 N 0 1 Y N N N N N 7.423 9.851 1.607 0.334 1.955 -0.256 N12 LL1 8
LL1 C13 C13 C 0 1 Y N N N N N 6.989 10.156 2.855 -0.056 0.713 -0.098 C13 LL1 9
LL1 C14 C14 C 0 1 Y N N N N N 5.603 10.185 3.295 -1.457 0.235 -0.048 C14 LL1 10
LL1 C15 C15 C 0 1 Y N N N N N 4.577 10.269 2.332 -1.811 -1.010 -0.579 C15 LL1 11
LL1 C16 C16 C 0 1 Y N N N N N 3.209 10.258 2.686 -3.127 -1.417 -0.511 C16 LL1 12
LL1 N17 N17 N 0 1 Y N N N N N 2.907 10.209 4.003 -4.045 -0.649 0.045 N17 LL1 13
LL1 C18 C18 C 0 1 Y N N N N N 3.795 10.112 5.001 -3.754 0.531 0.557 C18 LL1 14
LL1 C19 C19 C 0 1 Y N N N N N 5.203 10.099 4.669 -2.461 1.012 0.537 C19 LL1 15
LL1 H5 H5 H 0 1 N N N N N N 7.690 11.070 5.605 0.535 -2.161 0.300 H5 LL1 16
LL1 H6 H6 H 0 1 N N N N N N 10.049 11.461 6.311 2.822 -3.011 0.434 H6 LL1 17
LL1 H1 H1 H 0 1 N N N N N N 11.904 11.192 4.643 4.735 -1.479 0.244 H1 LL1 18
LL1 H2 H2 H 0 1 N N N N N N 11.378 10.326 2.329 4.386 0.914 -0.080 H2 LL1 19
LL1 H15 H15 H 0 1 N N N N N N 4.845 10.344 1.289 -1.064 -1.643 -1.036 H15 LL1 20
LL1 H16 H16 H 0 1 N N N N N N 2.435 10.288 1.934 -3.409 -2.376 -0.919 H16 LL1 21
LL1 H18 H18 H 0 1 N N N N N N 3.468 10.045 6.028 -4.537 1.127 1.003 H18 LL1 22
LL1 H19 H19 H 0 1 N N N N N N 5.946 10.025 5.449 -2.229 1.977 0.963 H19 LL1 23
LL1 HN11 HN11 H 0 0 N N N N N N 9.167 9.746 0.599 2.255 2.831 -0.357 HN11 LL1 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
LL1 C3 C4 DOUB Y N 1
LL1 C13 C4 SING Y N 2
LL1 C4 C5 SING Y N 3
LL1 C5 C6 DOUB Y N 4
LL1 C5 H5 SING N N 5
LL1 C1 C6 SING Y N 6
LL1 C6 H6 SING N N 7
LL1 C2 C1 DOUB Y N 8
LL1 C1 H1 SING N N 9
LL1 C3 C2 SING Y N 10
LL1 C2 H2 SING N N 11
LL1 N11 C3 SING Y N 12
LL1 N11 N12 SING Y N 13
LL1 N12 C13 DOUB Y N 14
LL1 C13 C14 SING Y N 15
LL1 C15 C14 DOUB Y N 16
LL1 C14 C19 SING Y N 17
LL1 C15 C16 SING Y N 18
LL1 C15 H15 SING N N 19
LL1 C16 N17 DOUB Y N 20
LL1 C16 H16 SING N N 21
LL1 N17 C18 SING Y N 22
LL1 C19 C18 DOUB Y N 23
LL1 C18 H18 SING N N 24
LL1 C19 H19 SING N N 25
LL1 N11 HN11 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
LL1 SMILES ACDLabs 10.04 n2c(c1ccccc1n2)c3ccncc3
LL1 SMILES_CANONICAL CACTVS 3.341 "[nH]1nc(c2ccncc2)c3ccccc13"
LL1 SMILES CACTVS 3.341 "[nH]1nc(c2ccncc2)c3ccccc13"
LL1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc2c(c1)c(n[nH]2)c3ccncc3
LL1 SMILES "OpenEye OEToolkits" 1.5.0 c1ccc2c(c1)c(n[nH]2)c3ccncc3
LL1 InChI InChI 1.03 InChI=1S/C12H9N3/c1-2-4-11-10(3-1)12(15-14-11)9-5-7-13-8-6-9/h1-8H,(H,14,15)
LL1 InChIKey InChI 1.03 MSRXUUDVRNWSTN-UHFFFAOYSA-N
#
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
LL1 "SYSTEMATIC NAME" ACDLabs 10.04 3-pyridin-4-yl-1H-indazole
LL1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 3-pyridin-4-yl-1H-indazole
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LL1 'Create component' 2008-07-04 PDBJ
LL1 'Modify aromatic_flag' 2011-06-04 RCSB
LL1 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id LL1
_pdbe_chem_comp_drugbank_details.drugbank_id DB08113
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 3-pyridin-4-yl-1H-indazole
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id LL1
_pdbe_chem_comp_drugbank_classification.drugbank_id DB08113
_pdbe_chem_comp_drugbank_classification.parent Indazoles
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Benzopyrazoles
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as indazoles. These are compounds containing an indazole, which is structurally characterized by a pyrazole fused to a benzene.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
LL1 DB08113 'cAMP-dependent protein kinase catalytic subunit alpha' Humans P17612 unknown 1
LL1 DB08113 'cAMP-dependent protein kinase inhibitor alpha' Humans P61925 unknown 2
#
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
LL1 C4 C 5.598 -0.947 1
LL1 C5 C 4.299 -0.197 2
LL1 C6 C 3.000 -0.947 3
LL1 C1 C 3.000 -2.447 4
LL1 C2 C 4.299 -3.197 5
LL1 C3 C 5.598 -2.447 6
LL1 N11 N 7.018 -2.904 7
LL1 N12 N 7.893 -1.697 8
LL1 C13 C 7.018 -0.490 9
LL1 C14 C 7.483 0.936 10
LL1 C15 C 6.482 2.053 11
LL1 C16 C 6.948 3.478 12
LL1 N17 N 8.415 3.788 13
LL1 C18 C 9.417 2.671 14
LL1 C19 C 8.951 1.246 15
#
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
LL1 C3 C4 SINGLE NONE 1
LL1 C13 C4 SINGLE NONE 2
LL1 C4 C5 DOUBLE NONE 3
LL1 C5 C6 SINGLE NONE 4
LL1 C1 C6 DOUBLE NONE 5
LL1 C2 C1 SINGLE NONE 6
LL1 C3 C2 DOUBLE NONE 7
LL1 N11 C3 SINGLE NONE 8
LL1 N11 N12 SINGLE NONE 9
LL1 N12 C13 DOUBLE NONE 10
LL1 C13 C14 SINGLE NONE 11
LL1 C15 C14 DOUBLE NONE 12
LL1 C14 C19 SINGLE NONE 13
LL1 C15 C16 SINGLE NONE 14
LL1 C16 N17 DOUBLE NONE 15
LL1 N17 C18 SINGLE NONE 16
LL1 C19 C18 DOUBLE 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
LL1 MurckoScaffold S1 scaffold 'c1ccc2c(-c3ccncc3)n[nH]c2c1' InChI=1S/C12H9N3/c1-2-4-11-10(3-1)12(15-14-11)9-5-7-13-8-6-9/h1-8H,(H,14,15) MSRXUUDVRNWSTN-UHFFFAOYSA-N
LL1 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
LL1 pyrazole F2 fragment 'c1cn[nH]c1' InChI=1S/C3H4N2/c1-2-4-5-3-1/h1-3H,(H,4,5) WTKZEGDFNFYCGP-UHFFFAOYSA-N
LL1 pyridine F3 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
LL1 C4 S1 1
LL1 C5 S1 1
LL1 C6 S1 1
LL1 C1 S1 1
LL1 C2 S1 1
LL1 C3 S1 1
LL1 N11 S1 1
LL1 N12 S1 1
LL1 C13 S1 1
LL1 C14 S1 1
LL1 C15 S1 1
LL1 C16 S1 1
LL1 N17 S1 1
LL1 C18 S1 1
LL1 C19 S1 1
LL1 C4 F1 1
LL1 C3 F1 1
LL1 C2 F1 1
LL1 C1 F1 1
LL1 C6 F1 1
LL1 C5 F1 1
LL1 C3 F2 1
LL1 C4 F2 1
LL1 C13 F2 1
LL1 N12 F2 1
LL1 N11 F2 1
LL1 C16 F3 1
LL1 C15 F3 1
LL1 C14 F3 1
LL1 C19 F3 1
LL1 C18 F3 1
LL1 N17 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LL1
_pdbe_chem_comp_rdkit_properties.exactmw 195.080
_pdbe_chem_comp_rdkit_properties.amw 195.225
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 99.490
_pdbe_chem_comp_rdkit_properties.tpsa 41.570
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.816
_pdbe_chem_comp_rdkit_properties.CrippenMR 55.797
_pdbe_chem_comp_rdkit_properties.chi0v 7.342
_pdbe_chem_comp_rdkit_properties.chi1v 4.094
_pdbe_chem_comp_rdkit_properties.chi2v 1.865
_pdbe_chem_comp_rdkit_properties.chi3v 1.865
_pdbe_chem_comp_rdkit_properties.chi4v 1.223
_pdbe_chem_comp_rdkit_properties.chi0n 16.342
_pdbe_chem_comp_rdkit_properties.chi1n 8.542
_pdbe_chem_comp_rdkit_properties.chi2n 1.865
_pdbe_chem_comp_rdkit_properties.chi3n 1.865
_pdbe_chem_comp_rdkit_properties.chi4n 1.223
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.160
_pdbe_chem_comp_rdkit_properties.kappa1 3.167
_pdbe_chem_comp_rdkit_properties.kappa2 3.203
_pdbe_chem_comp_rdkit_properties.kappa3 1.287
_pdbe_chem_comp_rdkit_properties.Phi 0.676
#
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
LL1 UniChem ChEMBL CHEMBL1234032
LL1 UniChem DrugBank DB08113
LL1 UniChem PDBe LL1
LL1 UniChem ZINC ZINC000039132370
LL1 UniChem SureChEMBL SCHEMBL10533662
LL1 UniChem BindingDb 50102624
LL1 UniChem 'Probes And Drugs' PD004734
LL1 UniChem PubChem 12412578
#
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
LL1 C4 -1.003 -0.047 -0.028 ETKDGv3 1
LL1 C5 -1.180 -1.283 -0.507 ETKDGv3 2
LL1 C6 -2.581 -1.749 -0.700 ETKDGv3 3
LL1 C1 -3.621 -0.923 -0.442 ETKDGv3 4
LL1 C2 -3.378 0.468 0.031 ETKDGv3 5
LL1 C3 -2.110 0.833 0.221 ETKDGv3 6
LL1 N11 -1.594 2.103 0.567 ETKDGv3 7
LL1 N12 -0.192 2.004 0.532 ETKDGv3 8
LL1 C13 0.177 0.795 0.207 ETKDGv3 9
LL1 C14 1.595 0.387 0.114 ETKDGv3 10
LL1 C15 2.532 1.267 -0.279 ETKDGv3 11
LL1 C16 3.943 0.841 -0.366 ETKDGv3 12
LL1 N17 4.279 -0.375 -0.047 ETKDGv3 13
LL1 C18 3.304 -1.331 0.402 ETKDGv3 14
LL1 C19 2.014 -0.985 0.491 ETKDGv3 15
LL1 H5 -0.347 -1.916 -0.777 ETKDGv3 16
LL1 H6 -2.766 -2.753 -1.059 ETKDGv3 17
LL1 H1 -4.636 -1.266 -0.594 ETKDGv3 18
LL1 H2 -4.194 1.159 0.193 ETKDGv3 19
LL1 H15 2.269 2.282 -0.552 ETKDGv3 20
LL1 H16 4.699 1.539 -0.698 ETKDGv3 21
LL1 H18 3.620 -2.327 0.683 ETKDGv3 22
LL1 H19 1.297 -1.700 0.871 ETKDGv3 23
LL1 HN11 -2.130 2.974 0.772 ETKDGv3 24
#