Structure of PDB 5kre Chain A Binding Site BS01

Receptor Information
>5kre Chain A (length=224) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLQRCIVSPAGRHSASLIFLHGSGDSGQGLRMWIKQVLNQDLTFQHIKII
YPTAPPRSYTPMKGGISNVWFDRFKITNDCPEHLESIDVMCQVLTDLIDE
EVKSGIKKNRILIGGFSMGGCMAMHLAYRNHQDVAGVFALSSFLNKASAV
YQALQKSNGVLPELFQCHGTADELVLHSWAEETNSMLKSLGVTTKFHSFP
NVYHELSKTELDILKLWILTKLPG
Ligand information
Ligand ID6WG
InChIInChI=1S/C12H15NO/c14-10-13-9-5-4-8-12(13)11-6-2-1-3-7-11/h1-3,6-7,10,12H,4-5,8-9H2/t12-/m1/s1
InChIKeyMUZIXORETQNNBG-GFCCVEGCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1ccc(cc1)[C@H]2CCCCN2C=O
CACTVS 3.385O=CN1CCCC[C@@H]1c2ccccc2
CACTVS 3.385O=CN1CCCC[CH]1c2ccccc2
OpenEye OEToolkits 2.0.5c1ccc(cc1)C2CCCCN2C=O
FormulaC12 H15 N O
Name(2~{R})-2-phenylpiperidine-1-carbaldehyde
ChEMBL
DrugBank
ZINCZINC000039235004
PDB chain5kre Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5kre Discovery of a Selective Covalent Inhibitor of Lysophospholipase-like 1 (LYPLAL1) as a Tool to Evaluate the Role of this Serine Hydrolase in Metabolism.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S30 Y66 R80 I83 S124 M125 L181 V182
Binding residue
(residue number reindexed from 1)		S23 Y59 R73 I76 S117 M118 L174 V175
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.23,IC50=0.059uM
Enzymatic activity
Catalytic site (original residue number in PDB) S30 S124 N165 D179 H211
Catalytic site (residue number reindexed from 1) S23 S117 N158 D172 H204
Enzyme Commision number 3.1.2.22: palmitoyl-protein hydrolase.
Gene Ontology
Molecular Function
GO:0004622 lysophospholipase activity
GO:0005515 protein binding
GO:0008474 palmitoyl-(protein) hydrolase activity
GO:0016298 lipase activity
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0052689 carboxylic ester hydrolase activity
Biological Process
GO:0008150 biological_process
GO:0098734 macromolecule depalmitoylation
GO:0160049 negative regulation of cGAS/STING signaling pathway
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5kre, PDBe:5kre, PDBj:5kre
PDBsum5kre
PubMed27391855
UniProtQ5VWZ2|LYPL1_HUMAN Lysophospholipase-like protein 1 (Gene Name=LYPLAL1)

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