Structure of PDB 5syn Chain A Binding Site BS01

Receptor Information
>5syn Chain A (length=223) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLLTDAATVSGAERETAAVIFLHGLGDTGHSWADALSTIRLPHVKYICPH
APRIPVTLNMKMVMPSWFDLMGLSPDAPEDEAGIKKAAENIKALIEHEMK
NGIPANRIVLGGFSQGGALSLYTALTCPHPLAGIVALSCWLPLHRAFPQA
ANGSAKDLAILQCHGELDPMVPVRFGALTAEKLRSVVTPARVQFKTYPGV
MHSSCPQEMAAVKEFLEKLLPPV
Ligand information
Ligand ID71T
InChIInChI=1S/C23H22N2O4S2/c1-29-18-8-6-17(7-9-18)24-10-12-25(13-11-24)23(26)20-14-16-15-31(27,28)21-5-3-2-4-19(21)22(16)30-20/h2-9,14H,10-13,15H2,1H3
InChIKeyYVIJPELUPZUEJX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1)N2CCN(CC2)C(=O)c3sc4c(C[S](=O)(=O)c5ccccc45)c3
OpenEye OEToolkits 2.0.5COc1ccc(cc1)N2CCN(CC2)C(=O)c3cc4c(s3)-c5ccccc5S(=O)(=O)C4
ACDLabs 12.01c5c(N1CCN(CC1)C(c4sc2c(CS(c3c2cccc3)(=O)=O)c4)=O)ccc(OC)c5
FormulaC23 H22 N2 O4 S2
Name2-[4-(4-methoxyphenyl)piperazine-1-carbonyl]-5lambda~6~-thieno[3,2-c][1]benzothiopyran-5,5(4H)-dione
ChEMBLCHEMBL1509398
DrugBank
ZINCZINC000009407519
PDB chain5syn 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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PDB5syn Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).
Resolution1.64 Å
Binding residue
(original residue number in PDB)		L33 L78 G80 L81 P83 S122 W148 H152 M178 F183 L186 T187
Binding residue
(residue number reindexed from 1)		L25 L70 G72 L73 P75 S114 W140 H144 M170 F175 L178 T179
Annotation score1
Binding affinityMOAD: Kd=240nM
PDBbind-CN: -logKd/Ki=6.62,Kd=240nM
BindingDB: Ki=120nM,Kd=240nM,IC50=1.1e+3nM
Enzymatic activity
Catalytic site (original residue number in PDB) L33 S122 A163 D176 H210
Catalytic site (residue number reindexed from 1) L25 S114 A155 D168 H202
Enzyme Commision number 3.1.2.-
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:0016787 hydrolase activity
GO:0045296 cadherin binding
GO:0052689 carboxylic ester hydrolase activity
Biological Process
GO:0002084 protein depalmitoylation
GO:0006631 fatty acid metabolic process
GO:0007411 axon guidance
GO:0046464 acylglycerol catabolic process
GO:1905344 prostaglandin catabolic process
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005795 Golgi stack
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5syn, PDBe:5syn, PDBj:5syn
PDBsum5syn
PubMed27748579
UniProtO95372|LYPA2_HUMAN Acyl-protein thioesterase 2 (Gene Name=LYPLA2)

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