Structure of PDB 5fp0 Chain A Binding Site BS01

Receptor Information
>5fp0 Chain A (length=543) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATT
RLMKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKI
NRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLI
ESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI
LVQDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLH
FVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSA
PPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPER
VRAVASLNTPFIPANPNMSPLESNPVFDYQLYFQEPGVAEAELEQNLSRT
FKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQF
KKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMS
QHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR
Ligand information
Ligand IDSZC
InChIInChI=1S/C19H18F3N3O2S/c20-19(21,22)13-10-8-12(9-11-13)18-23-15-6-3-7-16(17(15)24-18)28(26,27)25-14-4-1-2-5-14/h3,6-11,14,25H,1-2,4-5H2,(H,23,24)
InChIKeyBCAADIRANQOVRJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(c(c1)S(=O)(=O)NC3CCCC3)[nH]c(n2)c4ccc(cc4)C(F)(F)F
CACTVS 3.385FC(F)(F)c1ccc(cc1)c2[nH]c3c(cccc3[S](=O)(=O)NC4CCCC4)n2
FormulaC19 H18 F3 N3 O2 S
NameN-cyclopentyl-2-[4-(trifluoromethyl)phenyl]-3H-benzimidazole-4-sulfonamide
ChEMBL
DrugBank
ZINCZINC000584905687
PDB chain5fp0 Chain A Residue 1549 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5fp0 Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation-Structure-Based Hit Evaluation and Chemistry Exploration.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		F267 D335 W336 M339 Y383 Q384 Y466 M503 H524
Binding residue
(residue number reindexed from 1)		F266 D334 W335 M338 Y379 Q380 Y462 M499 H520
Annotation score1
Binding affinityMOAD: ic50=0.017uM
PDBbind-CN: -logKd/Ki=7.77,IC50=0.017uM
Enzymatic activity
Catalytic site (original residue number in PDB) F267 H334 D335 W336 N359 N378 Y383 Y466 D496 H524
Catalytic site (residue number reindexed from 1) F266 H333 D334 W335 N358 N374 Y379 Y462 D492 H520
Enzyme Commision number 3.1.3.76: lipid-phosphate phosphatase.
3.3.2.10: soluble epoxide hydrolase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004301 epoxide hydrolase activity
GO:0015643 toxic substance binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0033885 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity
GO:0042577 lipid phosphatase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0052642 lysophosphatidic acid phosphatase activity
Biological Process
GO:0006629 lipid metabolic process
GO:0009056 catabolic process
GO:0009636 response to toxic substance
GO:0010628 positive regulation of gene expression
GO:0016311 dephosphorylation
GO:0042632 cholesterol homeostasis
GO:0046272 stilbene catabolic process
GO:0046839 phospholipid dephosphorylation
GO:0090181 regulation of cholesterol metabolic process
GO:0097176 epoxide metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
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:5fp0, PDBe:5fp0, PDBj:5fp0
PDBsum5fp0
PubMed26845235
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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