Structure of PDB 5ndd Chain A Binding Site BS01

Receptor Information
>5ndd Chain A (length=567) Species: 562,9606,10665 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKA
IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL
INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV
ITTFRTGTWDAYIYEFFSVDEFSASVLTGKLTTVFLPIVYTIVFVVALPS
NGMALWVFLFRTKKKAPAVIYMANLALADLLSVIWFPLKIAYHIHGNNWI
YGEALCNVLIGFFYANMYCSILFLTCLSVQRAWEIVNPMGHSRKKANIAI
GISLAIWLLILLVTIPLYVVKQTIFIPALQITTCHDVLPEQLLVGDMFNY
FLSLAIGVFLFPAFLTASAYVLMIRALADLEDNWETLNDNLKVIEKADNA
AQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQID
DALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLENSEKKRKRAIKLAVTV
AAMYLICFTPSNLLLVVHYFLIKSQGQSHVYALYIVALCLSTLNSCIDPF
VYYFVSHDFRDHAKNAL
Ligand information
Ligand ID8TZ
InChIInChI=1S/C13H15FN2O/c1-2-3-9-8-10(14)4-5-11(9)12(17)13-15-6-7-16-13/h4-8,12,17H,2-3H2,1H3,(H,15,16)/t12-/m0/s1
InChIKeyIDFPQEHZYBXIFO-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCc1cc(F)ccc1[CH](O)c2[nH]ccn2
CACTVS 3.385CCCc1cc(F)ccc1[C@H](O)c2[nH]ccn2
OpenEye OEToolkits 2.0.6CCCc1cc(ccc1[C@@H](c2[nH]ccn2)O)F
OpenEye OEToolkits 2.0.6CCCc1cc(ccc1C(c2[nH]ccn2)O)F
FormulaC13 H15 F N2 O
Name(~{S})-(4-fluoranyl-2-propyl-phenyl)-(1~{H}-imidazol-2-yl)methanol
ChEMBLCHEMBL4127372
DrugBank
ZINC
PDB chain5ndd Chain A Residue 2201 [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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PDB5ndd Structural insight into allosteric modulation of protease-activated receptor 2.
Resolution2.801 Å
Binding residue
(original residue number in PDB)		Y82 Y134 H135 W141 F155 C226 H227 D228 I327 L330
Binding residue
(residue number reindexed from 1)		Y190 Y242 H243 W249 F263 C334 H335 D336 I535 L538
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.46,Kd=344nM
Enzymatic activity
Catalytic site (original residue number in PDB) E1011 D1020
Catalytic site (residue number reindexed from 1) E12 D21
Enzyme Commision number 3.2.1.17: lysozyme.
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0004930 G protein-coupled receptor activity
GO:0005506 iron ion binding
GO:0009055 electron transfer activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0007186 G protein-coupled receptor signaling pathway
GO:0009253 peptidoglycan catabolic process
GO:0016998 cell wall macromolecule catabolic process
GO:0022900 electron transport chain
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0044659 viral release from host cell by cytolysis
Cellular Component
GO:0016020 membrane
GO:0030430 host cell cytoplasm
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ndd, PDBe:5ndd, PDBj:5ndd
PDBsum5ndd
PubMed28445455
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
P0ABE7|C562_ECOLX Soluble cytochrome b562 (Gene Name=cybC);
P55085

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