Structure of PDB 5cgd Chain A Binding Site BS01

Receptor Information
>5cgd Chain A (length=408) Species: 9606,10665 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPVQYLRWGDPAPIAAVVFACLGLLATLFVTVVFIIYRDTPVVKSSSREL
CYIILAGICLGYLCTFCLIAKPKQIYCYLQRIGIGLSPAMSYSALVTKTY
RAARILAMSKKNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLN
AAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDS
LDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYN
QTPNRAKRVITTFRTGTWDAYKISACAQLVIAFILICIQLGIIVALFIME
PPDIMVYLICNTTNLGVVAPLGYNGLLILACTFYAFKTRNVPANFNEAKY
IAFTMYTTCIIWLAFVPIYFGSNYKIITMCFSVSLSATVALGCMFVPKVY
IILAKPER
Ligand information
Ligand ID51E
InChIInChI=1S/C16H8ClFN4/c17-12-4-10(7-19)3-11(5-12)15-6-16(22-9-21-15)14-2-1-13(18)8-20-14/h1-6,8-9H
InChIKeyFQAXDSVNYVVQSE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1c(cc(cc1Cl)C#N)c2ncnc(c2)c3ccc(cn3)F
OpenEye OEToolkits 1.9.2c1cc(ncc1F)c2cc(ncn2)c3cc(cc(c3)Cl)C#N
CACTVS 3.385Fc1ccc(nc1)c2cc(ncn2)c3cc(Cl)cc(c3)C#N
FormulaC16 H8 Cl F N4
Name3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile
ChEMBLCHEMBL3603923
DrugBank
ZINCZINC000220897715
PDB chain5cgd Chain A Residue 4005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cgd Fragment and Structure-Based Drug Discovery for a Class C GPCR: Discovery of the mGlu5 Negative Allosteric Modulator HTL14242 (3-Chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile).
Resolution2.603 Å
Binding residue
(original residue number in PDB)		G624 I625 I651 S654 P655 S658 Y659 L744 W785 F788 V806 S809
Binding residue
(residue number reindexed from 1)		G57 I58 I84 S87 P88 S91 Y92 L321 W362 F365 V383 S386
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.30,Ki=0.5nM
Enzymatic activity
Catalytic site (original residue number in PDB) E1011 D1020
Catalytic site (residue number reindexed from 1) E121 D130
Enzyme Commision number 3.2.1.17: lysozyme.
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0004930 G protein-coupled receptor activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0007186 G protein-coupled receptor signaling pathway
GO:0009253 peptidoglycan catabolic process
GO:0016998 cell wall macromolecule catabolic process
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

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Biological Process
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Cellular Component
External links
PDB RCSB:5cgd, PDBe:5cgd, PDBj:5cgd
PDBsum5cgd
PubMed26225459
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
P41594|GRM5_HUMAN Metabotropic glutamate receptor 5 (Gene Name=GRM5)

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