Structure of PDB 5cgc Chain A Binding Site BS01

Receptor Information
>5cgc Chain A (length=409) 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
IILAKPERN
Ligand information
Ligand ID51D
InChIInChI=1S/C14H7ClFN5/c15-11-5-9(7-17)4-10(14(11)16)12-6-13(19-8-18-12)21-3-1-2-20-21/h1-6,8H
InChIKeyUPDNOLJVPHHECL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cnn(c1)c2cc(ncn2)c3cc(cc(c3F)Cl)C#N
CACTVS 3.385Fc1c(Cl)cc(cc1c2cc(ncn2)n3cccn3)C#N
ACDLabs 12.01c1(c(cc(cc1Cl)C#N)c2ncnc(c2)n3cccn3)F
FormulaC14 H7 Cl F N5
Name3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile
ChEMBLCHEMBL3603915
DrugBank
ZINCZINC000219247130
PDB chain5cgc Chain A Residue 4006 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5cgc 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).
Resolution3.101 Å
Binding residue
(original residue number in PDB)		I625 I651 P655 L744 W785 F788 V806 S809 A810
Binding residue
(residue number reindexed from 1)		I58 I84 P88 L321 W362 F365 V383 S386 A387
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5cgc, PDBe:5cgc, PDBj:5cgc
PDBsum5cgc
PubMed26225459
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
P41594|GRM5_HUMAN Metabotropic glutamate receptor 5 (Gene Name=GRM5)

[Back to BioLiP]