Structure of PDB 5v83 Chain A Binding Site BS01

Receptor Information
>5v83 Chain A (length=364) Species: 9606,10665 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS
LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVY
DSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRW
YNQTPNRTKRVITTFRTGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDG
IQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIE
KLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGLDLEMAIAYWNLVLNG
RFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPV
LIDDFVEFARPQIA
Ligand information
Ligand ID8Z7
InChIInChI=1S/C20H22F3N3O/c21-20(22,23)16-7-4-8-18(13-16)25-19(27)24-17-9-11-26(12-10-17)14-15-5-2-1-3-6-15/h1-8,13,17H,9-12,14H2,(H2,24,25,27)
InChIKeyMXZRHPHRSQJCML-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CN2CCC(CC2)NC(=O)Nc3cccc(c3)C(F)(F)F
CACTVS 3.385FC(F)(F)c1cccc(NC(=O)NC2CCN(CC2)Cc3ccccc3)c1
ACDLabs 12.01C3C(NC(=O)Nc1cc(C(F)(F)F)ccc1)CCN(Cc2ccccc2)C3
FormulaC20 H22 F3 N3 O
NameN-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea
ChEMBLCHEMBL4086524
DrugBank
ZINCZINC000006730838
PDB chain5v83 Chain A Residue 401 [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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PDB5v83 Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.
Resolution2.002 Å
Binding residue
(original residue number in PDB)		I1086 F1089 P1097 A1098 V1102 I1105 A1106 A1111 Q1114 E1116 F1117 F1164 A1180 Y1181 L1184
Binding residue
(residue number reindexed from 1)		I201 F204 P212 A213 V217 I220 A221 A226 Q229 E231 F232 F279 A292 Y293 L296
Annotation score1
Binding affinityMOAD: ic50=7uM
PDBbind-CN: -logKd/Ki=5.16,IC50=6.91uM
Enzymatic activity
Catalytic site (original residue number in PDB) E11 D20
Catalytic site (residue number reindexed from 1) E23 D32
Enzyme Commision number 3.2.1.17: lysozyme.
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
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:0030430 host cell cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5v83, PDBe:5v83, PDBj:5v83
PDBsum5v83
PubMed28581483
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
Q96GG9|DCNL1_HUMAN DCN1-like protein 1 (Gene Name=DCUN1D1)

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