Structure of PDB 6bg5 Chain A Binding Site BS01

Receptor Information
>6bg5 Chain A (length=366) Species: 9606,10665 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HSQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSP
SLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPV
YDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSR
WYNQTPNRTKRVITTFRTGTWDAYKNLRKKLEQLYNRYKDPQDENKIGID
GIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSI
EKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNL
VLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEG
AWPVLIDDFVEFARPQ
Ligand information
Ligand IDDQD
InChIInChI=1S/C24H28F3N3O3/c1-2-10-29-11-8-20(9-12-29)30(15-17-6-7-21-22(13-17)33-16-32-21)23(31)28-19-5-3-4-18(14-19)24(25,26)27/h3-7,13-14,20H,2,8-12,15-16H2,1H3,(H,28,31)
InChIKeyPLBHVOJLFQGHAQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCN1CCC(CC1)N(Cc2ccc3c(c2)OCO3)C(=O)Nc4cccc(c4)C(F)(F)F
CACTVS 3.385CCCN1CCC(CC1)N(Cc2ccc3OCOc3c2)C(=O)Nc4cccc(c4)C(F)(F)F
ACDLabs 12.01FC(F)(F)c1cccc(c1)NC(=O)N(C2CCN(CC2)CCC)Cc3ccc4c(c3)OCO4
FormulaC24 H28 F3 N3 O3
NameN-[(2H-1,3-benzodioxol-5-yl)methyl]-N-(1-propylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea
ChEMBLCHEMBL4104419
DrugBank
ZINC
PDB chain6bg5 Chain A Residue 1301 [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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PDB6bg5 Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation.
Resolution1.1 Å
Binding residue
(original residue number in PDB)		I1083 I1086 F1089 P1097 A1106 Q1114 E1116 F1117 F1164 Y1181
Binding residue
(residue number reindexed from 1)		I199 I202 F205 P213 A222 Q230 E232 F233 F280 Y297
Annotation score1
Binding affinityMOAD: ic50=1uM
PDBbind-CN: -logKd/Ki=6.00,IC50=1uM
Enzymatic activity
Catalytic site (original residue number in PDB) E11 D20
Catalytic site (residue number reindexed from 1) E24 D33
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:6bg5, PDBe:6bg5, PDBj:6bg5
PDBsum6bg5
PubMed29547696
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
Q96GG9|DCNL1_HUMAN DCN1-like protein 1 (Gene Name=DCUN1D1)

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