Structure of PDB 4j59 Chain A Binding Site BS01

Receptor Information
>4j59 Chain A (length=164) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGS
TFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMA
NAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGR
TSKKIVITDCGQLS
Ligand information
Ligand ID671
InChIInChI=1S/C24H26N4O2/c25-19-12-10-17(11-13-19)15-26-24(30)27-16-23(29)28-14-4-9-22(28)21-8-3-6-18-5-1-2-7-20(18)21/h1-3,5-8,10-13,22H,4,9,14-16,25H2,(H2,26,27,30)/t22-/m1/s1
InChIKeyMRLPPIJHRIIWJS-JOCHJYFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc2c(c1)cccc2C3CCCN3C(=O)CNC(=O)NCc4ccc(cc4)N
ACDLabs 12.01O=C(N3C(c1cccc2c1cccc2)CCC3)CNC(=O)NCc4ccc(N)cc4
CACTVS 3.370Nc1ccc(CNC(=O)NCC(=O)N2CCC[CH]2c3cccc4ccccc34)cc1
OpenEye OEToolkits 1.7.6c1ccc2c(c1)cccc2[C@H]3CCCN3C(=O)CNC(=O)NCc4ccc(cc4)N
CACTVS 3.370Nc1ccc(CNC(=O)NCC(=O)N2CCC[C@@H]2c3cccc4ccccc34)cc1
FormulaC24 H26 N4 O2
Name1-(4-aminobenzyl)-3-{2-[(2R)-2-(naphthalen-1-yl)pyrrolidin-1-yl]-2-oxoethyl}urea
ChEMBL
DrugBank
ZINCZINC000098208536
PDB chain4j59 Chain A Residue 301 [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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PDB4j59 Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.
Resolution1.92 Å
Binding residue
(original residue number in PDB)		F102 M103 Q105 R124 A143 N144 Q153 F155 H168
Binding residue
(residue number reindexed from 1)		F59 M60 Q62 R81 A100 N101 Q110 F112 H125
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.85,IC50=1.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) R97 F102 Q105 N144 F155 L164 H168
Catalytic site (residue number reindexed from 1) R54 F59 Q62 N101 F112 L121 H125
Enzyme Commision number 5.2.1.8: peptidylprolyl isomerase.
Gene Ontology
Molecular Function
GO:0003755 peptidyl-prolyl cis-trans isomerase activity
Biological Process
GO:0000413 protein peptidyl-prolyl isomerization
GO:0006457 protein folding

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4j59, PDBe:4j59, PDBj:4j59
PDBsum4j59
PubMed27652979
UniProtP30405|PPIF_HUMAN Peptidyl-prolyl cis-trans isomerase F, mitochondrial (Gene Name=PPIF)

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