Structure of PDB 5n2d Chain A Binding Site BS01

Receptor Information

>5n2d Chain A (length=125) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQF
VHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMIS
YGGADYKRITVKVNAPYAAALEHHH

Ligand information

Ligand ID

8J8

InChI

InChI=1S/C27H32N2O4/c1-19-22(11-8-12-24(19)21-9-6-5-7-10-21)18-33-23-15-26(31-3)25(27(16-23)32-4)17-28-13-14-29-20(2)30/h5-12,15-16,28H,13-14,17-18H2,1-4H3,(H,29,30)

InChIKey

OYNIISWIMDFFAF-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	Cc1c(cccc1c2ccccc2)COc3cc(c(c(c3)OC)CNCCNC(=O)C)OC
CACTVS 3.385	COc1cc(OCc2cccc(c2C)c3ccccc3)cc(OC)c1CNCCNC(C)=O

Formula

C27 H32 N2 O4

Name

~{N}-[2-[[2,6-dimethoxy-4-[(2-methyl-3-phenyl-phenyl)methoxy]phenyl]methylamino]ethyl]ethanamide

PDB chain

5n2d Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5n2d Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1.
Resolution	2.35 Å
Binding residue (original residue number in PDB)	F19 Y56 M115 I116 S117 A121 D122 Y123
Binding residue (residue number reindexed from 1)	F2 Y39 M98 I99 S100 A104 D105 Y106
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=8.22,IC50~6nM BindingDB: Kd=<1000nM,IC50=6.0nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:5n2d, PDBe:5n2d, PDBj:5n2d
PDBsum	5n2d
PubMed	28613862
UniProt	Q9NZQ7\|PD1L1_HUMAN Programmed cell death 1 ligand 1 (Gene Name=CD274)

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