Structure of PDB 5n2f Chain B Binding Site BS01

Receptor Information

>5n2f Chain B (length=124) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQF
VHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMIS
YGGADYKRITVKVNAPYAAALEHH

Ligand information

Ligand ID

8HW

InChI

InChI=1S/C27H25F2NO6/c1-16-18(3-2-4-21(16)17-5-6-24-26(10-17)35-8-7-34-24)15-36-25-12-22(28)19(9-23(25)29)13-30-14-20(31)11-27(32)33/h2-6,9-10,12,30H,7-8,11,13-15H2,1H3,(H,32,33)

InChIKey

PRHIMIDCCNVQEI-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	Cc1c(cccc1c2ccc3c(c2)OCCO3)COc4cc(c(cc4F)CNCC(=O)CC(=O)O)F
CACTVS 3.385	Cc1c(COc2cc(F)c(CNCC(=O)CC(O)=O)cc2F)cccc1c3ccc4OCCOc4c3

Formula

C27 H25 F2 N O6

Name

4-[[4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-2,5-bis(fluoranyl)phenyl]methylamino]-3-oxidanylidene-butanoic acid

ChEMBL

DrugBank

ZINC

PDB chain

5n2f 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	5n2f 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	1.7 Å
Binding residue (original residue number in PDB)	I54 Y56 Q66 M115 I116 A121 D122
Binding residue (residue number reindexed from 1)	I37 Y39 Q49 M98 I99 A104 D105
Annotation score	1
Binding affinity	MOAD: ic50=80nM PDBbind-CN: -logKd/Ki=7.10,IC50=80nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:5n2f, PDBe:5n2f, PDBj:5n2f
PDBsum	5n2f
PubMed	28613862
UniProt	Q9NZQ7\|PD1L1_HUMAN Programmed cell death 1 ligand 1 (Gene Name=CD274)

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