SMTL ID : 7jra.1

HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}quinolin-6-yl)pyrimidin-2-yl]propan-2-ol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

1 x VGY: 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}quinolin-6-yl)pyrimidin-2-yl]propan-2-ol(Non-covalent)

VGY.1: 23 residues within 4Å: Chain A: K.14, L.60, Y.62, Y.122, V.126, I.158, A.159, L.160 Chain B: L.60, Y.62, Y.122, G.124, G.125, L.160 Chain C: L.60, Y.62, S.63, Y.122, L.123, G.124, Y.154, I.158, L.160 17 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: C:Y.62, C:Y.154, B:Y.62, B:Y.122, A:L.60, A:L.60, A:V.126, A:I.158, A:I.158 pi-Stacking: C:Y.62, A:Y.62 Hydrogen bonds: B:Y.122, B:Y.122, A:L.160, A:L.160 Water bridges: A:K.14, A:Y.122

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain B: P.120, I.121, Y.122 Chain C: K.101, P.120, I.121, Y.122 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.122, C:P.120, C:Y.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, H.Y. et al., Biologic-like In Vivo Efficacy with Small Molecule Inhibitors of TNF alpha Identified Using Scaffold Hopping and Structure-Based Drug Design Approaches. J.Med.Chem. (2020)

Release Date

2020-12-09

Peptides

Tumor necrosis factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Tumor necrosis factor