SMTL ID : 3lkj.1

Small Molecule Inhibition of the TNF Family Cyokine CD40 Ligand Through a Subunit Fracture Mechanism

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 6 residues within 4Å: Chain A: S.16, C.74, E.82, N.120, V.121 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.16, A:E.82 Water bridges: A:R.87 NAG.2: 4 residues within 4Å: Chain A: E.82, R.83, I.84 Ligands: NAG.1 No protein-ligand interaction detected (PLIP) NAG.3: 8 residues within 4Å: Chain B: I.70, S.72, E.82, R.87, N.120, V.121, T.122 Ligands: NAG.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.70, B:T.122 Hydrogen bonds: B:S.72, B:S.72, B:E.82, B:E.82, B:R.87 NAG.4: 3 residues within 4Å: Chain B: E.82, I.84 Ligands: NAG.3 No protein-ligand interaction detected (PLIP) NAG.6: 7 residues within 4Å: Chain C: I.70, S.72, C.74, E.82, N.120, V.121 Ligands: NAG.7 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.70 Hydrogen bonds: C:N.120 Water bridges: C:S.72, C:R.87 NAG.7: 3 residues within 4Å: Chain C: E.82, I.84 Ligands: NAG.6 No protein-ligand interaction detected (PLIP)

1 x LKJ: (2R)-{[(2'-[(biphenyl-3-ylmethyl)carbamoyl]-6'-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}-6-{[(2R)-2-(1H-pyrrol-1-ylmethyl)pyrrolidin-1-yl]carbonyl}-4,4'-bipyridin-2-yl)carbonyl]amino}(cyclohexyl)ethanoic acid(Non-covalent)

LKJ.5: 26 residues within 4Å: Chain A: L.48, Y.50, V.108, F.109, E.110, L.139, L.141 Chain B: Y.50, Y.52, A.53, H.104, L.105 Chain C: Q.1, A.3, H.5, G.24, Y.25, Y.26, Y.50, Y.52, A.53, H.104, L.105, G.106, L.139, L.141 26 PLIP interactions: 5 interactions with chain A, 17 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: A:L.48, A:Y.50, A:V.108, A:E.110, A:L.139, C:Q.1, C:A.3, C:H.5, C:Y.25, C:Y.26, C:Y.50, C:Y.52, C:Y.52, C:H.104, C:L.139, C:L.139, C:L.141, B:Y.50, B:Y.52, B:Y.52, B:H.104 Hydrogen bonds: C:Y.25, C:Y.26, C:Y.50 Salt bridges: C:H.5 pi-Stacking: C:Y.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvian, L.F. et al., Small Molecule Inhibition of the TNF Family Cytokine CD40 Ligand through a Subunit Fracture Mechanism. Acs Chem.Biol. (2011)

Release Date

2011-02-02

Peptides

CD40 ligand: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

CD40 ligand