SMTL ID : 4wx4.1

Crystal structure of adenovirus 8 protease in complex with a nitrile inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

hetero-oligomer

Ligands

1 x 3VF: N-[(2-cyanopyrimidin-4-yl)methyl]-3-[2-(3,5-dichlorophenyl)-2-methylpropanoyl]-4-methoxybenzamide(Covalent)

3VF.1: 23 residues within 4Å: Chain A: S.2, S.4, S.5, E.6, T.25, H.26, D.27, N.45, A.47, G.48, R.49, G.52, G.53, V.54, H.55, W.56, Q.116, S.120, A.121, A.122, C.123, M.202 Ligands: EPE.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.6, A:D.27, A:W.56 Hydrogen bonds: A:S.2, A:E.6, A:N.45, A:Q.116, A:S.120, A:C.123 Water bridges: A:H.55, A:H.55 pi-Stacking: A:W.56 Halogen bonds: A:T.25, A:A.47

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 7 residues within 4Å: Chain A: L.23, G.24, T.25, H.26, D.27, R.49 Ligands: 3VF.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.23, A:D.27 Salt bridges: A:R.49 pi-Cation interactions: A:H.26

1 x GLY: GLYCINE(Covalent)

GLY.3: 7 residues within 4Å: Chain A: Q.113, M.142, D.143, M.148, L.151, G.153 Chain B: V.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.143, A:G.153 Water bridges: B:K.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grosche, P. et al., Structure-based design and optimization of potent inhibitors of the adenoviral protease. Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-01-14

Peptides

Protease: A
peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Protease

peptide