SMTL ID : 6vql.1

CRYSTAL STRUCTURE OF INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4 (IRAK4-WT) COMPLEX WITH A NICOTINAMIDE INHIBITOR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

4 x R7S: 6-[(1,3-benzothiazol-6-yl)amino]-4-(cyclopropylamino)-N-[(2R)-2-fluoro-3-hydroxy-3-methylbutyl]pyridine-3-carboxamide(Non-covalent)

R7S.1: 19 residues within 4Å: Chain A: I.30, M.37, G.38, V.45, A.56, K.58, V.91, Y.107, V.108, Y.109, M.110, P.111, N.112, G.113, R.118, D.123, T.125, L.163, S.173 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.30, A:V.45, A:V.45, A:A.56, A:V.91, A:Y.107, A:Y.107, A:T.125, A:L.163 Hydrogen bonds: A:V.108, A:Y.109, A:M.110, A:M.110, A:G.113 Water bridges: A:S.114, A:R.118 pi-Stacking: A:Y.107 Halogen bonds: A:R.118 R7S.3: 19 residues within 4Å: Chain B: I.30, M.37, G.38, V.45, A.56, K.58, V.91, Y.107, V.108, Y.109, M.110, P.111, N.112, G.113, R.118, D.123, T.125, L.163, S.173 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.30, B:V.45, B:A.56, B:V.91, B:Y.107, B:T.125, B:L.163 Hydrogen bonds: B:V.108, B:Y.109, B:M.110, B:M.110, B:G.113, B:D.174 pi-Stacking: B:Y.107, B:Y.107 Halogen bonds: B:R.118 R7S.8: 17 residues within 4Å: Chain C: I.30, M.37, G.38, V.45, A.56, K.58, V.91, Y.107, V.108, Y.109, M.110, P.111, G.113, R.118, T.125, L.163, S.173 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.30, C:V.45, C:V.45, C:V.91, C:Y.107, C:T.125, C:L.163 Hydrogen bonds: C:V.108, C:M.110, C:M.110, C:G.113 Water bridges: C:D.174 pi-Stacking: C:Y.107, C:Y.107 R7S.12: 19 residues within 4Å: Chain D: I.30, M.37, G.38, V.45, A.56, K.58, V.91, Y.107, V.108, Y.109, M.110, P.111, N.112, G.113, R.118, D.123, T.125, L.163, S.173 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.30, D:V.45, D:V.45, D:A.56, D:V.91, D:Y.107, D:T.125, D:L.163 Hydrogen bonds: D:V.108, D:M.110, D:M.110, D:G.113 pi-Stacking: D:Y.107, D:Y.107 Halogen bonds: D:R.118

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: G.195, T.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.197 SO4.4: 4 residues within 4Å: Chain B: I.248, E.249, Y.275, S.279 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.249, B:S.279 SO4.5: 3 residues within 4Å: Chain B: F.10, H.11, S.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.12 Salt bridges: B:H.11 SO4.6: 4 residues within 4Å: Chain B: K.245, H.283, E.284, K.285 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.284, B:K.285 Salt bridges: B:K.245, B:H.283 SO4.7: 3 residues within 4Å: Chain B: G.195, T.196, T.197 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.195, B:T.197 SO4.9: 3 residues within 4Å: Chain A: N.52 Chain C: D.267, S.268 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.268, C:S.268, C:S.268, A:N.52 SO4.10: 3 residues within 4Å: Chain C: H.283, E.284, K.285 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.284, C:K.285 Salt bridges: C:H.283 SO4.11: 2 residues within 4Å: Chain A: H.11 Chain C: T.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.11 SO4.13: 3 residues within 4Å: Chain B: N.52 Chain D: D.267, S.268 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.268, B:N.52 SO4.14: 3 residues within 4Å: Chain D: F.10, H.11, S.12 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.12 Salt bridges: D:H.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nair, S. et al., Optimization of Nicotinamides as Potent and Selective IRAK4 Inhibitors with Efficacy in a Murine Model of Psoriasis. Acs Med.Chem.Lett. (2020)

Release Date

2020-06-24

Peptides

Interleukin-1 receptor-associated kinase 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Interleukin-1 receptor-associated kinase 4

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