SMTL ID : 9cj4.1

Dual phosphorylated human p38 alpha bound to BIRB796

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x B96: 1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA(Non-covalent)

B96.1: 22 residues within 4Å: Chain A: V.38, A.51, K.53, R.67, E.71, L.74, L.75, M.78, V.83, I.84, L.104, T.106, H.107, L.108, M.109, G.110, H.148, I.166, L.167, D.168, F.169 Ligands: PEG.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:A.51, A:K.53, A:K.53, A:R.67, A:E.71, A:E.71, A:L.75, A:V.83, A:I.84, A:I.84, A:L.104, A:T.106, A:I.166, A:D.168 Hydrogen bonds: A:K.53, A:E.71, A:E.71, A:E.71, A:M.109, A:G.110, A:D.168

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

SO4.2: 7 residues within 4Å: Chain A: K.152, F.169, G.170, L.171, A.172, R.173 Ligands: PEG.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.170, A:L.171, A:A.172, A:R.173 Water bridges: A:N.155 Salt bridges: A:K.152, A:R.173 SO4.4: 2 residues within 4Å: Chain A: R.57, Q.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.57, A:Q.60

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: H.107, L.108, M.109, N.159, E.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.107, A:N.159 EDO.9: 1 residues within 4Å: Chain A: S.254 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain A: R.256, Q.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.256, A:R.256, A:Q.260 EDO.14: 2 residues within 4Å: Chain A: R.330, L.332 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: E.81, N.82, Q.133, R.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.82 Water bridges: A:L.164, A:L.164

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: Q.11, Q.25, N.26, L.27 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.25, A:N.26, A:L.27 Water bridges: A:Y.9, A:Q.25, A:L.27 PEG.6: 6 residues within 4Å: Chain A: R.67, D.150, D.168, G.170 Ligands: B96.1, SO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.67, A:R.67 Water bridges: A:H.148, A:H.148, A:D.150, A:D.168 PEG.7: 4 residues within 4Å: Chain A: D.125, H.126, F.129, Y.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.125 PEG.8: 3 residues within 4Å: Chain A: R.186, R.189, H.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.186, A:R.189 Water bridges: A:T.185, A:I.193, A:H.228

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: L.217, F.274, I.275, A.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.217, A:F.274 GOL.11: 4 residues within 4Å: Chain A: Y.323, D.324, Q.325, S.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.323, A:Q.325 Water bridges: A:Q.325, A:Q.325 GOL.12: 5 residues within 4Å: Chain A: P.6, P.21, D.88, V.89, F.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.88, A:V.89 Water bridges: A:R.23, A:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stadnicki, E.J. et al., Dual-Action Kinase Inhibitors Influence p38 alpha MAP Kinase Dephosphorylation. Biorxiv (2024)

Release Date

2024-11-13

Peptides

Mitogen-activated protein kinase 14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitogen-activated protein kinase 14

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