SMTL ID : 9cj3.1

Dual phosphorylated human p38 alpha bound to pexmetinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: K.152, F.169, G.170, L.171, A.172, R.173 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.170, A:L.171, A:A.172, A:R.173 Water bridges: A:K.152, A:K.152, A:K.152, A:S.154, A:N.155, A:N.155, A:R.173, A:T.185 Salt bridges: A:K.152, A:R.173

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

EDO.2: 4 residues within 4Å: Chain A: L.217, I.275, G.276 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.275 EDO.3: 4 residues within 4Å: Chain A: D.124, G.276, N.278 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.278 Water bridges: A:N.278 EDO.5: 2 residues within 4Å: Chain A: F.129, Y.311 No protein-ligand interaction detected (PLIP) EDO.7: 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:R.186, A:R.189, A:H.228

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.294, K.295, R.296, I.297, Q.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.295, A:Q.301 Water bridges: A:K.295, A:R.296, A:Q.301

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 1 residues within 4Å: Chain A: R.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.189, A:R.189 DMS.9: 2 residues within 4Å: Chain A: Q.325, S.326 No protein-ligand interaction detected (PLIP)

1 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.8: 5 residues within 4Å: Chain A: R.67, D.150, D.168, G.170 Ligands: 01.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.67, A:R.67, A:G.170

1 x 01: Pexmetinib

01.10: 25 residues within 4Å: Chain A: V.38, A.51, K.53, R.67, E.71, L.74, L.75, M.78, I.84, L.86, L.104, V.105, T.106, H.107, L.108, M.109, G.110, A.111, H.148, A.157, I.166, L.167, D.168, F.169 Ligands: PDO.8 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.38, A:A.51, A:K.53, A:K.53, A:R.67, A:E.71, A:E.71, A:L.75, A:L.75, A:I.84, A:I.84, A:T.106, A:I.166, A:L.167, A:L.167, A:D.168, A:F.169 Hydrogen bonds: A:K.53, A:E.71, A:E.71, A:E.71, A:M.109, A:D.168 Water bridges: A:G.110

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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