SMTL ID : 5r9j.1

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N14231a in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x LXS: 3-ethyl-1-[(1~{R},8~{S},9~{S},10~{S})-10-oxidanyl-11-oxatricyclo[6.2.1.0^{2,7}]undeca-2(7),3,5-trien-9-yl]imidazolidine-2,4-dione(Non-covalent)

LXS.1: 12 residues within 4Å: Chain A: V.30, V.38, A.51, K.53, I.84, L.104, T.106, H.107, L.108, M.109, L.167, D.168 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.30, A:V.38, A:K.53, A:L.104, A:T.106 Hydrogen bonds: A:K.53, A:M.109, A:D.168

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: P.6, P.21, E.22, R.23 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: T.91, A.93, E.98, N.100, D.101 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: G.85, H.107, K.165 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.73, P.322, Y.323, D.324 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: N.114, K.152, P.153, S.154 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: A.144, P.322, Y.323 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain A: N.155, D.168 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.168, H2O.3, H2O.6, H2O.8, H2O.8

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

SO4.9: 3 residues within 4Å: Chain A: Y.182, R.220, T.221 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.182, A:T.221, A:T.221 Salt bridges: A:R.220

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

DMS.10: 3 residues within 4Å: Chain A: K.76, H.77, K.79 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nichols, C. et al., Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes. J.Med.Chem. (2020)

Release Date

2020-07-22

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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