SMTL ID : 6so1.1

Fragment N13569a in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x LO5: 1-(1,3-benzodioxol-5-yl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine(Non-covalent)

LO5.1: 9 residues within 4Å: Chain A: T.239, T.242, L.243, P.245, L.255, R.258, L.259, M.289, F.295 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.239 Hydrogen bonds: A:L.243, A:R.258 Water bridges: A:T.239

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

CL.2: 4 residues within 4Å: Chain A: P.27, P.42, E.43, R.44 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: T.112, A.114, E.119, N.121, D.122 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: I.105, G.106, H.128, K.186 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.94, P.343, Y.344, D.345 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: N.135, K.173, P.174, S.175 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: A.165, P.343, Y.344 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: M.289, N.290 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: N.176, D.189 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.189, H2O.1, H2O.5, H2O.6, H2O.7

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

SO4.10: 2 residues within 4Å: Chain A: R.241, T.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.242, A:T.242 Salt bridges: A:R.241 SO4.11: 4 residues within 4Å: Chain A: D.171, K.173, H.195, T.206 7 PLIP interactions: 7 interactions with chain A Water bridges: A:S.175, A:N.176, A:N.176, A:N.176, A:D.189 Salt bridges: A:K.173, A:H.195

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

2019-10-02

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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