SMTL ID : 6soi.1

Fragment N13788a in complex with MAP kinase p38-alpha

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x LOK: methyl ~{N}-[3-(methoxycarbonylamino)phenyl]carbamate(Non-covalent)

LOK.1: 6 residues within 4Å: Chain A: L.238, T.239, V.294, F.295, I.296, A.298 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.239 Hydrogen bonds: A:L.238, A:V.294

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

CL.2: 6 residues within 4Å: Chain A: T.112, P.113, A.114, E.119, N.121, D.122 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: V.104, G.106, H.128, K.186 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.94, P.343, Y.344, D.345 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: N.135, K.173, P.174, S.175 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: A.284, Q.285 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 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.2, H2O.5, H2O.6, H2O.7

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

SO4.8: 2 residues within 4Å: Chain A: R.241, T.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.242, A:T.242, A:T.242 Salt bridges: A:R.241 SO4.9: 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:D.189, A:D.189 Salt bridges: A:K.173, A:H.195

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

DMS.10: 3 residues within 4Å: Chain A: K.97, H.98, K.100 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.97

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