SMTL ID : 6sod.1

Fragment N14056a in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

1 x LOE: 1-[[(3~{S})-1,4-dioxaspiro[4.5]decan-3-yl]methyl]piperidine(Non-covalent)

LOE.1: 8 residues within 4Å: Chain A: T.239, R.241, T.242, L.243, L.255, L.259, M.289, V.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.239, A:R.241, A:L.259, A:V.294

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

CL.2: 5 residues within 4Å: Chain A: T.112, A.114, E.119, N.121, D.122 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: 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: 1 residues within 4Å: Chain A: E.184 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: M.289, N.290 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: N.217, M.219 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.3, H2O.4, H2O.4

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

SO4.10: 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 SO4.11: 2 residues within 4Å: Chain A: K.173, H.195 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.173, A:S.175, A:D.189 Salt bridges: A:K.173, A:H.195

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

DMS.12: 3 residues within 4Å: Chain A: K.97, H.98, K.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.98 Water bridges: A:R.94

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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