SMTL ID : 6spl.1

Fragment KCL615 in complex with MAP kinase p38-alpha

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

1 x SB4: 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE(Non-covalent)

SB4.1: 14 residues within 4Å: Chain A: V.31, S.33, G.34, V.39, A.52, K.54, L.87, L.105, V.106, T.107, H.108, L.109, M.110, L.168 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.52, A:K.54, A:T.107, A:L.168 Hydrogen bonds: A:M.110, A:M.110 Water bridges: A:D.113

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.355, E.357 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.355, A:D.355, A:E.357 CA.3: 2 residues within 4Å: Chain A: D.314, E.360 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.314, A:E.360, H2O.3, H2O.5, H2O.5 CA.4: 1 residues within 4Å: Chain A: D.316 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.316, H2O.1, H2O.2, H2O.10

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

CL.5: 4 residues within 4Å: Chain A: R.74, P.323, Y.324, D.325 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: R.74, D.325, S.327, F.328 Ligand excluded by PLIP

3 x LOW: (5~{S},7~{R})-3-azanyladamantan-1-ol(Non-covalent)

LOW.7: 6 residues within 4Å: Chain A: T.222, L.223, L.235, R.238, L.239, M.269 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.223, A:L.239, A:L.239 Hydrogen bonds: A:L.223 LOW.8: 4 residues within 4Å: Chain A: R.50, N.160, E.161, D.162 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.162 Hydrogen bonds: A:D.162 Water bridges: A:E.164, A:E.164 LOW.9: 6 residues within 4Å: Chain A: N.27, S.29, A.41, A.42, F.43, L.109 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.27, A:A.41, A:F.43, A:L.109 Hydrogen bonds: A:N.27 Water bridges: A:N.27

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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