SMTL ID : 6sov.1

Fragments KCL_615 and KCL_802 in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

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

SB4.1: 15 residues within 4Å: Chain A: V.31, S.33, G.34, V.39, A.52, K.54, I.85, L.87, L.105, V.106, T.107, H.108, L.109, M.110, L.168 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.52, A:K.54, A:I.85, A:T.107 Hydrogen bonds: A:M.110, A:M.110

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

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.2, H2O.3, H2O.3 CA.4: 1 residues within 4Å: Chain A: D.316 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.316, H2O.1, H2O.4 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x LOT: 6-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]pyridine-3-sulfonamide(Non-covalent)

LOT.6: 7 residues within 4Å: Chain A: L.218, T.219, V.274, F.275, I.276, A.278 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.278 Hydrogen bonds: A:I.276

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

LOW.7: 7 residues within 4Å: Chain A: T.222, L.223, L.235, R.238, L.239, M.269 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.223, A:L.239 Hydrogen bonds: A:L.223

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

SO4.8: 7 residues within 4Å: Chain A: T.219, R.221, T.222, L.223, V.274 Ligands: LOT.6, LOW.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.222

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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