SMTL ID : 6sp9.1

Fragment KCL802 in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.39, A:A.52, A:K.54, A:I.85, A:T.107 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.3, H2O.6 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.9

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

DMS.5: 7 residues within 4Å: Chain A: T.219, R.221, T.222, L.223, V.274, F.275 Ligands: LOT.7 No protein-ligand interaction detected (PLIP) DMS.6: 6 residues within 4Å: Chain A: L.123, T.124, D.125, V.128, L.218 Ligands: LOT.7 No protein-ligand interaction detected (PLIP)

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

LOT.7: 8 residues within 4Å: Chain A: L.218, T.219, V.274, F.275, I.276, A.278 Ligands: DMS.5, DMS.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.278 Hydrogen bonds: A:I.276 LOT.8: 9 residues within 4Å: Chain A: P.7, F.9, P.22, R.24, Y.25, D.89, F.91, T.92, A.94 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.9, A:P.22, A:F.91, A:T.92 Hydrogen bonds: A:R.24, A:D.89, A:T.92

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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