SMTL ID : 6y80.1

Fragment KCL_916 in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

1 x OFZ: 1-(2-adamantylmethyl)-3-ethyl-guanidine(Non-covalent)

OFZ.1: 10 residues within 4Å: Chain A: R.220, T.221, L.222, F.223, P.224, L.234, R.237, L.238, M.268 Ligands: SO4.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.223, A:P.224, A:L.234, A:L.238 Hydrogen bonds: A:T.221, A:L.222

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

SB4.2: 15 residues within 4Å: Chain A: V.30, S.32, G.33, V.38, A.51, K.53, I.84, L.86, L.104, V.105, T.106, H.107, L.108, M.109, L.167 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.51, A:K.53, A:I.84, A:T.106 Hydrogen bonds: A:M.109, A:M.109 Water bridges: A:D.112

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

CA.3: 2 residues within 4Å: Chain A: D.354, E.356 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.354, A:D.354, A:E.356 CA.4: 2 residues within 4Å: Chain A: D.313, E.359 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.313, A:E.359, H2O.4, H2O.4, H2O.5 CA.5: 1 residues within 4Å: Chain A: D.315 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.315, H2O.4, H2O.9, H2O.10 CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 4 residues within 4Å: Chain A: H.77, P.322, Y.323, D.324 Ligand excluded by PLIP

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

SO4.8: 7 residues within 4Å: Chain A: T.218, R.220, T.221, L.222, V.273, F.274 Ligands: OFZ.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.221

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

2020-03-11

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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