SMTL ID : 6so4.1

Fragment RZ132 in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

1 x LO8: (2~{S})-2-methyl-4-(oxetan-3-yl)-~{N}-(phenylmethyl)piperazine-2-carboxamide(Non-covalent)

LO8.1: 8 residues within 4Å: Chain A: T.239, R.241, T.242, L.243, R.258, V.294, F.295, I.296 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.239, A:V.294, A:F.295 Hydrogen bonds: A:T.239, A:T.242, A:R.258 Water bridges: A:V.294

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

CL.2: 4 residues within 4Å: Chain A: P.27, P.42, E.43, R.44 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: T.112, A.114, E.119, N.121, D.122 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: V.104, G.106, H.128, K.186 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.94, P.343, Y.344, D.345 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: N.135, K.173, P.174, S.175 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: A.284, Q.285 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: N.176, D.189 Ligands: SO4.10 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.189, H2O.1, H2O.1, H2O.3, H2O.7

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

SO4.9: 3 residues within 4Å: Chain A: Y.203, R.241, T.242 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.203, A:Y.203, A:T.242, A:T.242 Water bridges: A:G.240 Salt bridges: A:R.241 SO4.10: 5 residues within 4Å: Chain A: D.171, K.173, H.195, T.206 Ligands: MG.8 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.175, A:N.176, A:D.189 Salt bridges: A:K.173, A:H.195

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

2019-09-11

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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