SMTL ID : 5ra6.1

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N11338a in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x SVM: 1-[(1~{R},2~{R},4~{S})-2-bicyclo[2.2.1]heptanyl]-3-(2-pyridin-2-ylethyl)thiourea(Non-covalent)

SVM.1: 9 residues within 4Å: Chain A: A.51, K.53, L.75, I.84, L.104, T.106, M.109, A.111, D.112 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.53, A:K.53, A:L.75, A:I.84, A:L.104

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

CL.2: 4 residues within 4Å: Chain A: P.6, P.21, E.22, R.23 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: T.91, A.93, E.98, N.100, D.101 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: I.84, G.85, T.106, H.107, K.165 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.73, P.322, Y.323, D.324 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: N.114, K.152, P.153, S.154 Ligand excluded by PLIP

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

SO4.7: 3 residues within 4Å: Chain A: Y.182, R.220, T.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.221, A:T.221 Salt bridges: A:R.220

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

DMS.8: 3 residues within 4Å: Chain A: K.76, H.77, K.79 No protein-ligand interaction detected (PLIP)

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

2020-07-22

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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