SMTL ID : 6y7y.1

Fragments KCL_771 and KCL_802 in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

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

SB4.1: 14 residues within 4Å: Chain A: V.30, S.32, G.33, V.38, A.51, K.53, L.86, L.104, V.105, T.106, H.107, L.108, M.109, L.167 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.51, A:K.53, A:T.106, A:L.167 Hydrogen bonds: A:M.109, A:M.109 Water bridges: A:A.34, A:D.112, A:D.112

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.3: 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.3, H2O.4, H2O.6 CA.4: 1 residues within 4Å: Chain A: D.315 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.315, H2O.1, H2O.3 CA.5: 3 residues within 4Å: Chain A: H.142, Q.202, A.299 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.142, H2O.8, H2O.8

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

CL.6: 3 residues within 4Å: Chain A: H.77, P.322, D.324 Ligand excluded by PLIP

1 x OFQ: (2-azanyl-2-adamantyl)methanol(Non-covalent)

OFQ.7: 5 residues within 4Å: Chain A: L.222, L.234, R.237, L.238, M.268 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.222, A:L.234, A:R.237 Hydrogen bonds: A:L.222

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

LOT.8: 7 residues within 4Å: Chain A: L.217, T.218, R.220, V.273, F.274, I.275, A.277 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.277 Hydrogen bonds: A:I.275 LOT.9: 6 residues within 4Å: Chain A: K.267, E.286, K.287, V.290, K.295, I.297 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.290, A:K.295 Hydrogen bonds: A:K.295, A:I.297

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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