SMTL ID : 6y81.1

Fragment KCL_1088 in complex with MAP kinase p38-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 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.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, A:L.167 Hydrogen bonds: A:M.109, A:M.109

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

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 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.313, A:E.359, H2O.2, H2O.3 CA.4: 1 residues within 4Å: Chain A: D.315 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.315, H2O.7 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain A: D.283 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.283 CA.7: 3 residues within 4Å: Chain A: M.268, N.269, N.272 No protein-ligand interaction detected (PLIP)

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

CL.8: 3 residues within 4Å: Chain A: I.250, S.251, S.252 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: N.114, K.152, P.153, S.154 Ligand excluded by PLIP

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

DMS.10: 3 residues within 4Å: Chain A: A.144, P.322, Y.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.323 Salt bridges: A:D.145

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 5 residues within 4Å: Chain A: P.242, G.243, A.244, L.247, Q.260 No protein-ligand interaction detected (PLIP)

1 x OG5: (3~{R})-~{N}-[(2-azanyl-2-adamantyl)methyl]-3-[[6-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]pyridin-3-yl]sulfonylamino]-3-phenyl-propanamide(Non-covalent)

OG5.12: 13 residues within 4Å: Chain A: L.217, T.218, R.220, T.221, L.222, L.234, R.237, L.238, V.273, F.274, I.275, G.276, A.277 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.218, A:R.220, A:L.234, A:R.237, A:L.238, A:V.273, A:F.274, A:A.277 Hydrogen bonds: A:I.275

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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