SMTL ID : 6yz4.1

Crystal structure of MKK7 (MAP2K7) with ibrutinib bound at allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: H.46, V.47, R.156 Ligands: DMS.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.45, A:V.47 Water bridges: A:D.154, A:D.154, A:D.154 EDO.2: 8 residues within 4Å: Chain A: M.28, V.82, M.98, E.99, L.100, M.101, L.152, D.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.101, A:M.101, A:D.163 EDO.3: 3 residues within 4Å: Chain A: T.87 Ligands: EDO.4, DMS.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.87, A:T.87 EDO.4: 3 residues within 4Å: Chain A: T.87, I.89 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.87 EDO.5: 5 residues within 4Å: Chain A: P.117, E.118, M.249, G.250, F.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.118, A:G.250 Water bridges: A:R.119 EDO.6: 4 residues within 4Å: Chain A: E.137, K.138, H.139, G.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.137 EDO.7: 4 residues within 4Å: Chain A: Y.133, N.274, L.277, E.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.133, A:N.274 EDO.8: 5 residues within 4Å: Chain A: Y.224, C.227, T.229, D.230, V.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.228 EDO.9: 4 residues within 4Å: Chain A: Q.239, E.240, E.241, K.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.265, A:K.265

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

DMS.10: 7 residues within 4Å: Chain A: G.6, A.17, E.18, I.19, L.22, F.88 Ligands: 1E8.14 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.88 DMS.11: 4 residues within 4Å: Chain A: T.44, G.45, H.46 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.46 DMS.12: 6 residues within 4Å: Chain A: T.9, L.73, C.84, F.85, G.86 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.87 DMS.13: 4 residues within 4Å: Chain A: E.27, Q.35, V.36, W.37 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.37, A:W.37

1 x 1E8: 1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one(Non-covalent)

1E8.14: 14 residues within 4Å: Chain A: Y.7, L.8, I.19, L.22, N.24, W.37, M.39, V.50, G.86, T.87, F.88, F.95, A.97 Ligands: DMS.10 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.8, A:I.19, A:I.19, A:L.22, A:N.24, A:W.37, A:W.37, A:V.50, A:F.88, A:F.95, A:F.95, A:F.95, A:F.95, A:A.97 Water bridges: A:K.3 pi-Stacking: A:F.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, M. et al., Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities. Cell Chem Biol (2020)

Release Date

2020-08-12

Peptides

Dual specificity mitogen-activated protein kinase kinase 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dual specificity mitogen-activated protein kinase kinase 7

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