SMTL ID : 6yg2.1

Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric binding modes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: G.86, T.87 Ligands: DMS.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.87 Water bridges: A:T.87 EDO.2: 4 residues within 4Å: Chain A: Y.133, N.274, L.277, E.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.278 EDO.3: 1 residues within 4Å: Chain A: K.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.130 EDO.4: 4 residues within 4Å: Chain A: H.46, V.47, L.100 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.47, A:L.100 Water bridges: A:L.100 EDO.5: 4 residues within 4Å: Chain A: T.44, G.45, H.46 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.44 EDO.6: 4 residues within 4Å: Chain A: K.109, G.220, Q.221, F.222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.109, A:F.222 Water bridges: A:K.109, A:E.216, A:Q.221 EDO.7: 5 residues within 4Å: Chain A: M.28, G.102, T.103, K.107 Ligands: 8E8.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.103, A:K.107 EDO.8: 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

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

DMS.9: 6 residues within 4Å: Chain A: R.156, G.157, V.290, D.291, V.292, A.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.292, A:A.293 Salt bridges: A:D.291 DMS.10: 7 residues within 4Å: Chain A: G.6, A.17, E.18, I.19, L.22, F.88 Ligands: 1E8.13 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.88 DMS.11: 6 residues within 4Å: Chain A: T.9, L.73, C.84, F.85, G.86 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.9, A:T.87 DMS.12: 4 residues within 4Å: Chain A: P.117, E.118, M.249, G.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.118 Water bridges: A:R.119

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)

1E8.13: 13 residues within 4Å: Chain A: Y.7, L.8, I.19, L.22, N.24, W.37, M.39, G.86, T.87, F.88, F.95, A.97 Ligands: DMS.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.8, A:I.19, A:L.22, A:W.37, A:W.37, A:F.88, A:F.95, A:F.95, A:A.97 pi-Stacking: A:F.95

1 x 8E8: 1-[(3~{R})-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one(Covalent)

8E8.14: 20 residues within 4Å: Chain A: M.28, G.29, S.30, G.31, K.51, I.65, D.68, L.69, V.82, I.96, M.98, E.99, L.100, M.101, C.104, E.106, K.107, S.149, F.164 Ligands: EDO.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:M.28, A:K.51, A:I.65, A:D.68, A:L.69, A:I.96, A:M.98, A:F.164 Hydrogen bonds: A:E.99, A:M.101

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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