SMTL ID : 6szm.1 (1 other biounit)

Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2009

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

3 x M2Z: 1-[4-[4-methyl-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenyl]piperazine(Non-covalent)

M2Z.1: 11 residues within 4Å: Chain A: R.4, V.6, A.7, R.8, I.10, W.29, I.68, A.69, D.71, I.84 Ligands: M2Z.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.6, A:R.8 Hydrogen bonds: A:A.7, A:R.8 M2Z.2: 6 residues within 4Å: Chain A: R.4, W.29, E.32, I.68, A.69 Ligands: M2Z.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.29 Water bridges: A:R.4 M2Z.3: 22 residues within 4Å: Chain A: V.16, V.24, A.35, V.36, K.37, E.50, L.65, L.83, I.84, T.85, H.86, Y.87, H.88, E.89, G.91, S.92, D.95, K.142, N.143, L.145, A.155, D.156 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.16, A:V.16, A:A.35, A:Y.87, A:L.145 Hydrogen bonds: A:H.88 Water bridges: A:K.37, A:D.156

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

SO4.4: 5 residues within 4Å: Chain A: H.88, E.89, K.147, K.148, N.149 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.148 Water bridges: A:E.89, A:N.149 Salt bridges: A:H.88, A:K.148 SO4.11: 2 residues within 4Å: Chain A: P.260, N.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.261 Water bridges: A:N.258, A:N.261, A:R.262

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

EDO.5: 7 residues within 4Å: Chain A: F.233, D.235, V.236, Q.255, R.256, P.257, N.258 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.235, A:N.258, A:N.258 Water bridges: A:F.233, A:N.258, A:N.258 EDO.6: 9 residues within 4Å: Chain A: H.61, E.62, I.64, L.65, G.66, H.86, H.88, K.147, C.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.66, A:H.86, A:H.88 Water bridges: A:K.147 EDO.7: 7 residues within 4Å: Chain A: R.182, P.231, F.233, Y.234, V.237, P.238, N.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.182, A:R.182, A:V.237, A:P.238 EDO.8: 4 residues within 4Å: Chain A: K.45, F.48, R.49, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49, A:E.52, A:E.52 EDO.10: 5 residues within 4Å: Chain A: R.218, E.227, D.228, K.230, Y.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.218, A:R.218, A:Y.234 Water bridges: A:Y.234

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.9: 7 residues within 4Å: Chain A: K.45, R.49, R.137, L.159, N.175, P.176, R.177 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.45, A:R.49, A:R.49, A:R.137, A:R.177, A:R.177, A:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smil, D. et al., Leveraging an Open Science Drug Discovery Model to Develop CNS-Penetrant ALK2 Inhibitors for the Treatment of Diffuse Intrinsic Pontine Glioma. J.Med.Chem. (2020)

Release Date

2019-10-16

Peptides

Activin receptor type I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Activin receptor type I

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