SMTL ID : 8c7z.1

Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2308

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

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

NH4.1: 2 residues within 4Å: Chain A: S.92, D.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.92, A:D.95

1 x TZX: 9-piperazin-1-yl-4-(3,4,5-trimethoxyphenyl)-5,6-dihydro-[1]benzoxepino[5,4-c]pyridine(Non-covalent)

TZX.2: 20 residues within 4Å: Chain A: V.16, V.24, A.35, V.36, K.37, E.50, L.65, L.83, T.85, H.86, Y.87, H.88, G.91, S.92, D.95, K.142, N.143, L.145, A.155, D.156 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.16, A:V.16, A:V.24, A:V.24, A:A.35, A:Y.87, A:L.145, A:L.145 Hydrogen bonds: A:H.88, A:S.92, A:D.95

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

SO4.3: 4 residues within 4Å: Chain A: R.182, N.239, D.240, P.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.240 Salt bridges: A:R.182 SO4.4: 5 residues within 4Å: Chain A: H.86, Y.87, H.88, K.147, K.148 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.148 Water bridges: A:Y.87, A:K.148, A:N.149, A:N.149 Salt bridges: A:H.86, A:H.88, A:K.148 SO4.5: 3 residues within 4Å: Chain A: M.72, T.73, S.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.72, A:S.74 SO4.6: 2 residues within 4Å: Chain A: T.289, R.292 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.289, A:R.292 Salt bridges: A:R.292 SO4.7: 2 residues within 4Å: Chain A: Y.96, L.99 No protein-ligand interaction detected (PLIP)

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

EDO.8: 6 residues within 4Å: Chain A: M.58, L.59, R.60, H.120, I.125, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.60, A:R.60 EDO.9: 2 residues within 4Å: Chain A: R.109, Q.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.151 EDO.10: 3 residues within 4Å: Chain A: R.137, V.188, Y.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.137 EDO.11: 3 residues within 4Å: Chain A: K.181, S.242, F.243 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.243 Water bridges: A:K.181, A:D.240, A:S.242, A:E.244 EDO.12: 5 residues within 4Å: Chain A: I.123, K.202, T.289, A.290, L.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.202, A:A.290, A:L.291 EDO.13: 4 residues within 4Å: Chain A: E.23, W.25, I.38, Q.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.23, A:Q.80, A:Q.80 EDO.14: 9 residues within 4Å: Chain A: H.61, E.62, I.64, L.65, G.66, H.86, H.88, K.147, C.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.66, A:H.88 EDO.15: 5 residues within 4Å: Chain A: Y.96, T.101, L.102, D.103, S.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.96, A:Y.96, A:D.103, A:D.103, A:S.106 EDO.16: 3 residues within 4Å: Chain A: R.292, K.295, K.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.292, A:K.299 Water bridges: A:K.299 EDO.17: 2 residues within 4Å: Chain A: S.40, S.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.41 EDO.18: 6 residues within 4Å: Chain A: R.182, P.231, Y.234, V.237, P.238, N.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.182, A:R.182, A:P.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez-Alvarez, H. et al., Discovery of Conformationally Constrained ALK2 Inhibitors. J.Med.Chem. (2024)

Release Date

2023-02-01

Peptides

Activin receptor type I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Activin receptor type I

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