SMTL ID : 9d8f.1 (1 other biounit)

Crystal structure of the ACVR1 (ALK2) Kinase Domain in complex with inhibitor CDD-2281

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: Y.100, K.146, K.148, T.186, R.188, Y.189, P.237 Ligands: PO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.188 Water bridges: A:K.146, A:Y.189 Salt bridges: A:K.146, A:K.148 PO4.2: 8 residues within 4Å: Chain A: H.92, Y.93, H.94, E.95, K.153, K.154, N.155 Ligands: GOL.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.95, A:E.95, A:K.154 Water bridges: A:H.94, A:K.154, A:K.154, A:N.155 Salt bridges: A:H.92, A:H.94, A:K.154 PO4.3: 10 residues within 4Å: Chain A: H.67, E.68, I.70, L.71, G.72, H.92, H.94, K.153, C.159 Ligands: GOL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.67, A:G.72 Water bridges: A:K.153, A:K.153 Salt bridges: A:H.92, A:H.94, A:K.153 PO4.4: 6 residues within 4Å: Chain A: K.148, R.188, N.245, D.246, P.247 Ligands: PO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.246 Water bridges: A:K.146, A:R.188, A:D.246 Salt bridges: A:R.188 PO4.5: 7 residues within 4Å: Chain A: V.63, M.64, L.65, R.66, H.126, I.131, K.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.64, A:M.64, A:R.66 Salt bridges: A:H.126 PO4.6: 6 residues within 4Å: Chain A: H.67, A.125, H.126, I.129, I.131, L.297 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.125 Water bridges: A:H.67, A:A.125, A:H.126, A:K.300 Salt bridges: A:H.126

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: H.92, H.94, K.153, K.154 Ligands: PO4.2, PO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.154 Water bridges: A:K.153, A:K.154

1 x 01: N-[3-(dimethylamino)propyl]-1-[(1r,3r)-3-(methylcarbamoyl)cyclobutyl]-2-(3,4,5-trimethoxyphenyl)-1H-1,3-benzimidazole-6-carboxamide

01.8: 26 residues within 4Å: Chain A: V.22, G.23, Y.27, V.30, A.41, V.42, K.43, E.56, Y.60, L.71, L.89, I.90, T.91, Y.93, H.94, E.95, M.96, G.97, S.98, D.101, L.105, K.148, N.149, L.151, A.161, D.162 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.22, A:V.30, A:Y.93, A:L.151 Hydrogen bonds: A:Y.27 Water bridges: A:K.43, A:K.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jimmidi, R. et al., Discovery of highly potent and ALK2/ALK1 selective kinase inhibitors using DNA-encoded chemistry technology. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-11-27

Peptides

Activin receptor type-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Activin receptor type-1

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