SMTL ID : 9d8e.1 (1 other biounit)

Crystal structure of the ACVR1 (ALK2) Kinase Domain in complex with inhibitor CDD-2789

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: R.33, A.36, R.37, D.100, M.101, T.102, S.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.37, A:D.100, A:M.101, A:T.102 GOL.2: 4 residues within 4Å: Chain A: S.103, R.104, H.105, S.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.103, A:H.105, A:S.106

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

01.3: 26 residues within 4Å: Chain A: V.45, G.46, Y.50, V.53, A.64, V.65, K.66, E.79, L.94, L.112, I.113, T.114, Y.116, H.117, E.118, M.119, G.120, S.121, D.124, L.128, K.171, N.172, L.174, A.184, D.185, L.186 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.45, A:V.53, A:V.53, A:Y.116, A:L.174 Hydrogen bonds: A:T.114, A:Y.116 Water bridges: A:K.66

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

PO4.4: 7 residues within 4Å: Chain A: H.115, Y.116, H.117, E.118, K.176, K.177, N.178 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.116, A:K.177 Water bridges: A:H.115, A:H.115, A:H.115, A:E.118, A:K.177, A:N.178, A:N.178 Salt bridges: A:H.115, A:H.117, A:K.177 PO4.5: 8 residues within 4Å: Chain A: Y.123, K.169, K.171, T.209, R.211, Y.212, P.260 Ligands: PO4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.211 Water bridges: A:R.211 Salt bridges: A:K.169, A:K.171 PO4.6: 9 residues within 4Å: Chain A: H.90, E.91, I.93, L.94, G.95, H.115, H.117, K.176, C.182 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.91, A:G.95 Water bridges: A:H.115, A:K.176 Salt bridges: A:H.115, A:H.117, A:K.176 PO4.7: 6 residues within 4Å: Chain A: H.90, A.148, H.149, I.152, I.154, L.320 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.90, A:H.90 Salt bridges: A:H.149, A:K.323 PO4.8: 6 residues within 4Å: Chain A: K.171, R.211, N.268, D.269, P.270 Ligands: PO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.268, A:D.269, A:D.269 Water bridges: A:R.211 Salt bridges: A:R.211

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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