SMTL ID : 9mzz.1

Crystal structure of RIPK1 with compound 36

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

2 x 01: (2S,5S)-4-(3,3-difluoro-2,2-dimethylpropanoyl)-2,3,4,5-tetrahydro-2,5-methanopyrido[3,4-f][1,4]oxazepine-9-carbonitrile

01.1: 12 residues within 4Å: Chain A: M.61, L.64, V.70, M.86, V.128, H.130, I.148, A.149, D.150, L.151, S.155, F.156 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.150 Hydrogen bonds: A:D.150, A:S.155 Water bridges: A:S.155 01.5: 16 residues within 4Å: Chain B: M.61, L.64, V.70, L.72, L.84, M.86, L.123, V.128, H.130, I.148, A.149, D.150, L.151, L.153, S.155, F.156 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.72, B:D.150, B:L.153 Hydrogen bonds: B:D.150, B:S.155

7 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: E.253, F.279 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: Y.222, A.225 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: I.226, L.231 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: S.67, K.71 Chain B: E.276, R.280 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: R.68, H.145 Chain B: R.280 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain B: F.279 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: E.276, R.280 Chain B: S.67, K.71 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J.L. et al., The Discovery of Bridged Benzoazepine Amides as Selective Allosteric Modulators of RIPK1. Acs Med.Chem.Lett. (2025)

Release Date

2025-05-28

Peptides

Receptor-interacting serine/threonine-protein kinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Receptor-interacting serine/threonine-protein kinase 1