SMTL ID : 9mzy.1

Crystal structure of human RIPK1 with Compound 22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

2 x 01: 1-[(2S,5S)-2,3-dihydro-2,5-methano-1,4-benzoxazepin-4(5H)-yl]-3,3-difluoro-2,2-dimethylpropan-1-one

01.1: 14 residues within 4Å: Chain A: M.60, L.63, V.68, V.69, L.71, M.85, L.122, H.129, I.147, A.148, D.149, L.150, L.152, F.155 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.63, A:V.68, A:L.71, A:L.122, A:D.149, A:L.152, A:F.155 Hydrogen bonds: A:D.149 01.6: 14 residues within 4Å: Chain B: M.60, L.63, V.68, V.69, L.71, M.85, L.122, H.129, I.147, A.148, D.149, L.150, L.152, F.155 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.68, B:L.71, B:L.122, B:D.149, B:L.152, B:F.155 Hydrogen bonds: B:D.149

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

IOD.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: S.66, K.70 Chain B: E.275, R.279 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: A.224, Q.229, L.230 Ligand excluded by PLIP IOD.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x GLY: GLYCINE(Non-covalent)

GLY.5: 4 residues within 4Å: Chain A: I.245, E.247, C.249, I.254 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: R.279 Chain B: S.66, K.70 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