SMTL ID : 7xmk.1

Crystal structure of human RIPK1 kinase domain in complex with compound SKLB923

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

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

IOD.1: 2 residues within 4Å: Chain A: E.282, R.286 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain B: E.282, R.286 Ligand excluded by PLIP

2 x GO4: 5-[2-(cyclopropylcarbonylamino)-[1,2,4]triazolo[1,5-a]pyridin-7-yl]-N-[(1S)-1-(3-fluorophenyl)ethyl]-1-methyl-indole-3-carboxamide(Non-covalent)

GO4.2: 25 residues within 4Å: Chain A: V.31, I.43, K.45, M.67, V.75, V.76, L.78, L.90, M.92, E.93, Y.94, M.95, E.96, K.97, G.98, L.129, H.136, L.145, I.154, A.155, D.156, L.157, L.159, S.161, F.162 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.43, A:M.92, A:Y.94, A:L.145, A:D.156, A:L.157, A:F.162 Hydrogen bonds: A:M.95, A:M.95, A:D.156 GO4.4: 27 residues within 4Å: Chain B: L.23, V.31, I.43, K.45, M.67, V.75, V.76, K.77, L.78, L.90, M.92, E.93, Y.94, M.95, E.96, K.97, G.98, L.129, H.136, L.145, I.154, A.155, D.156, L.157, L.159, S.161, F.162 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.43, B:V.75, B:M.92, B:L.145, B:D.156, B:L.157, B:F.162 Hydrogen bonds: B:M.95, B:M.95, B:D.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., From Hit to Lead: Structure-Based Optimization of Novel Selective Inhibitors of Receptor-Interacting Protein Kinase 1 (RIPK1) for the Treatment of Inflammatory Diseases. J.Med.Chem. (2024)

Release Date

2023-04-26

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

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