SMTL ID : 7ydx.1

Crystal structure of human RIPK1 kinase domain in complex with compound RI-962

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

2 x 3CI: 1-methyl-5-[2-(2-methylpropanoylamino)-[1,2,4]triazolo[1,5-a]pyridin-7-yl]-N-[(1S)-1-phenylethyl]indole-3-carboxamide(Non-covalent)

3CI.1: 20 residues within 4Å: Chain A: L.23, I.43, K.45, M.67, L.70, V.75, V.76, L.78, M.92, E.93, M.95, G.98, L.145, I.154, A.155, D.156, L.157, L.159, S.161, F.162 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.23, A:I.43, A:L.70, A:V.75, A:L.78, A:M.92, A:L.145, A:D.156, A:L.157, A:F.162 Hydrogen bonds: A:M.95, A:M.95, A:D.156 3CI.6: 19 residues within 4Å: Chain B: V.31, L.33, I.43, K.45, V.75, V.76, M.92, E.93, M.95, E.96, G.98, H.136, L.145, I.154, A.155, D.156, L.157, L.159, S.161 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.31, B:L.33, B:I.43, B:K.45, B:V.75, B:M.92, B:L.145, B:D.156, B:L.157, B:L.157 Hydrogen bonds: B:M.95, B:M.95, B:D.156

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

IOD.2: 1 residues within 4Å: Chain A: K.284 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: E.282, R.286 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: F.35, L.41 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: R.286 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain B: F.285 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain B: R.286 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain B: R.286 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Generative deep learning enables the discovery of a potent and selective RIPK1 inhibitor. Nat Commun (2022)

Release Date

2023-04-19

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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