SMTL ID : 8uh6.1

Degrader-induced complex between PTPN2 and CRBN-DDB1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x WO8: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid

WO8.1: 26 residues within 4Å: Chain B: N.360, P.361, H.362, H.366, E.386, H.387, W.389, W.395, W.409, F.411 Chain C: R.28, N.29, S.31, H.32, D.33, Y.50, D.52, V.53, Y.56, K.124, D.184, G.223, R.224, M.258, L.260, Q.262 19 PLIP interactions: 10 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:D.33, C:D.52, C:V.53, B:P.361, B:E.386, B:H.387, B:W.389, B:W.395, B:W.395, B:W.395 Hydrogen bonds: C:S.31, C:D.184, C:R.224, C:Q.262, C:Q.262, B:N.360 Salt bridges: C:K.124, C:R.224 pi-Stacking: B:W.395

1 x ZN: ZINC ION

ZN.2: 5 residues within 4Å: Chain B: C.332, C.335, C.400, C.403, S.405 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.332, B:C.335, B:C.400, B:C.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hao, Q. et al., Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex. Commun Chem (2024)

Release Date

2024-09-11

Peptides

DNA damage-binding protein 1: A
Protein cereblon: B
Tyrosine-protein phosphatase non-receptor type 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

Tyrosine-protein phosphatase non-receptor type 2

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