SMTL ID : 8u0h.1 (1 other biounit)

Crystal structure of PTPN2 with a PROTAC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x UB0: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[2-(4-{3-[(3R)-2,6-dioxopiperidin-3-yl]-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl}piperidin-1-yl)acetamido]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid

UB0.1: 22 residues within 4Å: Chain A: R.28, N.29, S.31, H.32, D.33, Y.50, D.52, V.53, Y.56, K.124, D.184, F.185, C.218, S.219, A.220, I.222, G.223, R.224, M.258, G.259, Q.262, Q.266 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:D.33, A:V.53, A:M.258 Hydrogen bonds: A:R.28, A:Y.50, A:F.185, A:S.219, A:G.223, A:R.224, A:R.224, A:Q.262, A:Q.262, A:Q.266 Water bridges: A:Y.24, A:D.33, A:K.124, A:A.220, A:A.220, A:A.220, A:A.220, A:R.254, A:R.254, A:R.254 Salt bridges: A:K.124, A:R.224

1 x ACT: ACETATE ION

ACT.2: 5 residues within 4Å: Chain A: W.129, T.157, H.159, H.178, T.180 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.150 Salt bridges: A:H.159, A:H.178

1 x NA: SODIUM ION

NA.3: 2 residues within 4Å: Chain A: P.191, A.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.192 Water bridges: A:E.276, A:E.276

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

2024-09-04

Peptides

PTPN2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PTPN2

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