SMTL ID : 6sis.1 (1 other biounit)

Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human Brd4 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x LFE: ~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide(Non-covalent)

LFE.1: 27 residues within 4Å: Chain A: W.44, P.45, F.46, V.50, A.54, L.55, G.56, L.57, C.99, N.103, H.107, E.108, V.109, M.112 Chain D: N.16, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 21 PLIP interactions: 10 interactions with chain D, 11 interactions with chain A Hydrophobic interactions: D:W.37, D:F.40, D:I.58, D:W.66, A:W.44, A:W.44, A:P.45, A:P.45, A:F.46, A:V.50, A:L.55, A:V.109, A:V.109 Hydrogen bonds: D:W.37, D:Y.47, D:H.59, D:Y.61, D:H.64, A:N.103, A:N.103 pi-Stacking: D:Y.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Testa, A. et al., Structure-Based Design of a Macrocyclic PROTAC. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2019-12-04

Peptides

Bromodomain-containing protein 4: A
Elongin-B: B
Elongin-C: C
von Hippel-Lindau disease tumor suppressor: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Bromodomain-containing protein 4

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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