SMTL ID : 6pai.1

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 9 residues within 4Å: Chain A: G.17, C.18, E.65, K.168, H.261, N.262, R.263, Y.271 Ligands: EPE.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.18 Salt bridges: A:E.65, A:E.65, A:H.261 EPE.2: 6 residues within 4Å: Chain A: V.259, C.260, H.261, E.312, R.327 Ligands: EPE.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.261, A:R.327 Salt bridges: A:H.261, A:E.312, A:E.312

1 x O6M: 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide(Non-covalent)

O6M.3: 15 residues within 4Å: Chain B: T.236, F.237, Q.238, P.239, A.240, F.241, V.375, R.450, C.453, V.454, V.457, L.461 Chain C: D.34, M.35, G.38 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Q.238, B:A.240, B:F.241, B:V.375, B:V.454, B:V.457, B:L.461 Hydrogen bonds: B:F.237, B:A.240, B:F.241 pi-Stacking: B:F.241

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: C.199, C.202, C.217, H.220 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.199, B:C.202, B:C.217, B:H.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, X. et al., Structural Basis and Kinetic Pathway of RBM39 Recruitment to DCAF15 by a Sulfonamide Molecular Glue E7820. Structure (2019)

Release Date

2019-09-18

Peptides

DNA damage-binding protein 1: A
DDB1- and CUL4-associated factor 15: B
RNA-binding protein 39: C
DET1- and DDB1-associated protein 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

DNA damage-binding protein 1

DDB1- and CUL4-associated factor 15

RNA-binding protein 39

DET1- and DDB1-associated protein 1

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