SMTL ID : 9nfq.1

Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: I.40, G.41, G.43, S.46, V.48, A.61, K.63, I.95, L.111, E.112, A.114, D.118, K.163, N.166, F.168, D.179 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.43, A:S.46, A:E.112, A:A.114, A:D.118, A:D.118, A:N.166, A:D.179 Salt bridges: A:K.63, A:K.163

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.161, N.166, D.179, L.180, G.181 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.179

1 x 01: (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide

01.3: 12 residues within 4Å: Chain C: N.351, P.352, H.353, H.357, S.375, E.377, H.378, S.379, W.380, W.386, W.400, F.402 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:E.377, C:W.380, C:W.386, C:W.386, C:W.400 Hydrogen bonds: C:N.351, C:H.353, C:H.378, C:W.380

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain C: C.323, C.326, C.391, C.394 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.323, C:C.326, C:C.391, C:C.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petzold, G. et al., Mining the CRBN Target Space Redefines Rules for Molecular Glue-induced Neosubstrate Recognition. To Be Published

Release Date

2025-07-09

Peptides

Serine/threonine-protein kinase Nek7: A
DNA damage-binding protein 1: B
Protein cereblon: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Serine/threonine-protein kinase Nek7

DNA damage-binding protein 1

Protein cereblon

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