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

Crystal structure of SETDB1 Tudor domain in complex with MR46747

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x XRU: (3S)-N-(4-chloro-3-{[2-(diethylamino)ethyl]carbamoyl}phenyl)-3-(diethylamino)pyrrolidine-1-carboxamide(Non-covalent)

XRU.1: 14 residues within 4Å: Chain A: Y.90, D.92, W.97, Y.99, F.119, D.121, Y.123, W.180, W.185, F.201, D.203, D.204, R.206, E.208 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.99, A:Y.99, A:F.119, A:W.180, A:W.185, A:F.201, A:F.201 Hydrogen bonds: A:E.208, A:E.208 Water bridges: A:Y.90 Salt bridges: A:D.121, A:D.204 pi-Cation interactions: A:W.97, A:W.97, A:W.180

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: H.36, K.37, N.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.37 Water bridges: A:N.58 Salt bridges: A:H.36 SO4.3: 4 residues within 4Å: Chain A: A.77, D.78, L.80, Y.81 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.80

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: S.84, T.142 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.140, A:K.140 EDO.5: 3 residues within 4Å: Chain A: F.154, S.214, T.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.213, A:T.215 EDO.6: 5 residues within 4Å: Chain A: Y.90, K.91, D.92, S.125, W.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.90 Water bridges: A:S.125, A:S.125, A:Y.126 EDO.7: 4 residues within 4Å: Chain A: F.118, G.122, A.124, F.154 No protein-ligand interaction detected (PLIP)

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.8: 2 residues within 4Å: Chain A: G.182, W.184 No protein-ligand interaction detected (PLIP) UNX.9: 2 residues within 4Å: Chain A: I.149, R.152 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrestha, S. et al., Crystal structure of SETDB1 Tudor domain in complex with MR46747. To be published

Release Date

2023-11-22

Peptides

Histone-lysine N-methyltransferase SETDB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETDB1

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