SMTL ID : 7cd9.1

Crystal Structure of SETDB1 tudor domain in complexed with Compound 6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x FVR: 3-methyl-2-[[(3R,5R)-1-methyl-5-(4-phenylmethoxyphenyl)piperidin-3-yl]amino]-5H-pyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

FVR.1: 19 residues within 4Å: Chain A: T.40, T.42, H.44, Y.98, D.100, W.105, Y.107, F.127, D.129, G.130, Y.131, W.188, E.216, R.224 Chain B: D.100, Q.103, W.105, D.129 Ligands: FVR.3 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.40, A:T.42, A:Y.98, A:W.105, A:W.105, A:Y.107, A:Y.131 Hydrogen bonds: A:Y.98, A:E.216, B:Q.103 Water bridges: A:R.224 Salt bridges: A:D.129 pi-Cation interactions: A:Y.98 pi-Stacking: B:W.105 FVR.3: 18 residues within 4Å: Chain A: D.100, Q.103, W.105, D.129 Chain B: T.40, T.42, H.44, Y.98, W.105, Y.107, F.127, D.129, G.130, Y.131, W.188, E.216, R.224 Ligands: FVR.1 16 PLIP interactions: 2 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:Q.103, B:Y.98, B:E.216, B:E.216 pi-Stacking: A:W.105, B:W.105 Hydrophobic interactions: B:T.40, B:T.42, B:Y.98, B:W.105, B:W.105, B:Y.107, B:Y.131 Water bridges: B:R.224 Salt bridges: B:D.129 pi-Cation interactions: B:Y.98

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 11 residues within 4Å: Chain A: F.126, F.127, G.130, Y.131, A.132, C.159, F.162, I.163, I.218, Y.219, S.222 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.126, A:Y.219 Hydrogen bonds: A:G.130, A:G.130, A:G.130, A:Y.131, A:Y.219, A:S.222 Water bridges: A:G.130, A:T.223, A:R.224 CIT.4: 11 residues within 4Å: Chain B: F.126, F.127, G.130, Y.131, A.132, C.159, F.162, I.163, I.218, Y.219, S.222 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.126, B:F.126, B:Y.219 Hydrogen bonds: B:G.130, B:G.130, B:Y.131, B:Y.219 Water bridges: B:G.130, B:S.222, B:S.222, B:T.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Structure-Guided Discovery of a Potent and Selective Cell-Active Inhibitor of SETDB1 Tudor Domain. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2021-04-07

Peptides

Histone-lysine N-methyltransferase SETDB1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase SETDB1

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