SMTL ID : 5nrr.1

Human DNMT3B PWWP domain in complex with 5-[(2-Hydroxyethyl)(propyl)amino]-1-pentanol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 96E: 5-[2-hydroxyethyl(propyl)amino]pentan-1-ol(Non-covalent)

96E.1: 7 residues within 4Å: Chain A: I.28, F.31, W.34, W.58, D.61, K.63, S.92 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.28, A:F.31, A:F.31, A:F.31, A:W.34, A:W.34, A:W.34 Hydrogen bonds: A:W.58, A:S.92 Water bridges: A:S.92 Salt bridges: A:D.61 96E.5: 7 residues within 4Å: Chain B: I.28, F.31, W.34, W.58, D.61, K.63, S.92 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.28, B:F.31, B:W.34, B:W.58 Hydrogen bonds: B:S.92 Water bridges: B:F.64, B:S.65 Salt bridges: B:D.61

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

SO4.2: 4 residues within 4Å: Chain A: K.46, R.47, W.55 Chain B: H.99 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:R.47, A:R.47 Salt bridges: A:K.46, A:R.47, B:H.99 SO4.3: 4 residues within 4Å: Chain A: K.27, K.29, G.30, F.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.30 Salt bridges: A:K.27 SO4.4: 4 residues within 4Å: Chain A: K.103, R.107, P.145, N.146 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.146 Water bridges: A:K.103, A:R.107 Salt bridges: A:K.103, A:R.107 SO4.6: 2 residues within 4Å: Chain B: K.46, R.47 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.46, B:R.47 SO4.7: 5 residues within 4Å: Chain A: D.70 Chain B: K.103, R.107, P.145, N.146 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.16, B:K.103, B:R.107 Hydrogen bonds: B:N.146, B:N.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rondelet, G. et al., Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors. To be published

Release Date

2018-05-30

Peptides

DNA (cytosine-5)-methyltransferase 3B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA (cytosine-5)-methyltransferase 3B

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