SMTL ID : 5nv2.1

Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x 9AE: (2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine(Non-covalent)

9AE.1: 5 residues within 4Å: Chain A: I.28, F.31, W.34, W.58, D.61 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.31, A:F.31, A:W.34, A:W.34, A:W.58 9AE.7: 6 residues within 4Å: Chain B: I.28, F.31, W.34, W.58, D.61, S.92 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.28, B:F.31, B:W.34, B:W.34, B:W.34, B:W.58, B:W.58

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

SO4.2: 4 residues within 4Å: Chain A: K.103, R.107, P.145, N.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.146, A:N.146 Salt bridges: A:K.103, A:R.107 SO4.3: 2 residues within 4Å: Chain A: R.105, T.111 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.105 SO4.4: 4 residues within 4Å: Chain A: K.46, R.47 Chain B: H.99 Ligands: SO4.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.47 Salt bridges: A:K.46, A:R.47, B:H.99 SO4.5: 3 residues within 4Å: Chain A: K.27, K.29, G.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.30 Salt bridges: A:K.27, A:K.29 SO4.6: 5 residues within 4Å: Chain A: K.46, R.47 Chain B: G.60, K.95 Ligands: SO4.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.47 Salt bridges: A:R.47, B:K.95 SO4.8: 5 residues within 4Å: Chain A: D.70 Chain B: K.103, R.107, P.145, N.146 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.146, B:N.146 Salt bridges: B:K.103, B:R.107 SO4.9: 3 residues within 4Å: Chain B: K.46, R.47, W.55 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.46, B:R.47 SO4.10: 2 residues within 4Å: Chain B: K.27, W.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.33 Water bridges: B:N.83 Salt bridges: B:K.27

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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