SMTL ID : 5nv0.1

Human DNMT3B PWWP domain in complex with 4-(dipropylamino)butyronitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 9AH: 4-(dipropylamino)butanenitrile(Non-covalent)

9AH.1: 8 residues within 4Å: Chain A: I.28, F.31, W.34, W.58, D.61, K.63, L.90, S.92 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.28, A:F.31, A:F.31, A:W.34, A:W.34, A:W.58, A:K.63 Hydrogen bonds: A:S.92 Salt bridges: A:D.61 pi-Cation interactions: A:F.31 9AH.7: 6 residues within 4Å: Chain B: I.28, F.31, W.34, W.58, D.61, S.92 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.28, B:F.31, B:W.34, B:W.34, B:W.34, B:W.58 Hydrogen bonds: B:S.92 Salt bridges: B:D.61

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

SO4.2: 4 residues within 4Å: Chain A: K.46, R.47 Chain B: H.99 Ligands: SO4.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.46, A:R.47, B:H.99 SO4.3: 4 residues within 4Å: Chain A: K.103, R.107, P.145, N.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.146 Salt bridges: A:K.103, A:R.107 SO4.4: 5 residues within 4Å: Chain A: K.27, I.28, K.29, G.30, F.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.30, A:F.31 Salt bridges: A:K.27 SO4.5: 3 residues within 4Å: Chain A: K.46, R.47 Ligands: SO4.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.47, B:K.95 SO4.6: 2 residues within 4Å: Chain A: K.71 Chain B: R.105 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.71, B:R.105 SO4.8: 1 residues within 4Å: Chain B: K.71 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.71 SO4.9: 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 SO4.10: 6 residues within 4Å: Chain A: K.16, D.70 Chain B: K.103, R.107, P.145, N.146 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.146 Salt bridges: B:K.103, B:R.107, A:K.16 SO4.11: 2 residues within 4Å: Chain B: K.27, W.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.33

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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