SMTL ID : 5nrv.1

Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

2 x 96K: 6-dipropylamino-1-hexanol(Non-covalent)

96K.1: 8 residues within 4Å: Chain A: I.28, F.31, W.34, W.58, D.61, F.64, S.65, 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.34, A:W.34, A:W.58 Water bridges: A:E.66, A:E.66 96K.8: 8 residues within 4Å: Chain B: I.28, F.31, W.34, W.58, D.61, F.64, S.65, S.92 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.28, B:F.31, B:W.34, B:W.34, B:W.34, B:W.34, B:W.58, B:W.58 Water bridges: B:E.66

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

SO4.2: 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 SO4.3: 2 residues within 4Å: Chain A: G.139, I.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.140 Water bridges: A:K.136, A:T.138, A:E.141 SO4.4: 3 residues within 4Å: Chain A: K.46, K.63, F.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.64 Salt bridges: A:K.46 SO4.5: 5 residues within 4Å: Chain A: K.46, R.47, W.55 Chain B: H.99 Ligands: SO4.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.99, A:K.46, A:R.47 SO4.6: 3 residues within 4Å: Chain A: L.90, V.91, S.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.91, A:S.92, A:S.92 Water bridges: A:S.92, A:S.92 SO4.7: 4 residues within 4Å: Chain A: K.46, R.47 Chain B: K.95 Ligands: SO4.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:G.60 Salt bridges: B:K.95, A:R.47 SO4.9: 4 residues within 4Å: Chain B: K.27, K.29, G.30, F.31 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.30, B:F.31 Water bridges: B:K.27, B:K.27, B:K.27, B:I.28 Salt bridges: B:K.27 SO4.10: 4 residues within 4Å: Chain B: F.78, S.79, Q.80, H.132 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.78, B:S.79, B:S.79, B:Q.80, B:Q.80, B:H.132 SO4.11: 4 residues within 4Å: Chain A: Q.48 Chain B: K.46, K.63, F.64 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.48, B:F.64 Water bridges: A:Q.48 Salt bridges: B:K.46 SO4.12: 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

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

2018-06-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

DNA (cytosine-5)-methyltransferase 3B

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