SMTL ID : 6au2.1

Crystal structure of SETDB1 Tudor domain with aryl triazole fragments

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x CGJ: 1-methyl-4H,6H-[1,2,4]triazolo[4,3-a][4,1]benzoxazepine(Non-covalent)

CGJ.1: 11 residues within 4Å: Chain A: F.107, F.108, G.111, Y.112, A.113, C.140, F.143, I.144, Y.200, S.203 Ligands: BME.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.107, A:F.143, A:F.143, A:I.144, A:I.144 Water bridges: A:Y.200, A:S.203, A:S.203, A:T.204 pi-Stacking: A:F.143

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 4 residues within 4Å: Chain A: G.111, S.139, C.140 Ligands: CGJ.1 No protein-ligand interaction detected (PLIP) BME.3: 4 residues within 4Å: Chain A: R.187, L.189, R.195, C.196 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: R.14, K.26, D.61 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.14 SO4.5: 3 residues within 4Å: Chain A: W.174, K.175, D.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.175, A:D.192 SO4.6: 5 residues within 4Å: Chain A: L.52, L.53, S.54, H.57 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.54 Water bridges: A:K.40 Salt bridges: A:K.40, A:H.57 SO4.7: 3 residues within 4Å: Chain A: T.117, Q.118, S.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.119, A:S.119 Water bridges: A:Q.118, A:Q.118 SO4.8: 3 residues within 4Å: Chain A: H.25, K.26 Ligands: UNX.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.26 Water bridges: A:K.26 Salt bridges: A:H.25

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 4 residues within 4Å: Chain A: Y.70, S.73, P.127, T.131 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.68 EDO.10: 8 residues within 4Å: Chain A: K.18, K.19, R.20, K.22, L.53, H.57 Ligands: SO4.6, EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.22, A:K.22, A:H.57 EDO.11: 3 residues within 4Å: Chain A: P.65, A.66, Q.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.66, A:Q.118 EDO.12: 4 residues within 4Å: Chain A: K.18, K.22, H.57 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.18, A:K.22 Water bridges: A:H.57 EDO.13: 3 residues within 4Å: Chain A: D.67, L.69, Y.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.67 EDO.14: 4 residues within 4Å: Chain A: E.168, W.169, E.170, R.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.170

13 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.15: 4 residues within 4Å: Chain A: E.1, N.2, Q.33, T.34 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain A: K.19, R.20, S.51 No protein-ligand interaction detected (PLIP) UNX.17: 4 residues within 4Å: Chain A: K.19, T.21, T.23, H.25 No protein-ligand interaction detected (PLIP) UNX.18: 4 residues within 4Å: Chain A: W.24, H.25, L.87 Ligands: SO4.8 No protein-ligand interaction detected (PLIP) UNX.19: 1 residues within 4Å: Chain A: Y.122 No protein-ligand interaction detected (PLIP) UNX.20: 3 residues within 4Å: Chain A: S.114, Y.115, L.185 No protein-ligand interaction detected (PLIP) UNX.21: 1 residues within 4Å: Chain A: W.173 No protein-ligand interaction detected (PLIP) UNX.22: 1 residues within 4Å: Chain A: F.190 No protein-ligand interaction detected (PLIP) UNX.23: 2 residues within 4Å: Chain A: W.169, W.174 No protein-ligand interaction detected (PLIP) UNX.24: 2 residues within 4Å: Chain A: L.159, K.160 No protein-ligand interaction detected (PLIP) UNX.25: 1 residues within 4Å: Chain A: P.127 No protein-ligand interaction detected (PLIP) UNX.26: 3 residues within 4Å: Chain A: N.56, R.126, L.128 No protein-ligand interaction detected (PLIP) UNX.27: 2 residues within 4Å: Chain A: R.126, P.127 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mader, P. et al., Identification and characterization of the first fragment hits for SETDB1 Tudor domain. Bioorg.Med.Chem. (2019)

Release Date

2017-10-11

Peptides

Histone-lysine N-methyltransferase SETDB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETDB1

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