SMTL ID : 5kch.1

SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

UNX.1: 2 residues within 4Å: Chain A: L.80, Y.81 Ligand excluded by PLIP UNX.2: 1 residues within 4Å: Chain A: Y.15 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: L.64, S.65, H.68 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: K.30, R.31, S.62 Ligand excluded by PLIP UNX.5: 4 residues within 4Å: Chain A: N.67, R.137 Ligands: UNX.17, UNX.37 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: D.92, G.93, N.94, Q.95 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: Q.95, V.96 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: S.125, Y.126, L.196 Ligands: UNX.13 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: T.160, A.161 Ligand excluded by PLIP UNX.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: W.184, F.221 Ligand excluded by PLIP UNX.12: 4 residues within 4Å: Chain A: E.105, N.108, R.165, S.195 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Chain A: D.193, L.196, W.209 Ligands: UNX.8 Ligand excluded by PLIP UNX.14: 2 residues within 4Å: Chain A: R.114, T.128 Ligand excluded by PLIP UNX.15: 5 residues within 4Å: Chain A: K.50, Y.52, R.137 Ligands: UNX.16, UNX.17 Ligand excluded by PLIP UNX.16: 1 residues within 4Å: Ligands: UNX.15 Ligand excluded by PLIP UNX.17: 7 residues within 4Å: Chain A: K.50, Y.52, S.65, G.66 Ligands: UNX.5, UNX.15, UNX.30 Ligand excluded by PLIP UNX.18: 1 residues within 4Å: Chain A: K.171 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: Q.174, L.175 Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Chain A: G.194 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: Y.90, D.92 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain A: K.30, T.32, T.34, H.36 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: R.165, P.166, M.167 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain A: M.167, M.220 Ligand excluded by PLIP UNX.25: 4 residues within 4Å: Chain A: K.141, W.143, E.144, E.156 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain A: E.179, R.216 Ligands: UNX.27, UNX.33 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain A: E.179 Ligands: UNX.26 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain A: R.85, I.135, P.138 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain A: T.160 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: G.49, K.50 Ligands: UNX.17 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain A: L.169, R.212 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain A: K.112, R.114, D.193 Ligand excluded by PLIP UNX.33: 4 residues within 4Å: Chain A: D.121, R.216 Ligands: UNX.26, 6RN.54 Ligand excluded by PLIP UNX.34: 2 residues within 4Å: Chain A: T.128, S.130 Ligand excluded by PLIP UNX.35: 3 residues within 4Å: Chain A: E.157, A.161, P.166 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain A: W.180, W.185 Ligand excluded by PLIP UNX.37: 2 residues within 4Å: Chain A: P.138 Ligands: UNX.5 Ligand excluded by PLIP UNX.38: 4 residues within 4Å: Chain A: G.122, R.216 Ligands: UNX.39, 6RN.54 Ligand excluded by PLIP UNX.39: 6 residues within 4Å: Chain A: Y.123, E.208, W.209, I.210, R.216 Ligands: UNX.38 Ligand excluded by PLIP UNX.40: 3 residues within 4Å: Chain A: R.152, D.153, E.156 Ligand excluded by PLIP UNX.41: 2 residues within 4Å: Chain A: M.24, R.25 Ligand excluded by PLIP UNX.42: 3 residues within 4Å: Chain A: D.92, Q.95, W.97 Ligand excluded by PLIP UNX.43: 2 residues within 4Å: Chain A: H.74, Y.133 Ligand excluded by PLIP UNX.44: 3 residues within 4Å: Chain A: L.14, A.42, I.43 Ligand excluded by PLIP UNX.45: 6 residues within 4Å: Chain A: K.29, K.33, W.35, Y.99, A.100 Ligands: UNX.46 Ligand excluded by PLIP UNX.46: 3 residues within 4Å: Chain A: K.29, D.120 Ligands: UNX.45 Ligand excluded by PLIP UNX.47: 2 residues within 4Å: Chain A: P.48, K.50 Ligand excluded by PLIP UNX.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.49: 4 residues within 4Å: Chain A: E.12, N.13, Q.44, T.45 Ligand excluded by PLIP UNX.50: 1 residues within 4Å: Chain A: F.201 Ligand excluded by PLIP

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.51: 5 residues within 4Å: Chain A: K.29, K.30, K.33, L.64, H.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.33

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

SO4.52: 2 residues within 4Å: Chain A: H.36, K.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.37 Water bridges: A:K.37 Salt bridges: A:H.36 SO4.53: 1 residues within 4Å: Chain A: R.31 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.31

1 x 6RN: 4-methoxy-N-[(pyridin-2-yl)methyl]aniline(Non-covalent)

6RN.54: 12 residues within 4Å: Chain A: F.118, F.119, G.122, Y.123, S.150, C.151, F.154, I.155, S.214, R.216 Ligands: UNX.33, UNX.38 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.118, A:F.154, A:I.155 Hydrogen bonds: A:S.150, A:S.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tempel, W. et al., SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy. To Be Published

Release Date

2016-07-27

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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