SMTL ID : 5kco.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: H.36, K.37 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.37 Water bridges: A:H.36, A:H.36, A:K.37 Salt bridges: A:H.36 SO4.2: 3 residues within 4Å: Chain A: W.185, K.186, D.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.186, A:D.203

1 x 6RO: ~{N}-(4-chlorophenyl)methanesulfonamide(Non-covalent)

6RO.3: 10 residues within 4Å: Chain A: F.118, G.122, A.124, S.150, C.151, F.154, Y.211, S.214, T.215 Ligands: UNX.27 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.122 Water bridges: A:G.122, A:Y.211, A:S.214 pi-Stacking: A:F.154

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

UNX.4: 1 residues within 4Å: Chain A: L.80 Ligand excluded by PLIP UNX.5: 1 residues within 4Å: Chain A: Y.15 Ligand excluded by PLIP UNX.6: 5 residues within 4Å: Chain A: L.64, S.65, H.68 Ligands: UNX.41, UNX.49 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: R.31, S.62 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: V.22, I.41 Ligands: UNX.9 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: S.23, L.40 Ligands: UNX.8 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: V.22, I.41, A.42 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: N.67, R.137 Ligands: UNX.25 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: K.91, S.125 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: D.92, N.94, Q.95 Ligand excluded by PLIP UNX.14: 1 residues within 4Å: Chain A: V.96 Ligand excluded by PLIP UNX.15: 4 residues within 4Å: Chain A: S.125, Y.126, L.196 Ligands: UNX.21 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: T.160, A.161 Ligand excluded by PLIP UNX.17: 1 residues within 4Å: Chain A: S.172 Ligand excluded by PLIP UNX.18: 1 residues within 4Å: Chain A: K.140 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: W.184, F.221 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: E.105, R.165, S.195 Ligand excluded by PLIP UNX.21: 4 residues within 4Å: Chain A: D.193, L.196, W.209 Ligands: UNX.15 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain A: R.114, T.128 Ligand excluded by PLIP UNX.23: 5 residues within 4Å: Chain A: K.50, Y.52, R.137 Ligands: UNX.24, UNX.25 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain A: R.137 Ligands: UNX.23 Ligand excluded by PLIP UNX.25: 7 residues within 4Å: Chain A: K.50, Y.52, S.65, G.66 Ligands: UNX.11, UNX.23, UNX.43 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain A: L.170, K.171 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain A: G.122 Ligands: 6RO.3 Ligand excluded by PLIP UNX.28: 2 residues within 4Å: Chain A: Q.174, L.175 Ligand excluded by PLIP UNX.29: 4 residues within 4Å: Chain A: N.67, H.68, D.145 Ligands: UNX.41 Ligand excluded by PLIP UNX.30: 1 residues within 4Å: Chain A: G.194 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain A: Y.90, D.92, W.97 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain A: K.30, H.36 Ligands: UNX.33 Ligand excluded by PLIP UNX.33: 5 residues within 4Å: Chain A: K.30, T.32, T.34, H.36 Ligands: UNX.32 Ligand excluded by PLIP UNX.34: 2 residues within 4Å: Chain A: P.166, M.167 Ligand excluded by PLIP UNX.35: 3 residues within 4Å: Chain A: M.167, V.168, M.220 Ligand excluded by PLIP UNX.36: 4 residues within 4Å: Chain A: K.141, W.143, E.144, E.156 Ligand excluded by PLIP UNX.37: 2 residues within 4Å: Chain A: D.204, R.206 Ligand excluded by PLIP UNX.38: 5 residues within 4Å: Chain A: E.179, W.180, E.181, R.216 Ligands: UNX.39 Ligand excluded by PLIP UNX.39: 4 residues within 4Å: Chain A: E.179, E.181, G.182 Ligands: UNX.38 Ligand excluded by PLIP UNX.40: 3 residues within 4Å: Chain A: R.85, I.135, P.138 Ligand excluded by PLIP UNX.41: 4 residues within 4Å: Chain A: S.65, H.68 Ligands: UNX.6, UNX.29 Ligand excluded by PLIP UNX.42: 1 residues within 4Å: Chain A: T.160 Ligand excluded by PLIP UNX.43: 3 residues within 4Å: Chain A: G.49, K.50 Ligands: UNX.25 Ligand excluded by PLIP UNX.44: 2 residues within 4Å: Chain A: L.169, R.212 Ligand excluded by PLIP UNX.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.46: 4 residues within 4Å: Chain A: Y.123, A.124, W.209 Ligands: UNX.50 Ligand excluded by PLIP UNX.47: 3 residues within 4Å: Chain A: T.128, Q.129 Ligands: UNX.48 Ligand excluded by PLIP UNX.48: 2 residues within 4Å: Chain A: S.130 Ligands: UNX.47 Ligand excluded by PLIP UNX.49: 3 residues within 4Å: Chain A: L.63, L.64 Ligands: UNX.6 Ligand excluded by PLIP UNX.50: 3 residues within 4Å: Chain A: E.208, W.209 Ligands: UNX.46 Ligand excluded by PLIP

3 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 DMS.52: 4 residues within 4Å: Chain A: W.180, W.185, F.201, D.204 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.204 Salt bridges: A:D.204 pi-Cation interactions: A:W.185 DMS.53: 5 residues within 4Å: Chain A: E.12, N.13, Q.44, T.45, V.46 No protein-ligand interaction detected (PLIP)

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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