SMTL ID : 5th7.1

Complex of SETD8 with MS453

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 7BY: N-(3-{[6,7-dimethoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)propanamide(Covalent)

7BY.1: 19 residues within 4Å: Chain A: Y.54, G.78, C.79, Y.80, M.81, Y.82, R.104, I.106, N.107, T.116, L.127, Y.143, Y.145 Chain B: E.68, Q.73, P.75, C.79 Ligands: EDO.13, UNX.17 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.54, A:Y.80, A:Y.82, A:T.116, A:L.127, A:Y.143, B:P.75 Hydrogen bonds: A:C.79, A:Y.145, B:E.68, B:E.68 7BY.14: 21 residues within 4Å: Chain A: E.68, P.75, C.79, M.81 Chain B: Y.54, G.78, C.79, Y.80, M.81, Y.82, R.104, L.105, I.106, N.107, T.116, L.127, L.129, Y.143, Y.145 Ligands: EDO.13, UNX.22 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:P.75, B:Y.80, B:Y.82, B:T.116, B:L.127, B:L.129, B:Y.143 Hydrogen bonds: A:E.68, A:E.68, B:C.79, B:Y.145

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

UNX.2: 2 residues within 4Å: Chain A: R.133, D.134 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: E.17, E.20, S.21 Ligand excluded by PLIP UNX.4: 2 residues within 4Å: Chain A: R.37, L.105 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: F.45, F.50 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: Y.82, F.84, L.127 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: S.76, T.77 Chain B: S.76 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: K.28, I.29 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: E.53, G.56, L.58, V.93 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: Q.44, A.136, A.137 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: S.46, D.49 Ligand excluded by PLIP UNX.12: 1 residues within 4Å: Chain A: L.58 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain B: E.24, N.100, L.102 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain B: V.124, H.126 Ligand excluded by PLIP UNX.17: 5 residues within 4Å: Chain B: Q.73, D.74, P.75, G.78 Ligands: 7BY.1 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: K.65 Chain B: F.84, Q.85 Ligand excluded by PLIP UNX.19: 4 residues within 4Å: Chain B: R.37, G.38, L.105, N.107 Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Chain B: R.67 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Chain B: E.139, E.140 Ligands: UNX.24 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain B: Y.80, R.104, L.105 Ligands: 7BY.14 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain B: E.53, G.56, L.58, V.93 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain B: N.113, E.140, L.142 Ligands: UNX.21 Ligand excluded by PLIP

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

EDO.13: 8 residues within 4Å: Chain A: C.79, M.81, Y.83 Chain B: C.79, M.81, Y.83 Ligands: 7BY.1, 7BY.14 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.68, A:E.68, A:M.81, A:Y.83, A:Y.83, A:Y.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Butler, K.V. et al., Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase. J. Med. Chem. (2016)

Release Date

2016-11-09

Peptides

N-lysine methyltransferase KMT5A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-lysine methyltransferase KMT5A

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