SMTL ID : 7lzd.1

Crystal Structure of SETD2 bound to Compound 35

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.66, C.68, C.83, C.87 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.68, A:C.83, A:C.87 ZN.2: 5 residues within 4Å: Chain A: C.83, C.96, C.100, C.106 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.96, A:C.100, A:C.106 ZN.3: 4 residues within 4Å: Chain A: C.198, C.245, C.247, C.252 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.198, A:C.245, A:C.247, A:C.252

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.4: 19 residues within 4Å: Chain A: K.127, G.128, W.129, I.169, H.170, Y.171, Y.172, R.192, F.193, M.194, N.195, H.196, Q.243, K.244, C.245, F.246, C.247, L.256 Ligands: YHY.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:W.129, A:Y.171, A:Y.171, A:Y.172, A:N.195, A:N.195, A:H.196, A:H.196, A:Q.243, A:Q.243, A:F.246 Salt bridges: A:H.170

1 x YHY: N-{3-[4-(dimethylamino)piperidin-1-yl]phenyl}-4-fluoro-7-methyl-1H-indole-2-carboxamide(Non-covalent)

YHY.5: 15 residues within 4Å: Chain A: Y.146, Y.171, Y.172, F.173, M.194, H.196, F.231, Y.233, Y.238, K.240, E.241, L.256 Ligands: SAM.4, EDO.6, EDO.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.146, A:Y.171, A:F.173, A:F.231, A:Y.233 Hydrogen bonds: A:F.173, A:F.173 Salt bridges: A:E.241 pi-Stacking: A:Y.171, A:Y.233, A:Y.233

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

EDO.6: 7 residues within 4Å: Chain A: F.235, Q.236, R.237, Y.238, G.257, G.258 Ligands: YHY.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.237, A:Y.238, A:Y.238, A:G.258 EDO.7: 4 residues within 4Å: Chain A: F.235, Q.236, Y.238, E.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.236, A:E.259 EDO.8: 6 residues within 4Å: Chain A: K.114, H.116, F.142, L.144, E.145, N.189 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.114, A:E.145, A:E.145, A:N.189 Water bridges: A:K.114, A:E.145 EDO.9: 4 residues within 4Å: Chain A: L.49, E.155, R.159, E.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.155, A:R.159 Water bridges: A:R.159, A:E.162 EDO.10: 5 residues within 4Å: Chain A: V.160, A.164, G.239, K.240 Ligands: YHY.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.240, A:K.240 Water bridges: A:K.240 EDO.11: 4 residues within 4Å: Chain A: Y.48, E.51, R.52, Q.212 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain A: Y.163, N.166, N.168, Q.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.166, A:N.168 EDO.13: 5 residues within 4Å: Chain A: E.199, P.200, N.201, E.228, T.230 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.199, A:T.230 EDO.14: 1 residues within 4Å: Chain A: N.140 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.110, A:R.110, A:N.140

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

DMS.15: 5 residues within 4Å: Chain A: D.104, Y.105, C.106, S.107, Q.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lampe, J.W. et al., Discovery of a First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable for Preclinical Studies. Acs Med.Chem.Lett. (2021)

Release Date

2021-09-22

Peptides

Histone-lysine N-methyltransferase SETD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETD2

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