SMTL ID : 7lzb.1

Crystal Structure of SETD2 bound to Compound 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 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: YJ1.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.127, A:W.129, A:H.170, 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 YJ1: N-[(1r,4r)-4-(beta-alanylamino)cyclohexyl]-7-methyl-1H-indole-2-carboxamide(Non-covalent)

YJ1.5: 12 residues within 4Å: Chain A: Y.146, V.160, Y.171, Y.172, F.173, M.194, H.196, F.231, Y.233, Y.238, E.241 Ligands: SAM.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.146, A:V.160, A:Y.171, A:F.231 Hydrogen bonds: A:F.173, A:F.173, A:Y.238, A:E.241 pi-Stacking: A:Y.233, A:Y.233

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

BME.6: 5 residues within 4Å: Chain A: S.15, D.20, R.26, C.30, M.36 No protein-ligand interaction detected (PLIP)

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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