SMTL ID : 8pj7.1

MLLT3 in complex with compound PFI-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

1 x ZJ9: ~{N}-[(1~{R})-2,3-dihydro-1~{H}-inden-1-yl]-5-[4-(dimethylcarbamoyl)-3-oxidanyl-phenyl]-1,2-oxazole-3-carboxamide(Non-covalent)

ZJ9.1: 13 residues within 4Å: Chain A: E.26, F.28, H.56, S.58, F.59, P.60, E.75, S.76, G.77, Y.78, A.79, G.80, F.81 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.28, A:F.28, A:F.59, A:F.59, A:F.59, A:P.60, A:F.81 Hydrogen bonds: A:S.58, A:S.58, A:E.75, A:Y.78, A:A.79 pi-Cation interactions: A:H.56

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

EDO.2: 8 residues within 4Å: Chain A: V.9, K.10, S.42, I.44, F.47, A.138, G.139, G.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.10, A:G.139 EDO.3: 4 residues within 4Å: Chain A: V.65, C.66, K.67, D.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.67, A:D.68 Water bridges: A:D.68 EDO.4: 2 residues within 4Å: Chain A: E.93, E.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.94 Water bridges: A:E.94 EDO.6: 4 residues within 4Å: Chain A: R.16, D.31, W.32, M.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.74, A:E.74 Water bridges: A:W.32 EDO.7: 3 residues within 4Å: Chain A: E.94, P.95, R.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:E.94, A:E.94 EDO.8: 4 residues within 4Å: Chain A: D.31, E.74, E.75, S.76 No protein-ligand interaction detected (PLIP)

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

DMS.5: 3 residues within 4Å: Chain A: P.95, L.122, T.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.123 pi-Cation interactions: A:F.124

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 1 residues within 4Å: Chain A: R.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raux, B. et al., Discovery of PFI-6, a small-molecule chemical probe for the YEATS domain of MLLT1 and MLLT3. Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-11-22

Peptides

Protein AF-9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein AF-9