SMTL ID : 7sea.1

Crystal structure of human Fibrillarin in complex with compound 2 from cocktail soak

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 8 residues within 4Å: Chain A: R.62, S.63, K.64, Y.86, A.90, T.93, T.94, V.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.93, A:T.94, A:T.94 Water bridges: A:G.92, A:T.93 FMT.2: 3 residues within 4Å: Chain A: F.113, S.114, H.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.113, A:H.115 FMT.3: 5 residues within 4Å: Chain A: P.133, V.134, I.135, E.136, L.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.135, A:E.136 FMT.4: 5 residues within 4Å: Chain A: D.191, A.194, A.198, V.199, S.202 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.202 FMT.5: 7 residues within 4Å: Chain A: G.88, A.90, E.112, D.157, V.158, A.159 Ligands: 8XF.7 No protein-ligand interaction detected (PLIP)

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

DMS.6: 5 residues within 4Å: Chain A: K.83, M.150, V.151, D.152, R.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.83 Salt bridges: A:D.152

1 x 8XF: 6-(trifluoromethyl)pyrimidin-4-amine(Non-covalent)

8XF.7: 13 residues within 4Å: Chain A: G.88, A.90, V.111, E.112, F.113, E.136, D.137, A.138, R.139, V.158, Q.160, I.166 Ligands: FMT.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.112, A:F.113, A:A.138 pi-Stacking: A:F.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Discovery of Cofactor Competitive Inhibitors against the Human Methyltransferase Fibrillarin. Pharmaceuticals (2021)

Release Date

2022-02-09

Peptides

rRNA 2'-O-methyltransferase fibrillarin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

rRNA 2'-O-methyltransferase fibrillarin

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