SMTL ID : 7se9.1 (1 other biounit)

Crystal structure of human Fibrillarin in complex with compound 1 from single soak

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x 8W1: (5S)-3-methyl-7-(trifluoromethyl)pyrrolo[1,2-a]pyrazin-1(2H)-one(Non-covalent)

8W1.1: 13 residues within 4Å: Chain A: L.87, G.88, A.90, E.112, F.113, A.138, A.156, D.157, V.158, Q.163, I.166, V.167 Ligands: FMT.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.112, A:F.113 Water bridges: A:S.114, A:S.114

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

FMT.2: 7 residues within 4Å: Chain A: F.113, D.137, A.138, R.139, Q.163, I.166 Ligands: 8W1.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.139, A:Q.163 Water bridges: A:A.138, A:D.162 FMT.3: 8 residues within 4Å: Chain A: R.62, S.63, K.64, Y.86, A.90, T.93, T.94, D.157 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:G.92 FMT.4: 4 residues within 4Å: Chain A: F.113, S.114, H.115, R.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.113, A:H.115 FMT.5: 4 residues within 4Å: Chain A: S.37, G.40, E.41, R.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.37, A:R.43, A:R.43 Water bridges: A:S.37 FMT.6: 6 residues within 4Å: Chain A: Y.39, G.40, E.41, K.42, N.59, R.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59, A:R.62

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

DMS.7: 10 residues within 4Å: Chain A: M.150, A.171, H.172, T.173, F.174, L.175, R.176, N.177, Y.234, P.236 No protein-ligand interaction detected (PLIP)

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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