SMTL ID : 8q8g.1

Crystal structure of HsRNMT complexed with inhibitor DDD1870799

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 18 residues within 4Å: Chain A: K.16, G.41, C.42, G.43, D.63, I.64, A.96, D.97, S.98, S.99, Q.120, F.121, V.122, Y.125, M.136 Ligands: O94.2, SO4.3, GOL.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.41, A:I.64, A:D.97, A:S.98, A:Q.120 Water bridges: A:S.68, A:S.68, A:S.99, A:Q.120 Salt bridges: A:K.16 SAH.6: 19 residues within 4Å: Chain B: K.16, G.41, C.42, G.43, D.63, I.64, A.65, A.96, D.97, S.98, S.99, Q.120, F.121, V.122, Y.125, M.136 Ligands: O94.7, SO4.8, SO4.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.64, B:A.65, B:D.97, B:S.98, B:Q.120 Water bridges: B:K.16, B:C.42, B:Q.120 Salt bridges: B:K.16

2 x O94: 2-(4-fluorophenyl)-1-[(3~{S})-3-(6-oxidanyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)piperidin-1-yl]ethanone(Non-covalent)

O94.2: 12 residues within 4Å: Chain A: L.8, N.12, F.121, Y.125, F.196, L.198, V.201, V.202, A.263, Y.267 Ligands: SAH.1, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.121, A:F.196, A:L.198, A:V.202, A:V.202, A:Y.267 O94.7: 11 residues within 4Å: Chain B: L.8, N.12, F.121, Y.125, F.196, L.198, V.202, A.263, Y.267 Ligands: SAH.6, SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.121, B:F.196, B:L.198, B:V.202, B:Y.267

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: R.9, G.46, R.75 Ligands: SAH.1, GOL.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.13, A:N.13 Salt bridges: A:R.9, A:R.75 SO4.8: 4 residues within 4Å: Chain B: R.9, G.46, R.75 Ligands: SAH.6 6 PLIP interactions: 6 interactions with chain B Water bridges: B:N.13, B:G.45, B:G.46, B:G.46 Salt bridges: B:R.9, B:R.75 SO4.9: 4 residues within 4Å: Chain B: G.43, K.44 Ligands: SAH.6, O94.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.44 Water bridges: B:G.45, B:S.68

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: C.42, G.43, K.44, G.46 Ligands: SAH.1, O94.2, SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.44, A:G.45, A:G.46 Water bridges: A:S.68 GOL.5: 6 residues within 4Å: Chain A: D.66, K.70, Q.73, F.93, I.94, T.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.95, A:T.95 Water bridges: A:F.93, A:F.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pearson, L.A. et al., Characterisation of RNA guanine-7 methyltransferase (RNMT) using a small molecule approach. Biochem.J. (2025)

Release Date

2024-08-28

Peptides

mRNA cap guanine-N7 methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

mRNA cap guanine-N7 methyltransferase

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