SMTL ID : 9g4s.1

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 56

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: 4-[(3~{R})-3-(cyclopropylmethylamino)piperidin-1-yl]-1-[(1~{R})-1-[4-[5-(dimethylamino)pyridin-3-yl]-1,2,3-triazol-1-yl]ethyl]pyridin-2-one

01.1: 22 residues within 4Å: Chain A: C.12, D.13, I.14, R.15, D.31, P.32, P.33, Y.42, G.43, T.44, L.45, W.67, W.93, E.117, H.148, K.149, F.170, G.171, R.172, G.184, N.185, Q.186 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.33, A:W.67, A:W.93, A:E.117, A:K.149, A:F.170, A:R.172 Hydrogen bonds: A:I.14, A:D.31, A:N.185 Water bridges: A:Q.186, A:Q.186, A:Q.186 pi-Stacking: A:H.148

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: F.130, Q.132 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:F.130 CA.3: 2 residues within 4Å: Chain A: Q.132 Chain B: P.162 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.162, H2O.5 CA.4: 2 residues within 4Å: Chain A: Q.98, E.142 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.142, A:E.142, H2O.5, H2O.5, H2O.5 CA.6: 2 residues within 4Å: Chain B: E.60, W.96 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain A: E.74 Chain B: R.134, R.139, R.140 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 2 residues within 4Å: Chain A: H.174, V.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.174, A:V.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dutheuil, G. et al., Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 56. To Be Published

Release Date

2025-02-12

Peptides

N6-adenosine-methyltransferase catalytic subunit: A
N6-adenosine-methyltransferase non-catalytic subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N6-adenosine-methyltransferase catalytic subunit

N6-adenosine-methyltransferase non-catalytic subunit