SMTL ID : 3uwp.1

Crystal structure of Dot1l in complex with 5-iodotubercidin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x 5ID: (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL(Non-covalent)

5ID.1: 12 residues within 4Å: Chain A: E.147, G.181, G.183, E.204, K.205, A.206, G.239, D.240, F.241, N.259, F.263 Ligands: IOD.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.205 Hydrogen bonds: A:G.183, A:K.205, A:D.240, A:D.240, A:F.241, A:N.259 Water bridges: A:N.259 pi-Stacking: A:F.241

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: L.242 Ligands: 5ID.1 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: G.264, V.267 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: K.70, L.71, M.73, N.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.73, A:N.75

6 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 5 residues within 4Å: Chain A: W.107, G.109, T.110, T.111, P.113 No protein-ligand interaction detected (PLIP) UNX.6: 5 residues within 4Å: Chain A: N.145, Y.146, E.147, F.149, S.150 No protein-ligand interaction detected (PLIP) UNX.7: 5 residues within 4Å: Chain A: H.199, H.200, Y.201, Y.234, T.235 No protein-ligand interaction detected (PLIP) UNX.8: 5 residues within 4Å: Chain A: L.161, L.314, S.315, S.329, Y.330 No protein-ligand interaction detected (PLIP) UNX.9: 4 residues within 4Å: Chain A: T.138, D.139, P.140, E.141 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain A: M.73, E.74 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, W. et al., Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors. Nat Commun (2012)

Release Date

2012-03-14

Peptides

Histone-lysine N-methyltransferase, H3 lysine-79 specific: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase, H3 lysine-79 specific