SMTL ID : 4er3.1

Crystal Structure of Human DOT1L in complex with inhibitor EPZ004777

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x 0QK: 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine(Non-covalent)

0QK.1: 22 residues within 4Å: Chain A: L.144, M.148, D.162, L.163, G.164, S.165, G.166, V.170, V.186, E.187, K.188, A.189, G.222, D.223, F.224, V.241, N.242, F.246, V.268, S.269, Y.313 Ligands: UNX.9 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.144, A:V.170, A:F.224, A:N.242, A:F.246, A:Y.313 Hydrogen bonds: A:D.162, A:D.162, A:G.166, A:K.188, A:D.223, A:F.224 Water bridges: A:G.168, A:N.242

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

SO4.2: 3 residues within 4Å: Chain A: N.100, T.101, R.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.102 Salt bridges: A:R.102 SO4.3: 2 residues within 4Å: Chain A: S.104, T.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.105 SO4.4: 4 residues within 4Å: Chain A: K.67, S.68, F.69, E.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.68, A:F.69, A:E.70 SO4.5: 3 residues within 4Å: Chain A: H.118, E.202, K.205 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.118, A:K.205 SO4.6: 3 residues within 4Å: Chain A: R.204, K.208, H.214 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.204, A:K.208

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: V.161, Y.184, R.232, T.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.236 EDO.8: 3 residues within 4Å: Chain A: R.230, Q.253, R.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.230, A:R.230, A:R.257, A:R.257

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

UNX.9: 1 residues within 4Å: Ligands: 0QK.1 No protein-ligand interaction detected (PLIP) UNX.10: 1 residues within 4Å: Ligands: UNX.11 No protein-ligand interaction detected (PLIP) UNX.11: 1 residues within 4Å: Ligands: UNX.10 No protein-ligand interaction detected (PLIP) UNX.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.13: 1 residues within 4Å: Chain A: L.126 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain A: A.19, K.205, W.206, W.209 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

2012-05-16

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