SMTL ID : 5vbq.1 (1 other biounit)

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRDT IN COMPLEX WITH BI2536

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x R78: 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide(Non-covalent)

R78.1: 14 residues within 4Å: Chain A: W.26, P.27, F.28, V.32, K.36, L.37, Q.38, L.39, Y.42, C.81, Y.84, N.85, I.91 Ligands: EDO.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.32, A:L.37, A:Q.38, A:L.39, A:Y.42, A:Y.84, A:I.91 Hydrogen bonds: A:N.85

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: R.30, N.53 Ligand excluded by PLIP

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

EDO.3: 9 residues within 4Å: Chain A: I.45, I.46, K.47, N.48, P.49, T.76, N.80, L.83 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.45, A:K.47, A:N.48, A:N.48, A:N.80 EDO.4: 5 residues within 4Å: Chain A: T.76, S.79, N.80, L.83 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 EDO.5: 6 residues within 4Å: Chain A: V.32, D.33, A.34, V.35, K.36, Y.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.33, A:A.34, A:V.35 Water bridges: A:Y.43 EDO.6: 6 residues within 4Å: Chain A: R.30, P.31, D.51, N.53, T.54, K.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.53 EDO.7: 1 residues within 4Å: Chain A: K.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.47 Water bridges: A:Y.43, A:K.47, A:K.47 EDO.8: 9 residues within 4Å: Chain A: W.26, P.27, R.30, P.31, V.32, D.33, K.36, L.37 Ligands: R78.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.27, A:D.33 EDO.9: 3 residues within 4Å: Chain A: T.54, R.58, Y.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58, A:R.58 EDO.10: 5 residues within 4Å: Chain A: N.48, M.50, R.58, Y.63, D.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.58, A:R.58, A:D.73 Water bridges: A:N.48, A:N.48 EDO.11: 4 residues within 4Å: Chain A: L.16, K.17, W.20, K.56 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: T.5, L.8, Q.9, Q.12, K.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.62 Water bridges: A:L.8, A:Q.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karim, R.M. et al., Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. J.Med.Chem. (2021)

Release Date

2018-04-04

Peptides

Bromodomain testis-specific protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain testis-specific protein

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