SMTL ID : 5vbr.2 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x IBI: N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide(Non-covalent)

IBI.1: 13 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 9 PLIP interactions: 9 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 Water bridges: A:P.27

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

EDO.2: 3 residues within 4Å: Chain A: T.76, S.79, N.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 EDO.3: 2 residues within 4Å: Chain A: Y.43, K.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.47 Water bridges: A:Y.43 EDO.4: 3 residues within 4Å: Chain A: P.31, P.49, D.51 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: L.16, W.20, K.56 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: Q.38, L.39, P.40, D.41, Y.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.41

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

CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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
B

Bromodomain testis-specific protein

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