PDBsum entry 5eic

Transferase

PDB id: 5eic

Contents

Protein chains

113 a.a.

Ligands

EDO ×2

5J5

Waters ×215

PDB id:

5eic

Name:

Transferase

Title:

Crystal structure of the bromodomain of human crebbp in complex with ayc

Structure:

Creb-binding protein. Chain: a, b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: crebbp, cbp. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.50Å R-factor: 0.174 R-free: 0.209

Authors:

J.Dong,A.Caflisch

Key ref:

J.Zhu et al. (2018). Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules. ACS Med Chem Lett, 9, 929-934. PubMed id: 30258543

Date:

29-Oct-15 Release date: 16-Nov-16

Protein chains

Q92793  (CBP_HUMAN) -  CREB-binding protein from Homo sapiens

Seq: 2442 a.a.

Struc: 113 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.3.1.- - ?????
• Enzyme class 2: E.C.2.3.1.48 - histone acetyltransferase.
• Reaction: L-lysyl-[protein] + acetyl-CoA = N₆-acetyl-L-lysyl-[protein] + CoA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

ACS Med Chem Lett 9:929-934 (2018)

PubMed id: 30258543

Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules.

J.Zhu, J.Dong, L.Batiste, A.Unzue, A.Dolbois, V.Pascanu, P.Śledź, C.Nevado, A.Caflisch.

ABSTRACT

We analyze 20 crystal structures of complexes between the CBP bromodomain and small-molecule ligands that belong to eight different chemotypes identified by docking. The binding motif of the moiety that mimics the natural ligand (acetylated side chain of lysine) at the bottom of the binding pocket is conserved. In stark contrast, the rest of the ligands form different interactions with different side chains and backbone polar groups on the outer rim of the binding pocket. Hydrogen bonds are direct or water-bridged. van der Waals contacts are optimized by rotations of hydrophobic side chains and a slight inward displacement of the ZA loop. Rare types of interactions are observed for some of the ligands.