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Structure of crebbp bromodomain with compound 2 bound

Analyse Structure of crebbp bromodomain with compound 2 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QST
Type: protein
Length: 454 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Creb-binding protein
EC: 2.3.1.48
UniProt: Q92793
Ligands: JGK
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Creb-binding protein (EC 2.3.1.48)	protein	116	66% helix, 0% strand	Q92793
B	Creb-binding protein (EC 2.3.1.48)	protein	112	69% helix, 0% strand	Q92793
C, D	Creb-binding protein (EC 2.3.1.48)	protein	113	68% helix, 0% strand	Q92793

Ligands and binding sites

JGK · ~{N}-[3-(3-azanyl-5-methyl-1,2-oxazol-4-yl)-5-(5-ethanoyl-2-ethoxy-phenyl)phenyl]furan-2-carboxamide · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	693	0.75	0.80	55	JGK
2	618	0.75	0.81	55	JGK
3	268	0.49	0.73	22	empty

Interfaces

3 interfaces between chains.

A–B · 409 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 290 Å² buried · 1 hydrogen bond · protein-protein
B–C · 211 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6QST · Structure of CREBBP bromodomain with compound 2 bound · the same entry in another collection · chain C against C, TM-score 1.00
Q92793 · AlphaFold monomer V2.0 prediction for creb-binding protein (Q92793) · a predicted model of the same protein · chain D against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q92793
Elsewhere: RCSB PDB 6QST · PDBe 6QST · UniProt Q92793

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