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Crystal structure of the cbp bromodomain in complex with CPI703

Analyse Crystal structure of the cbp bromodomain in complex with CPI703 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DBM
Type: protein
Length: 345 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Creb-binding protein
EC: 2.3.1.48
UniProt: Q92793
Ligands: 58N
Pockets: 7 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Creb-binding protein (EC 2.3.1.48)	protein	114	68% helix, 0% strand	Q92793
B	Creb-binding protein (EC 2.3.1.48)	protein	113	65% helix, 0% strand	Q92793
C	Creb-binding protein (EC 2.3.1.48)	protein	118	63% helix, 0% strand	Q92793

Ligands and binding sites

58N · (4R)-6-(1-tert-butyl-1H-pyrazol-4-yl)-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one · ligand · 3 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.50	0.82	18	58N
2	86	0.48	0.82	16	58N
3	74	0.48	0.82	15	58N
4	189	0.47	0.75	23	empty
5	111	0.36	0.74	20	empty

Interfaces

2 interfaces between chains.

B–C · 483 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 419 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5DBM · Crystal structure of the CBP bromodomain in complex with CPI703 · the same entry in another collection · chain A against A, TM-score 1.00
Q92793 · AlphaFold monomer V2.0 prediction for creb-binding protein (Q92793) · a predicted model of the same protein · chain B 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 5DBM · PDBe 5DBM · UniProt Q92793

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