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Crystal structure of the crebbp bromodomain in complex with a benzo- diazepine ligand

Analyse Crystal structure of the crebbp bromodomain in complex with a benzo- diazepine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YIJ
Type: protein
Length: 813 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Crebbp
EC: 2.3.1.48, 2.3.1.-
UniProt: Q92793
Ligands: OSN
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Crebbp (EC 2.3.1.48, 2.3.1.-)	protein	119	61% helix, 0% strand	Q92793
C	Crebbp (EC 2.3.1.48, 2.3.1.-)	protein	118	63% helix, 0% strand	Q92793
D	Crebbp (EC 2.3.1.48, 2.3.1.-)	protein	113	65% helix, 0% strand	Q92793
E	Crebbp (EC 2.3.1.48, 2.3.1.-)	protein	114	69% helix, 0% strand	Q92793
F	Crebbp (EC 2.3.1.48, 2.3.1.-)	protein	118	61% helix, 0% strand	Q92793
G	Crebbp (EC 2.3.1.48, 2.3.1.-)	protein	112	66% helix, 0% strand	Q92793

Ligands and binding sites

OSN · (4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one · ligand · 7 copies · chains A, B, C, D, E, F, G

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1096	0.82	0.83	97	OSN
2	588	0.69	0.78	62	empty
3	176	0.55	0.79	32	OSN
4	134	0.54	0.81	19	empty
5	108	0.54	0.83	20	OSN

Interfaces

11 interfaces between chains.

B–E · 523 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 518 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 513 Å² buried · 5 hydrogen bonds · protein-protein
F–G · 501 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 463 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6YIJ · Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand · the same entry in another collection · chain G against G, TM-score 1.00
Q92793 · AlphaFold monomer V2.0 prediction for creb-binding protein (Q92793) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 6YIJ · PDBe 6YIJ · UniProt Q92793

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