MolNFT v1 · #111205 · protein

Crystal structure of the cbp bromodomain in complex with CPI098

4YK0 · Creb-binding protein: “Crystal structure of the cbp bromodomain in complex with CPI098”. X-ray diffraction, 1 ligand (986), 5 pockets (best druggability 0.80). MolNFT v1 #111205 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4YK0
Type: protein
Length: 416 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: 986
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, 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	99	68% helix, 0% strand	Q92793
D	Creb-binding protein (EC 2.3.1.48)	protein	91	65% helix, 0% strand	Q92793

Ligands and binding sites

986 · (4R)-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	932	0.80	0.82	78	986
2	160	0.60	0.83	25	empty
3	135	0.52	0.80	23	986
4	94	0.51	0.82	18	986
5	68	0.38	0.79	18	empty

Interfaces

5 interfaces between chains.

A–B · 484 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 474 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 364 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 218 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 189 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4YK0 · Crystal structure of the CBP bromodomain in complex with CPI098 · the same entry in another collection · chain D against D, 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 4YK0 · PDBe 4YK0 · UniProt Q92793

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.