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Crystal structure of the cbp in complex with the Y08188

Analyse Crystal structure of the cbp in complex with the Y08188 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7XM7
Type: protein
Length: 453 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: GAY, NO3
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Creb-binding protein (EC 2.3.1.48)	protein	113	65% helix, 0% strand	Q92793
B	Creb-binding protein (EC 2.3.1.48)	protein	114	62% helix, 0% strand	Q92793

Ligands and binding sites

GAY · 3-ethanoyl-~{N}-[2-fluoranyl-3-(1-methylpyrazol-4-yl) phenyl]-7-methoxy-indolizine-1-carboxamide · ligand · 2 copies · chains A, D, B, C
NO3 · Nitrate ion · ion · 2 copies · chains B, C
EDO · 1,2-ethanediol · additive · 2 copies · chains D
GOL · Glycerol · additive · chains A
DMS · Dimethyl sulfoxide · additive · chains B
PEG · Di(hydroxyethyl)ether · additive · chains 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	591	0.72	0.80	60	GAY, GOL
2	524	0.72	0.80	58	GAY, DMS
3	562	0.62	0.74	42	PEG, NO3

Interfaces

3 interfaces between chains.

A–D · 426 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 417 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 76 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7XM7 · Crystal Structure of the CBP in complex with the Y08188 · 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 0.98

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 7XM7 · PDBe 7XM7 · UniProt Q92793

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