MolNFT v1 · #142246 · protein

Crystal structure of cert start domain in complex with compound E5

5ZYH · Lipid-transfer protein cert: “Crystal structure of cert start domain in complex with compound E5”. X-ray diffraction, 1 ligand (9N0), 3 pockets (best druggability 0.84). MolNFT v1 #142246 on GenesisL1: 3D structure, binding sites…

PDB: 5ZYH
Type: protein
Length: 228 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipid-transfer protein cert
UniProt: Q9Y5P4
Ligands: 9N0
Pockets: 3 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipid-transfer protein cert	protein	228	27% helix, 39% strand	Q9Y5P4

Ligands and binding sites

9N0 · 2-[4-[3-~{tert}-butyl-5-[(1~{R},2~{S})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	526	0.84	0.90	52	9N0
2	103	0.36	0.74	17	empty
3	60	0.29	0.74	19	empty

Compared structures

5ZYH · Crystal structure of CERT START domain in complex with compound E5 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5P4 · AlphaFold monomer V2.0 prediction for ceramide transfer protein (Q9Y5P4) · a predicted model of the same protein · chain A 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 Q9Y5P4
Elsewhere: RCSB PDB 5ZYH · PDBe 5ZYH · UniProt Q9Y5P4

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