MolNFT v1 · #142250 · protein
Crystal structure of cert start domain in complex with compound E25A
5ZYL · Lipid-transfer protein cert: “Crystal structure of cert start domain in complex with compound E25A”. X-ray diffraction, 1 ligand (9MC), 3 pockets (best druggability 0.85). MolNFT v1 #142250 on GenesisL1: 3D structure, binding sites…
- PDB
- 5ZYL
- Type
- protein
- Length
- 235 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipid-transfer protein cert
- UniProt
- Q9Y5P4
- Ligands
- 9MC
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipid-transfer protein cert | protein | 235 | 26% helix, 38% strand | Q9Y5P4 |
Ligands and binding sites
- 9MC · 2-[4-[4-cyclopentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol · ligand · chains A
- GOL · Glycerol · additive · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.85 | 0.91 | 48 | 9MC |
| 2 | 63 | 0.30 | 0.75 | 15 | empty |
| 3 | 65 | 0.29 | 0.74 | 17 | GOL |
Compared structures
- 5ZYL · Crystal structure of CERT START domain in complex with compound E25A · 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 5ZYL · PDBe 5ZYL · UniProt Q9Y5P4
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