MolNFT v1 · #173895 · protein
Structure of human programmed cell death 1 ligand 1 (pd-L1) with inhibitor
7BEA: “Structure of human programmed cell death 1 ligand 1 (pd-L1) with inhibitor”. X-ray diffraction, 1 ligand (TK2), 1 pocket (best druggability 0.64). MolNFT v1 #173895 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BEA
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Ligands
- TK2
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death 1 ligand 1 | protein | 126 | 16% helix, 45% strand | Q9NZQ7 |
| B | Programmed cell death 1 ligand 1 | protein | 123 | 10% helix, 46% strand | Q9NZQ7 |
Ligands and binding sites
- TK2 · 2-(aminomethyl)-6-[(2-methyl-3-phenyl-phenyl)methoxy]-~{N}-(2-phenylethyl)imidazo[1,2-a]pyridin-3-amine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.64 | 0.87 | 25 | TK2 |
Interfaces
1 interface between chains.
- A–B · 583 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7BEA · Structure of human Programmed cell death 1 ligand 1 (PD-L1) with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9NZQ7
- Elsewhere: RCSB PDB 7BEA · PDBe 7BEA · UniProt Q9NZQ7
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