MolNFT v1 · #127636 · protein
Structure of pd-L1/SMALL-molecule inhibitor complex
5N2D · Programmed cell death 1 ligand 1: “Structure of pd-L1/SMALL-molecule inhibitor complex”. X-ray diffraction, 1 ligand (8J8), 5 pockets (best druggability 0.64). MolNFT v1 #127636 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5N2D
- Type
- protein
- Length
- 500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Ligands
- 8J8
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death 1 ligand 1 | protein | 125 | 16% helix, 45% strand | Q9NZQ7 |
| B, D | Programmed cell death 1 ligand 1 | protein | 124 | 17% helix, 44% strand | Q9NZQ7 |
| C | Programmed cell death 1 ligand 1 | protein | 127 | 17% helix, 46% strand | Q9NZQ7 |
Ligands and binding sites
- 8J8 · ~{N}-[2-[[2,6-dimethoxy-4-[(2-methyl-3-phenyl-phenyl) methoxy]phenyl]methylamino]ethyl]ethanamide · ligand · 2 copies · chains A, B, C, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.64 | 0.86 | 33 | 8J8 |
| 2 | 171 | 0.64 | 0.84 | 30 | 8J8 |
| 3 | 229 | 0.51 | 0.75 | 28 | empty |
| 4 | 192 | 0.51 | 0.77 | 28 | empty |
| 5 | 159 | 0.44 | 0.75 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–C · 610 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 555 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 530 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 511 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5N2D · Structure of PD-L1/small-molecule inhibitor complex · 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 5N2D · PDBe 5N2D · UniProt Q9NZQ7
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