MolNFT v1 · #183311 · protein
Structure of human programmed cell death 1 ligand 1 (pd-L1) with low molecular mass inhibitor
7NLD: “Structure of human programmed cell death 1 ligand 1 (pd-L1) with low molecular mass inhibitor”. X-ray diffraction, 1 ligand (UGZ), 4 pockets (best druggability 0.75). MolNFT v1 #183311 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7NLD
- Type
- protein
- Length
- 696 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Ligands
- UGZ
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | Programmed cell death 1 ligand 1 | protein | 116 | 11% helix, 47% strand | Q9NZQ7 |
| A | Programmed cell death 1 ligand 1 | protein | 118 | 10% helix, 47% strand | Q9NZQ7 |
| B | Programmed cell death 1 ligand 1 | protein | 117 | 11% helix, 49% strand | Q9NZQ7 |
| D | Programmed cell death 1 ligand 1 | protein | 114 | 13% helix, 48% strand | Q9NZQ7 |
| F | Programmed cell death 1 ligand 1 | protein | 115 | 9% helix, 45% strand | Q9NZQ7 |
Ligands and binding sites
- UGZ · N-(2-((2'-chloro-3'-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-3-methoxy-[1,1'-biphenyl]-4-yl)(methyl)amino) ethyl)methanesulfonamide · ligand · 3 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.75 | 0.78 | 98 | UGZ |
| 2 | 672 | 0.68 | 0.77 | 60 | empty |
| 3 | 441 | 0.67 | 0.79 | 54 | UGZ |
| 4 | 198 | 0.50 | 0.77 | 20 | empty |
Interfaces
9 interfaces between chains.
- C–A · 530 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 529 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 434 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 431 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 233 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7NLD · Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass… · the same entry in another collection · chain C against C, 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 7NLD · PDBe 7NLD · UniProt Q9NZQ7
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