MolNFT v1 · #16242 · protein
Thrombin in complex with selective macrocyclic inhibitor
1NT1: “Thrombin in complex with selective macrocyclic inhibitor”. X-ray diffraction, 1 ligand (T76), 1 pocket (best druggability 0.56). MolNFT v1 #16242 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NT1
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- T76
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 276 | 17% helix, 33% strand | P00734 |
| H | Hirudin | protein | 11 | 36% helix, 0% strand | P28504 |
Ligands and binding sites
- T76 · (6r,21as)-17-chloro-6-cyclohexyl-2,3,6,7,10,11,19,20-octahydro-1H,5H-pyrrolo[1,2-k][1,4,8,11,14]benzoxatetraaza-cycloheptadecine-5,8,12,21(9h,13h,21ah)-tetrone · ligand · chains A
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 | 279 | 0.56 | 0.76 | 42 | T76 |
Interfaces
1 interface between chains.
- A–H · 680 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
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 P00734
- Every structure of UniProt P28504
- Elsewhere: RCSB PDB 1NT1 · PDBe 1NT1 · UniProt P00734 · UniProt P28504
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