MolNFT v1 · #49905 · protein
2-(2-chloro-6-FLUOROPHENYL)ACETAMIDES as potent thrombin inhibitors
2R2M · Thrombin light chain: “2-(2-chloro-6-FLUOROPHENYL)ACETAMIDES as potent thrombin inhibitors”. X-ray diffraction, 1 ligand (I50), 3 pockets (best druggability 0.56). MolNFT v1 #49905 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2R2M
- Type
- protein
- Length
- 286 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin-3A
- EC
- 3.4.21.5
- UniProt
- P00734, P28507
- Ligands
- I50
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 15% helix, 35% strand | P00734 |
| H | Hirudin-3A | protein | 11 | 0% helix, 0% strand | P28507 |
Ligands and binding sites
- I50 · N-[2-({[amino(imino)methyl]amino}oxy)ethyl]-2-{6-chloro-3-[(2,2-difluoro-2-phenylethyl)amino]-2-fluorophenyl}acetamide · ligand · chains B
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 | 276 | 0.56 | 0.77 | 43 | I50 |
| 2 | 51 | 0.31 | 0.77 | 16 | empty |
| 3 | 56 | 0.29 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1088 Ų buried · 26 hydrogen bonds · protein-protein
- B–H · 610 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 P28507
- Elsewhere: RCSB PDB 2R2M · PDBe 2R2M · UniProt P00734 · UniProt P28507
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