MolNFT v1 · #32615 · protein
Human thrombin complexed with fragment-based small molecules occupying the S1 pocket
2BVR · Alpha thrombin: “Human thrombin complexed with fragment-based small molecules occupying the S1 pocket”. X-ray diffraction, 1 ligand (4CP), 2 pockets (best druggability 0.56). MolNFT v1 #32615 on GenesisL1: 3D structure, binding…
- PDB
- 2BVR
- Type
- protein
- Length
- 288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- 4CP
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Alpha thrombin (EC 3.4.21.5) | protein | 250 | 15% helix, 34% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 0% helix, 0% strand | P09945 |
| L | Alpha thrombin (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
Ligands and binding sites
- 4CP · 2-[2-(4-chloro-phenylsulfanyl)-acetylamino]-3-(4-guanidino-phenyl)-propionamide · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.56 | 0.76 | 37 | 4CP |
| 2 | 51 | 0.30 | 0.76 | 12 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1095 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 589 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 2BVR · Human thrombin complexed with fragment-based small molecules occupying the S1 pocket · the same entry in another collection · chain L against L, TM-score 1.00
- P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.53
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 P09945
- Elsewhere: RCSB PDB 2BVR · PDBe 2BVR · UniProt P00734 · UniProt P09945
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