MolNFT v1 · #70214 · protein
Discovery and clinical evaluation of rwj-671818, a thrombin inhibitor with an oxyguanidine P1 motif
3LDX · Thrombin light chain: “Discovery and clinical evaluation of rwj-671818, a thrombin inhibitor with an oxyguanidine P1 motif”. X-ray diffraction, 1 ligand (NLI), 2 pockets (best druggability 0.56). MolNFT v1 #70214 on GenesisL1: 3D…
- PDB
- 3LDX
- 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 variant-1
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- NLI
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 15% helix, 36% strand | P00734 |
| I | Hirudin variant-1 | protein | 11 | 36% helix, 0% strand | P01050 |
Ligands and binding sites
- NLI · N-[2-(carbamimidamidooxy)ethyl]-2-{3-[(2,2-difluoro-2-phenylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}acetamide · 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 | 271 | 0.56 | 0.77 | 43 | NLI |
| 2 | 53 | 0.31 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1080 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 602 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3LDX · Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an… · the same entry in another collection · chain L against L, TM-score 1.00
- P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain I against A, TM-score 0.43
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 P01050
- Elsewhere: RCSB PDB 3LDX · PDBe 3LDX · UniProt P00734 · UniProt P01050
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