MolNFT v1 · #145798 · protein
Reversible covalent direct thrombin inhibitors
6CYM · Prothrombin: “Reversible covalent direct thrombin inhibitors”. X-ray diffraction, 3 ligands (71F, NAG, NA), 3 pockets (best druggability 0.76). MolNFT v1 #145798 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CYM
- Type
- protein
- Length
- 562 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 71F, NAG, NA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 250 | 15% helix, 35% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 27 | 44% helix, 0% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 257 | 14% helix, 34% strand | P00734 |
| D | Prothrombin (EC 3.4.21.5) | protein | 28 | 43% helix, 0% strand | P00734 |
Ligands and binding sites
- 71F · 2-methoxybenzoic acid · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.76 | 0.78 | 80 | 71F |
| 2 | 219 | 0.53 | 0.77 | 35 | 71F |
| 3 | 79 | 0.50 | 0.83 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1119 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1114 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 469 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6CYM · Reversible Covalent Direct Thrombin Inhibitors · the same entry in another collection · chain A against A, 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 P00734
- Elsewhere: RCSB PDB 6CYM · PDBe 6CYM · UniProt P00734
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