MolNFT v1 · #16078 · protein
Design of weakly basic thrombin inhibitors incorporating novel P1 binding functions: molecular and X-ray crystallographic studies.
1NO9 · Alpha thrombin: “Design of weakly basic thrombin inhibitors incorporating novel P1 binding functions: molecular and X-ray…”. X-ray diffraction, 2 ligands (4ND, NAG), 2 pockets (best druggability 0.54). MolNFT v1 #16078 on GenesisL1…
- PDB
- 1NO9
- Type
- protein
- Length
- 300 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P28501
- Ligands
- 4ND, NAG
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha thrombin (EC 3.4.21.5) | protein | 36 | 28% helix, 0% strand | P00734 |
| H | Alpha thrombin (EC 3.4.21.5) | protein | 253 | 13% helix, 34% strand | P00734 |
| I | Hirugen | protein | 11 | 36% helix, 0% strand | P28501 |
Ligands and binding sites
- 4ND · N4-(N,N-diphenylcarbamoyl)-aminoguanidine · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 | 247 | 0.54 | 0.77 | 40 | 4ND |
| 2 | 50 | 0.30 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1495 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 645 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, sulfation).
Compared structures
- 1NO9 · Design of weakly basic thrombin inhibitors incorporating novel P1 binding functions… · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P28501
- Elsewhere: RCSB PDB 1NO9 · PDBe 1NO9 · UniProt P00734 · UniProt P28501
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