Crystal Structure of Thrombin in complex with compound10. Determined by X-ray diffraction at 1.8 Å resolution. Released 26 Aug 2020.
Explore 6ZUG in 3D Show helices and sheets RCSB PDB PDBe
6ZUG contains 17 α-helices and 24 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 17 | 1 | 1 |
| β-strand | 20-21 | 2 | 2 |
| α-helix | 22-23 | 2 | |
| β-strand | 30-36 | 7 | 3 |
| β-strand | 38-46 | 9 | 3 |
| β-strand | 51-54 | 4 | 3 |
| α-helix | 56-58 | 3 | |
| β-strand | 60-60A | 2 | 4 |
| α-helix | 60B-60D | 3 | |
| β-strand | 60F-60G | 2 | 4 |
| α-helix | 61-63 | 3 | |
| β-strand | 64-68 | 5 | 3 |
| β-strand | 72 | 1 | 5 |
| β-strand | 81-90 | 10 | 3 |
| β-strand | 95 | 1 | 6 |
| β-strand | 100 | 1 | 6 |
| β-strand | 104-108 | 5 | 3 |
| α-helix | 111-114 | 4 | |
| β-strand | 115 | 1 | 7 |
| β-strand | 118 | 1 | 7 |
| α-helix | 120-121 | 2 | |
| β-strand | 122 | 1 | 2 |
| α-helix | 123-124 | 2 | |
| α-helix | 126-129C | 7 | |
| β-strand | 135-140 | 6 | 2 |
| β-strand | 154 | 1 | 5 |
| β-strand | 156-162 | 7 | 2 |
| α-helix | 165-170 | 6 | |
| α-helix | 175-176 | 2 | |
| β-strand | 180-183 | 4 | 2 |
| α-helix | 186-186B | 3 | |
| β-strand | 189 | 1 | 1 |
| β-strand | 198-202 | 5 | 2 |
| β-strand | 207-216 | 10 | 2 |
| β-strand | 226-230 | 5 | 2 |
| α-helix | 232-234 | 3 | |
| α-helix | 235-244 | 10 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 11-15 | 5 | |
| α-helix | 16-18 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14I | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Prothrombin | L | protein | 29 | Homo sapiens | P00734 (AlphaFold model) |
| Prothrombin | H | protein | 258 | Homo sapiens | P00734 (AlphaFold model) |
| Hirudin-2 | I | protein | 11 | Hirudo medicinalis | P28504 (AlphaFold model) |
>6ZUG_1 Prothrombin (chains L) EADCGLRPLFEKKSLEDKTERELLESYID
>6ZUG_2 Prothrombin (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFG
>6ZUG_3 Hirudin-2 (chains I) GDFEEIPEEYL
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| QPW | 2-[(3-chlorophenyl)methylamino]-7-methoxy-~{N}-[[(3~{S})-oxolan-3-yl]methyl]-~{… | C24 H28 Cl N3 O4 | 1 |
Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics. Hillisch, A., Gericke, K.M., Allerheiligen, S. et al. J Med Chem (2020) 63:12574-12594. DOI 10.1021/acs.jmedchem.0c01035 · PubMed
Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 6ZUG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.