Exploring thrombin S3 pocket
Brandt, T., Baum, B., Hangauer, D., Heine, A., Klebe, G.To be published.
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
Find similar proteins by: Sequence  |  Structure
Entity ID: 1 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
Thrombin light chain | L | 36 | Homo sapiens | Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5 |
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734 |
Entity ID: 2 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
Thrombin heavy chain | H | 259 | Homo sapiens | Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5 |
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734 |
Entity ID: 3 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
Hirudin variant-2 | I | 12 | Hirudo medicinalis | Mutation(s): 0  |
Find proteins for P09945 (Hirudo medicinalis) Go to UniProtKB:  P09945 |
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
12U Query on 12U | H | N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[2-(cycloheptylamino)ethanoyl]pyrrolidine-2-carboxamide C22 H33 N5 O2 BYTJPDBCLWUEBU-IBGZPJMESA-N | ![]() |  Ligand Interaction | |
NA Query on NA | H | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N | ![]() |  Ligand Interaction |
Biologically Interesting Molecules 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000588 (12U) Query on PRD_000588 | H | N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide | Peptide-like / Thrombin inhibitor | ![]() | -- |
Modified Residues  1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
TYS Query on TYS | I | L-PEPTIDE LINKING | C9 H11 N O6 S | ![]() | TYR |
Length (Å) | Angle (°) |
---|---|
a = 68.900 | α = 90.00 |
b = 71.500 | β = 99.10 |
c = 71.300 | γ = 90.00 |
Software Name | Purpose |
---|---|
SHELX | model building |
SHELXL-97 | refinement |
CrystalClear | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |