Exploring thrombin S3 pocket
Brandt, T., Baum, B., Hangauer, D., Heine, A., Klebe, G.To be published.
Experimental Data Snapshot
Starting Model: experimental
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Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Thrombin light chain | A [auth L] | 36 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Thrombin heavy chain | B [auth H] | 259 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Hirudin variant-2 | C [auth I] | 12 | Hirudo medicinalis | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P09945 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 3 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
49U Query on 49U | F [auth H] | (S)-N-(4-carbamimidoylbenzyl)-1-(3-cyclopentylpropanoyl)pyrrolidine-2-carboxamide C21 H30 N4 O2 BNCHHUFGEOJCNH-SFHVURJKSA-N | |||
GOL Query on GOL | G [auth H] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
NA Query on NA | D [auth H], E [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
TYS Query on TYS | C [auth I] | L-PEPTIDE LINKING | C9 H11 N O6 S | TYR |
Entity ID: 5 | |||||
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ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000606 (49U) Query on PRD_000606 | F [auth H] | (S)-N-(4-carbamimidoylbenzyl)-1-(3-cyclopentylpropanoyl)pyrrolidine-2-carboxamide | Peptide-like / Thrombin inhibitor |
Length ( Å ) | Angle ( ˚ ) |
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a = 70.4 | α = 90 |
b = 71.2 | β = 100.3 |
c = 72.2 | γ = 90 |
Software Name | Purpose |
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SHELX | model building |
SHELXL-97 | refinement |
CrystalClear | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |