3qtv Summary

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Thrombin Inhibition by Pyridin Derivatives

The structure was published by Biela, A., Khayat, M., Tan, H., et al., Heine, A., Hangauer, D., and Klebe, G., in 2012 in a paper entitled "Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.63 Å and deposited in 2011.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely Thrombin light chain, Thrombin heavy chain, and Hirudin variant-2.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotrimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
L Thrombin light chain P00734 (328-363) (THRB_HUMAN)search Homo sapienssearch 93% 36 77%
H Thrombin heavy chain P00734 (364-622) (THRB_HUMAN)search Homo sapienssearch 93% 259 96%
I Hirudin variant-2 P09945 (60-72) (HIRV2_HIRME)search Hirudo medicinalissearch 100% 13 92%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P00734 (328 - 363) Thrombin light chain Homo sapiens
P09945 (60 - 72) Hirudin variant-2 Hirudo medicinalis

Chain Sequence family (Pfam)
L (P00734) PF09396: Thrombin light chainsearch
H (P00734) PF00089: Trypsinsearch
I (P09945) PF00713: Hirudinsearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
L (P00734) blood coagulationsearch proteolysissearch serine-type endopeptidase activitysearch extracellular regionsearch
H (P00734) proteolysissearch blood coagulationsearch serine-type endopeptidase activitysearch calcium ion bindingsearch catalytic activitysearch

Chain InterPro annotation
L Thrombin light chainsearch
H Peptidase S1search Peptidase S1A, chymotrypsin-typesearch Prothrombin/thrombinsearch Trypsin-like cysteine/serine peptidase domainsearch Peptidase S1, trypsin family, active sitesearch
I