Brand  (β version)

PDB ID: 4UD9

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Ligands
Code Name Style Show Link
DMS Dimethyl sulfoxide PoSSuM
EDO 1,2-ethanediol PoSSuM
FQI 5-chloro-2-thiophenecarboxamide PoSSuM
GOL Glycerol PoSSuM
NA Sodium ion PoSSuM
PO4 Phosphate ion PoSSuM
Non-standard Residues
Code Name Show
TYS O-sulfo-L-tyrosine
Glycosylation
Code Name Emphasize
NAG 2-acetamido-2-deoxy-beta-D-glucopyranose
Modification
Code Name Show

Structure summary

Code : 4UD9   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Thrombin in complex with 5-chlorothiophene-2-carboxamide
Release Data : 2015-08-26
Compound :
mol_id molecule chains
1 Thrombin heavy chain H
ec: 3.4.21.5
fragment: THROMBIN HEAVY CHAIN, UNP RESIDUES 364-622
mol_id molecule chains synonym
2 Hirudin-2 I Hirudin II
other_details: HIRUDIN (54-65) (SULFATED)
mol_id molecule chains synonym
3 Prothrombin L Coagulation factor II
ec: 3.4.21.5
fragment: THROMBIN LIGHT CHAIN, UNP RESIDUES 333-360
Source :
mol_id organism_scientific organism_common
1 Homo sapiens  (taxid:9606) Human
other_details: PURIFIED FROM HUMAN BLOOD PLASMA
mol_id organism_scientific organism_common
2 Hirudo medicinalis  (taxid:6421) Medicinal leech
synthetic: yes
mol_id organism_scientific organism_common
3 Homo sapiens  (taxid:9606) Human
other_details: PURIFIED FROM HUMAN BLOOD PLASMA
Authors : Ruehmann, E., Heine, A., Klebe, G.
Keywords : HYDROLASE, HYDROLASE INHIBITOR COMPLEX, SERINE PROTEASE, BLOOD COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, BLOOD CLOTTING INHIBITOR, THROMBIN INHIBITOR, FRAGMENT, GLYCOSYLATION, BLOOD
Exp. method : X-RAY DIFFRACTION ( 1.124 Å )
Citation :

Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.

Ruehmann, E.,Betz, M.,Heine, A.  et al.
(2015)  J.Med.Chem.  58 : 6960

PubMed: 26270568
DOI: 10.1021/ACS.JMEDCHEM.5B00812

Reaction

Chain : L
UniProt : P00734 (THRB_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B. 3.4.21.5 -
-
Chain : I
UniProt : P28504 (HIR2_HIRME)
Reaction : -