PDBsum entry 2jh6

Hydrolase/hydrolase inhibitor

PDB id

2jh6

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Contents

			Protein chains

					28 a.a. *


					251 a.a. *

			Ligands

					ASP-PHE-GLU-GLU- ILE-PRO-GLU-GLU- TYS-LEU


					894

			Metals

					_CA


					_NA

			Waters ×182

* Residue conservation analysis

PDB id:

2jh6

Links
- PDBe
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- Proteopedia
- CATH
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Name:

Hydrolase/hydrolase inhibitor

Title:

Human thrombin hirugen inhibitor complex

Structure:

Thrombin light chain. Chain: c. Fragment: light chain, residues 328-363. Synonym: coagulation factor ii, alpha thrombin. Other_details: light chain has one disulphide bond to heavy chain. Thrombin heavy chain. Chain: d. Fragment: heavy chain, residues 364-622. Synonym: coagulation factor ii, alpha thrombin.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood plasma. Synthetic: yes. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421

Resolution:

2.21Å

R-factor:

0.165

R-free:

0.196

Authors:

S.Senger,C.Chan,M.A.Convery,J.A.Hubbard,R.J.Young,G.P.Shah,N.S.Watson

Key ref:

S.Senger et al. (2007). Sulfonamide-related conformational effects and their importance in structure-based design. Bioorg Med Chem Lett, 17, 2931-2934. PubMed id: 17336062 DOI: 10.1016/j.bmcl.2007.02.034

Date:

20-Feb-07

Release date:

08-May-07

PROCHECK

	Headers

	References

Protein chain

P00734 (THRB_HUMAN) - Prothrombin from Homo sapiens

Seq: Struc:

Seq: Struc:					622 a.a. 28 a.a.

Protein chain

P00734 (THRB_HUMAN) - Prothrombin from Homo sapiens

Seq: Struc:

Seq: Struc:					622 a.a. 251 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

Chains C, D: E.C.3.4.21.5 - thrombin.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

DOI no: 10.1016/j.bmcl.2007.02.034	Bioorg Med Chem Lett 17:2931-2934 (2007)
PubMed id: 17336062

Sulfonamide-related conformational effects and their importance in structure-based design.
S.Senger, C.Chan, M.A.Convery, J.A.Hubbard, G.P.Shah, N.S.Watson, R.J.Young.

ABSTRACT

Structure-based design (SBD) is a challenging endeavour since even localised SAR can hardly ever be explained by the variation of just one dominating factor. Here, we present a rare example where structural information combined with ab initio calculations clearly indicate that the observed difference in biological activity is dominated by conformational effects. The learnings discussed are successfully put to the test and have the potential to be of general use as a qualitative guide in SBD efforts.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18711721

K.T.Butler, F.J.Luque, and X.Barril (2009).
Toward accurate relative energy predictions of the bioactive conformation of drugs.

J Comput Chem, 30, 601-610.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.