PDBsum entry 2cn0

Hydrolase/hydrolase inhibitor

PDB id: 2cn0

Contents

Protein chains

250 a.a. *

28 a.a. *

Ligands

SIN-PHE-GLU-GLU-ILE-PRO

F25

Metals

_CA

_NA

Waters ×397

* Residue conservation analysis

PDB id:

2cn0

Name:

Hydrolase/hydrolase inhibitor

Title:

Complex of recombinant human thrombin with a designed inhibitor

Structure:

Prothrombin precursor. Chain: h. Fragment: residues 364-620. Synonym: coagulation factor ii, thrombin. Engineered: yes. Hirudin iia. Chain: i. Fragment: hirudin c-terminus, residues 56-65. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: ovary. Synthetic: yes. Hirudo medicinalis. Medicinal leech.

Biol. unit:

Trimer (from PQS)

Resolution:

1.30Å R-factor: 0.185 R-free: 0.204

Authors:

A.Hoffmann-Roder,E.Schweizer,J.Egger,P.Seiler,U.Obst-Sander,B.Wagner, M.Kansy,D.W.Banner,F.Diederich

Key ref:

A.Hoffmann-Röder et al. (2006). Mapping the fluorophilicity of a hydrophobic pocket: synthesis and biological evaluation of tricyclic thrombin inhibitors directing fluorinated alkyl groups into the p pocket. Chemmedchem, 1, 1205-1215. PubMed id: 17001711

Date:

17-May-06 Release date: 06-Nov-06

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 250 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

Enzyme reactions

• Enzyme class: Chains H, L: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

Chemmedchem 1:1205-1215 (2006)

PubMed id: 17001711

Mapping the fluorophilicity of a hydrophobic pocket: synthesis and biological evaluation of tricyclic thrombin inhibitors directing fluorinated alkyl groups into the p pocket.

A.Hoffmann-Röder, E.Schweizer, J.Egger, P.Seiler, U.Obst-Sander, B.Wagner, M.Kansy, D.W.Banner, F.Diederich.

ABSTRACT

In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics followed by oxidation/deoxyfluorination, as well as oxidation/reduction/deoxyfluorination sequences. In contrast, the incorporation of perfluoroalkyl groups required a stereoselective nucleophilic addition reaction at the "upper" carbonyl group of the tricycles, thereby yielding scaffolds with an additional OH, F, or OMe group, respectively. All newly prepared inhibitors showed potent biological activity, with inhibitory constants (K(i) values) in the range of 0.008-0.163 microM. The X-ray crystal structure of a protein-ligand complex revealed the exact positioning of a difluoromethyl substituent in the tight P pocket. Fluorophilic characteristics are attributed to this hydrophobic pocket, although the potency of the inhibitors was found to be modulated by steric rather than electronic factors.