PDBsum entry 2c93

Hydrolase/hydrolase inhibitor

PDB id: 2c93

Contents

Protein chains

29 a.a. *

251 a.a. *

11 a.a. *

Ligands

DMS ×2

C4M

Metals

_NA

Waters ×299

* Residue conservation analysis

PDB id:

2c93

Name:

Hydrolase/hydrolase inhibitor

Title:

Thrombin inhibitors

Structure:

Thrombin, light chain. Chain: a. Fragment: fragment alpha thrombin, residues 328-363. Thrombin heavy chain. Chain: b. Fragment: fragment alpha thrombin, residues 364-622. Hirudin variant-2. Chain: i. Fragment: peptide fragment of hirugen, residues 61-72.

Source:

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

Biol. unit:

Trimer (from PDB file)

Resolution:

2.20Å R-factor: 0.168 R-free: 0.242

Authors:

N.Howard,C.Abell,W.Blakemore,R.Carr,G.Chessari,M.Congreve,S.Howard, H.Jhoti,C.W.Murray,L.C.A.Seavers,R.L.M.Van Montfort

Key ref:

N.Howard et al. (2006). Application of fragment screening and fragment linking to the discovery of novel thrombin inhibitors. J Med Chem, 49, 1346-1355. PubMed id: 16480269 DOI: 10.1021/jm050850v

Date:

09-Dec-05 Release date: 04-Jul-06

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 29 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 251 a.a.

Protein chain

P09945  (HIRV2_HIRME) -  Hirudin variant-2 (Fragment) from Hirudo medicinalis

Seq: 72 a.a.

Struc: 11 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

DOI no: 10.1021/jm050850v

J Med Chem 49:1346-1355 (2006)

PubMed id: 16480269

Application of fragment screening and fragment linking to the discovery of novel thrombin inhibitors.

N.Howard, C.Abell, W.Blakemore, G.Chessari, M.Congreve, S.Howard, H.Jhoti, C.W.Murray, L.C.Seavers, R.L.van Montfort.

ABSTRACT

The screening of fragments is an alternative approach to high-throughput screening for the identification of leads for therapeutic targets. Fragment hits have been discovered using X-ray crystallographic screening of protein crystals of the serine protease enzyme thrombin. The fragment library was designed to avoid any well-precedented, strongly basic functionality. Screening hits included a novel ligand (3), which binds exclusively to the S2-S4 pocket, in addition to smaller fragments which bind to the S1 pocket. The structure of these protein-ligand complexes are presented. A chemistry strategy to link two such fragments together and to synthesize larger drug-sized compounds resulted in the efficient identification of hybrid inhibitors with nanomolar potency (e.g., 7, IC50 = 3.7 nM). These potent ligands occupy the same area of the active site as previously described peptidic inhibitors, while having very different chemical architecture.