PDBsum entry 2bdy

Hydrolase/hydrolase inhibitor

PDB id: 2bdy

Contents

Protein chain

276 a.a. *

Ligands

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

UNB

Metals

_NA

Waters ×357

* Residue conservation analysis

PDB id:

2bdy

Name:

Hydrolase/hydrolase inhibitor

Title:

Thrombin in complex with inhibitor

Structure:

Thrombin. Chain: a. Fragment: heavy and light chain, residues 334-622. Hirudin iiib'. Chain: b. Fragment: residues 55-64. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Hirudo medicinalis. Organism_taxid: 6421. Other_details: this sequence occurs naturally in hirudo medicinalis (medicinal leech).

Biol. unit:

Dimer (from PQS)

Resolution:

1.61Å R-factor: 0.194 R-free: 0.225

Authors:

Y.Xue

Key ref:

S.Hanessian et al. (2006). Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure. Bioorg Med Chem Lett, 16, 1032-1036. PubMed id: 16290930 DOI: 10.1016/j.bmcl.2005.10.082

Date:

21-Oct-05 Release date: 24-Oct-06

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 276 a.a.

Enzyme reactions

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

DOI no: 10.1016/j.bmcl.2005.10.082

Bioorg Med Chem Lett 16:1032-1036 (2006)

PubMed id: 16290930

Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure.

S.Hanessian, E.Therrien, W.A.van Otterlo, M.Bayrakdarian, I.Nilsson, O.Fjellström, Y.Xue.

ABSTRACT

Prototypical thrombin inhibitors were synthesized based on a trisubstituted phenol as a core motif. A naphthylsulfonamide analogue showed excellent antithrombin activity. An X-ray co-crystal structure showed the expected interactions.