PDBsum entry 1ets

Hydrolase/hydrolase inhibitor

PDB id: 1ets

Contents

Protein chains

36 a.a. *

259 a.a. *

Ligands

MID

Waters ×684

* Residue conservation analysis

PDB id:

1ets

Name:

Hydrolase/hydrolase inhibitor

Title:

Refined 2.3 angstroms x-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors napap, 4-tapap and mqpa: a starting point for improving antithrombotics

Structure:

Epsilon-thrombin. Chain: l. Engineered: yes. Epsilon-thrombin. Chain: h. Engineered: yes

Source:

Bos taurus. Cow. Organism_taxid: 9913. Organism_taxid: 9913

Biol. unit:

Trimer (from PQS)

Resolution:

2.30Å R-factor: 0.178

Authors:

W.Bode,H.Brandstetter

Key ref:

H.Brandstetter et al. (1992). Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics. J Mol Biol, 226, 1085-1099. PubMed id: 1518046 DOI: 10.1016/0022-2836(92)91054-S

Date:

06-Jul-92 Release date: 31-Jan-94

Protein chain

P00735  (THRB_BOVIN) -  Prothrombin from Bos taurus

Seq: 625 a.a.

Struc: 36 a.a.

Protein chain

P00735  (THRB_BOVIN) -  Prothrombin from Bos taurus

Seq: 625 a.a.

Struc: 259 a.a.

Enzyme reactions

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

DOI no: 10.1016/0022-2836(92)91054-S

J Mol Biol 226:1085-1099 (1992)

PubMed id: 1518046

Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.

H.Brandstetter, D.Turk, H.W.Hoeffken, D.Grosse, J.Stürzebecher, P.D.Martin, B.F.Edwards, W.Bode.

ABSTRACT

Well-diffracting crystals of bovine epsilon-thrombin in complex with several "non-peptidic" benzamidine and arginine-based thrombin inhibitors have been obtained by co-crystallization. The 2.3 A crystal structures of three complexes formed either with NAPAP, 4-TAPAP, or MQPA, were solved by Patterson search methods and refined to crystallographic R-values of 0.167 to 0.178. The active-site environment of thrombin is only slightly affected by binding of the different inhibitors; in particular, the exposed "60-insertion loop" essentially maintains its typical projecting structure. The D-stereoisomer of NAPAP and the L-stereoisomer of MQPA bind to thrombin with very similar conformations, as previously inferred from their binding to bovine trypsin; the arginine side-chain of the latter inserts into the specificity pocket in a "non-canonical" manner. The L-stereoisomer of 4-TAPAP, whose binding geometry towards trypsin was only poorly defined, is bound to the thrombin active-site in a compact conformation. In contrast to NAPAP, the distal p-amidino/guanidino groups of 4-TAPAP and MQPA do not interact with the carboxylate group of Asp189 in the thrombin specificity pocket in a "symmetrical" twin N-twin O manner, but through "lateral" single N-twin O contacts; in contrast to the p-amidino group of 4-TAPAP, however, the guanidyl group of MQPA packs favourably in the pocket due to an elaborate hydrogen bond network, which includes two entrapped water molecules. These thrombin structures confirm previous conclusions of the important role of the intermolecular hydrogen bonds formed with Gly216, and of the good sterical fit of the terminal bulky hydrophobic inhibitor groups with the hydrophobic aryl binding site and the S2-cavity, respectively, for tight thrombin active site binding of these non-peptidic inhibitors. These accurate crystal structures are presumed to be excellent starting points for the design and the elaboration of improved antithrombotics.

Selected figure(s)

Figure 1.
Figure 1. Chemical ormulas of NAPAP (with residues XasIl. GlypI2, Papal3 and Pipn14): (~cr-(2-napthyl-s~Ilphotl~l-

Figure 4.
Figure 4. ctive site region f the complex formed between NAPAP (thick lines) and bovine thrombin (thin lines) superimposed with the final 2F,,, -Fcslf electron denity. The view is (similar to Figs 2 and 3) towards the thrombin surface; the active site residues are o the ight, the specificity pocket is in the back. Contou surface is at @9a.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 226, 1085-1099) copyright 1992.

Figures were selected by an automated process.