PDBsum entry 1d3d

Hydrolase/hydrolase inhibitor

PDB id: 1d3d

Contents

Protein chains

28 a.a.

250 a.a. *

12 a.a. *

Ligands

NAG

BZT

Metals

_NA ×2

Waters ×119

* Residue conservation analysis

PDB id:

1d3d

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of human alpha thrombin in complex with benzothiophene inhibitor 4

Structure:

Alpha-thrombin. Chain: a. Alpha-thrombin. Chain: b. Hirugen. Chain: h

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

2.04Å R-factor: 0.175 R-free: 0.223

Authors:

N.Y.Chirgadze

Key ref:

N.Y.Chirgadze et al. (2000). The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors. Protein Sci, 9, 29-36. PubMed id: 10739244 DOI: 10.1110/ps.9.1.29

Date:

29-Sep-99 Release date: 04-Oct-00

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 250 a.a.

Protein chain

P01050  (HIRV1_HIRME) -  Hirudin variant-1 from Hirudo medicinalis

Seq: 65 a.a.

Struc: 12 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: 10.1110/ps.9.1.29

Protein Sci 9:29-36 (2000)

PubMed id: 10739244

The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors.

N.Y.Chirgadze, D.J.Sall, S.L.Briggs, D.K.Clawson, M.Zhang, G.F.Smith, R.W.Schevitz.

ABSTRACT

The crystal structures of four active site-directed thrombin inhibitors, 1-4, in a complex with human alpha-thrombin have been determined and refined at up to 2.0 A resolution using X-ray crystallography. These compounds belong to a structurally novel family of inhibitors based on a 2,3-disubstituted benzo[b]thiophene structure. Compared to traditional active-site directed inhibitors, the X-ray crystal structures of these complexes reveal a novel binding mode. Unexpectedly, the lipophilic benzo[b]thiophene nucleus of the inhibitor appears to bind in the S1 specificity pocket. At the same time, the basic amine of the C-3 side chain of the inhibitor interacts with the mostly hydrophobic proximal, S2, and distal, S3, binding sites. The second, basic amine side chain at C-2 was found to point away from the active site, occupying a location between the S1 and S1' sites. Together, the aromatic rings of the C-2 and C-3 side chains sandwich the indole ring of Trp60D contained in the thrombin S2 insertion loop defined by the sequence "Tyr-Pro-Pro-Trp." [The thrombin residue numbering used in this study is equivalent to that reported for chymotrypsinogen (Hartley BS, Shotton DM, 1971, The enzymes, vol. 3. New York: Academic Press. pp 323-373).] In contrast to the binding mode of more classical thrombin inhibitors (D-Phe-Pro-Arg-H, NAPAP, Argatroban), this novel class of benzo[b]thiophene derivatives does not engage in hydrogen bond formation with Gly216 of the thrombin active site. A detailed analysis of the three-dimensional structures not only provides a clearer understanding of the interaction of these agents with thrombin, but forms a foundation for rational structure-based drug design. The use of the data from this study has led to the design of derivatives that are up to 2,900-fold more potent than the screening hit 1.