ISDA

Entry Detail

PDB ID:

3C1K

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

Crystal structure of thrombin in complex with inhibitor 15

Biological Source:

Source Organism:

Homo sapiens, Hirudo medicinalis

PDB Version:

Deposition Date:

2008-01-23

Release Date:

2008-03-18

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.84 Å

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Prothrombin
Chain IDs:A
Chain Length:287
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P00734 Pfam ID:PF09396, PF00089 EC:3.4.21.5

Protein Blast

Polymer Type:polypeptide(L)
Description:Hirugen
Chain IDs:B
Chain Length:11
Number of Molecules:1
Biological Source:Hirudo medicinalis

UniProt ID:P28511 EC:3.4.21.5

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
TYS	B	TYR	O-SULFO-L-TYROSINE

Ligand Molecules

T15

Primary Citation

Structure-based design of novel groups for use in the P1 position of thrombin inhibitor scaffolds. Part 2: N-acetamidoimidazoles.

Isaacs, R.C, Solinsky, M.G, Cutrona, K.J, Newton, C.L, Naylor-Olsen, A.M, McMasters, D.R, Krueger, J.A, Lewis, S.D, Lucas, B.J, Kuo, L.C, Yan, Y, Lynch, J.J, Lyle, E.A.Show

Bioorg.Med.Chem.Lett. 18 2062 2066 (2008)

PMID: 18291642 DOI: 10.1016/j.bmcl.2008.01.098

Abstact

Guided by X-ray crystallography of thrombin-inhibitor complexes and molecular modeling, alkylation of the N1 nitrogen of the imidazole P1 ligand of the pyridinoneacetamide thrombin inhibitor 1 with various acetamide moieties furnished inhibitors with significantly improved thrombin potency, trypsin selectivity, functional in vitro anticoagulant potency and in vivo antithrombotic efficacy. In the pyrazinoneacetamide series, oral bioavailability was also improved.

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Primary Citation of related structures