ISDA

Deposition Date 2004-11-01

Release Date 2005-01-27

Last Version Date 2024-10-23

Entry Detail

PDB ID:

1WBG

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

Active site thrombin inhibitors

Biological Source:

Source Organism:

HIRUDO MEDICINALIS (Taxon ID: 6421)
HOMO SAPIENS (Taxon ID: 9606)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.26

R-Value Work:

0.16

R-Value Observed:

0.17

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:THROMBIN LIGHT CHAIN
Gene (Uniprot):F2
Chain IDs:A
Chain Length:36
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)
Molecule:THROMBIN HEAVY CHAIN
Gene (Uniprot):F2
Chain IDs:B
Chain Length:259
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)
Molecule:HIRUGEN
Chain IDs:C (auth: I)
Chain Length:10
Number of Molecules:1
Biological Source:HIRUDO MEDICINALIS

UniProt ID:P09945

Modified Residue

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

Ligand Molecules

DMS

L03

Primary Citation

Fragment-Based Lead Discovery Using X-Ray Crystallography

Hartshorn, M.J, Murray, C.W, Cleasby, A, Frederickson, M, Tickle, I.J, Jhoti, H.Show

J.Med.Chem. 48 403 ? (2005)

PMID: 15658854 DOI: 10.1021/JM0495778

Abstact

Fragment screening offers an alternative to traditional screening for discovering new leads in drug discovery programs. This paper describes a fragment screening methodology based on high throughput X-ray crystallography. The method is illustrated against five proteins (p38 MAP kinase, CDK2, thrombin, ribonuclease A, and PTP1B). The fragments identified have weak potency (>100 microM) but are efficient binders relative to their size and may therefore represent suitable starting points for evolution to good quality lead compounds. The examples illustrate that a range of molecular interactions (i.e., lipophilic, charge-charge, neutral hydrogen bonds) can drive fragment binding and also that fragments can induce protein movement. We believe that the method has great potential for the discovery of novel lead compounds against a range of targets, and the companion paper illustrates how lead compounds have been identified for p38 MAP kinase starting from fragments such as those described in this paper.

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Disease

Primary Citation of related structures