PDBsum entry 5am3

Hydrolase

PDB id: 5am3

Contents

Protein chain

546 a.a.

Ligands

SO4

GOL

PEG ×2

AUB

Waters ×137

PDB id:

5am3

Name:

Hydrolase

Title:

Ligand complex structure of soluble epoxide hydrolase

Structure:

Bifunctional epoxide hydrolase 2. Chain: a. Synonym: epoxide hydratase, soluble epoxide hydrolase, seh. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9

Resolution:

2.20Å R-factor: 0.201 R-free: 0.236

Authors:

L.Oster,S.Tapani,Y.Xue,H.Kack

Key ref:

L.Öster et al. (2015). Successful generation of structural information for fragment-based drug discovery. Drug Discov Today, 20, 1104-1111. PubMed id: 25931264 DOI: 10.1016/j.drudis.2015.04.005

Date:

09-Mar-15 Release date: 13-May-15

Protein chain

P34913  (HYES_HUMAN) -  Bifunctional epoxide hydrolase 2 from Homo sapiens

Seq: 555 a.a.

Struc: 546 a.a.

Enzyme reactions

• Enzyme class 2: E.C.3.1.3.76 - lipid-phosphate phosphatase.
• Reaction: (9S,10S)-10-hydroxy-9-(phosphooxy)octadecanoate + H2O = (9S,10S)-9,10- dihydroxyoctadecanoate + phosphate
• Cofactor: Mg(2+)
• Enzyme class 3: E.C.3.3.2.10 - soluble epoxide hydrolase.
• Reaction: an epoxide + H2O = an ethanediol

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.drudis.2015.04.005

Drug Discov Today 20:1104-1111 (2015)

PubMed id: 25931264

Successful generation of structural information for fragment-based drug discovery.

L.Öster, S.Tapani, Y.Xue, H.Käck.

ABSTRACT

Fragment-based drug discovery relies upon structural information for efficient compound progression, yet it is often challenging to generate structures with bound fragments. A summary of recent literature reveals that a wide repertoire of experimental procedures is employed to generate ligand-bound crystal structures successfully. We share in-house experience from setting up and executing fragment crystallography in a project that resulted in 55 complex structures. The ligands span five orders of magnitude in affinity and the resulting structures are made available to be of use, for example, for development of computational methods. Analysis of the results revealed that ligand properties such as potency, ligand efficiency (LE) and, to some degree, clogP influence the success of complex structure generation.