PDBsum entry 4aht

Transferase

PDB id: 4aht

Contents

Protein chains

151 a.a.

Ligands

SO4 ×8

EDO ×3

TAM ×2

Q6T ×2

ACY

Waters ×178

PDB id:

4aht

Name:

Transferase

Title:

Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification

Structure:

Integrase. Chain: a, b. Fragment: integrase, residues 1197-1359. Synonym: in. Engineered: yes. Mutation: yes. Other_details: n-term his-tag not removed from protein

Source:

Human immunodeficiency virus. HIV. Organism_taxid: 12721. Strain: type 1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.162 R-free: 0.198

Authors:

J.Wielens,S.J.Heady,D.I.Rhodes,R.J.Mulder,O.Dolezal,J.J.Deadman, J.Newman,D.K.Chalmers,M.W.Parker,T.S.Peat,M.J.Scanlon

Key ref:

J.Wielens et al. (2013). Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? J Biomol Screen, 18, 147-159. PubMed id: 23139382

Date:

07-Feb-12 Release date: 19-Dec-12

Protein chains

P12497  (POL_HV1N5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

Seq: 1435 a.a.

Struc: 151 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.1.-.-
• Enzyme class 5: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 6: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

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

J Biomol Screen 18:147-159 (2013)

PubMed id: 23139382

Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?

J.Wielens, S.J.Headey, D.I.Rhodes, R.J.Mulder, O.Dolezal, J.J.Deadman, J.Newman, D.K.Chalmers, M.W.Parker, T.S.Peat, M.J.Scanlon.

ABSTRACT

Fragment screening is becoming widely accepted as a technique to identify hit compounds for the development of novel lead compounds. In neighboring laboratories, we have recently, and independently, performed a fragment screening campaign on the HIV-1 integrase core domain (IN) using similar commercially purchased fragment libraries. The two campaigns used different screening methods for the preliminary identification of fragment hits; one used saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR), and the other used surface plasmon resonance (SPR) spectroscopy. Both initial screens were followed by X-ray crystallography. Using the STD-NMR/X-ray approach, 15 IN/fragment complexes were identified, whereas the SPR/X-ray approach found 6 complexes. In this article, we compare the approaches that were taken by each group and the results obtained, and we look at what factors could potentially influence the final results. We find that despite using different approaches with little overlap of initial hits, both approaches identified binding sites on IN that provided a basis for fragment-based lead discovery and further lead development. Comparison of hits identified in the two studies highlights a key role for both the conditions under which fragment binding is measured and the criteria selected to classify hits.