PDBsum entry 2ykn

Hydrolase

PDB id: 2ykn

Contents

Protein chains

558 a.a.

411 a.a.

Ligands

YKN

Metals

_CA

Waters ×276

PDB id:

2ykn

Name:

Hydrolase

Title:

Crystal structure of HIV-1 reverse transcriptase (rt) in complex with a difluoromethylbenzoxazole (dfmb) pyrimidine thioether derivative, a non-nucleoside rt inhibitor (nnrti)

Structure:

Reverse transcriptase/ribonuclease h. Chain: a. Fragment: residues 600-1156. Synonym: exoribonuclease h, p66rt. Ec: 2.7.7.49 , 2.7.7.7 , 3.1.26.13. Engineered: yes. Mutation: yes. Reverse transcriptase/ribonuclease h. Chain: b.

Source:

Human immunodeficiency virus type 1 bh10. Organism_taxid: 11678. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Resolution:

2.12Å R-factor: 0.230 R-free: 0.279

Authors:

J.Boyer,E.Arnoult,M.Medebielle,J.Guillemont,T.Unge,J.Unge,D.Jochmans

Key ref:

J.Boyer et al. (2011). Difluoromethylbenzoxazole pyrimidine thioether derivatives: a novel class of potent non-nucleoside HIV-1 reverse transcriptase inhibitors. J Med Chem, 54, 7974-7985. PubMed id: 22017513

Date:

28-May-11 Release date: 17-Aug-11

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 558 a.a.*

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 411 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B: 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: Chains A, B: 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: Chains A, B: E.C.3.1.-.-
• Enzyme class 5: Chains A, B: 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: Chains A, B: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: Chains A, B: 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 Med Chem 54:7974-7985 (2011)

PubMed id: 22017513

Difluoromethylbenzoxazole pyrimidine thioether derivatives: a novel class of potent non-nucleoside HIV-1 reverse transcriptase inhibitors.

J.Boyer, E.Arnoult, M.Médebielle, J.Guillemont, J.Unge, D.Jochmans.

ABSTRACT

No abstract given.