SMTL ID : 6x4d.1

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-(cyclopropylmethyl)-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-8-methyl-2-naphthonitrile (JLJ678), a Non-nucleoside Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x UO4: 5-(cyclopropylmethyl)-7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-8-methylnaphthalene-2-carbonitrile(Non-covalent)

UO4.1: 18 residues within 4Å: Chain A: P.97, L.102, K.103, K.104, K.105, V.108, V.110, V.181, Y.183, Y.190, V.191, G.192, F.229, W.231, L.236, H.237, P.238, Y.320 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.97, A:K.105, A:V.108, A:V.181, A:Y.183, A:Y.183, A:Y.190, A:Y.190, A:W.231, A:L.236 Hydrogen bonds: A:K.105, A:P.238 pi-Stacking: A:Y.190, A:W.231

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.336, A:Q.336 Water bridges: A:K.333 Salt bridges: A:K.333, A:K.514 SO4.3: 4 residues within 4Å: Chain A: R.279, R.358, M.359, R.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.358 Salt bridges: A:R.279, A:R.358, A:R.360

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duong, V.N. et al., Structural investigation of 2-naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site. Protein Sci. (2020)

Release Date

2020-07-22

Peptides

Reverse transcriptase/ribonuclease H: A
p51 RT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase/ribonuclease H

p51 RT

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