SMTL ID : 9mxb.1

Crystal Structure of WT HIV-1 Reverse Transcriptase in Complex with 5-{2-[2-(2-oxo-4-sulfanylidene-3,4-dihydropyrimidin-1(2H)-yl)ethoxy] phenoxy}naphthalene-2-carbonitrile (JLJ648), a non-nucleoside inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

hetero-1-1-mer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: K.355, Y.356, A.357, K.376 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: Q.526, K.530 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: D.17, R.83 Ligand excluded by PLIP

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

SO4.3: 3 residues within 4Å: Chain A: Q.280, K.283, Q.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.280, A:Q.280 Salt bridges: A:K.283 SO4.6: 3 residues within 4Å: Chain B: E.370, Q.373, Q.407 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.407

1 x 01: 5-{2-[2-(2-oxo-4-sulfanylidene-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}naphthalene-2-carbonitrile

01.4: 17 residues within 4Å: Chain A: L.102, K.103, K.104, K.105, V.108, V.110, V.181, Y.183, Y.190, G.192, P.227, F.229, W.231, L.236, H.237, P.238, Y.320 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.102, A:K.105, A:V.108, A:V.108, A:V.110, A:V.181, A:Y.190, A:Y.190, A:F.229, A:W.231, A:L.236 Hydrogen bonds: A:K.105, A:K.225, A:P.238 pi-Stacking: A:Y.183, A:Y.190, A:W.231, A:W.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hollander, K. et al., Mechanistic basis for a novel dual-function Gag-Pol dimerizer potentiating CARD8 inflammasome activation and clearance of HIV-infected cells. Npj Drug Discov (2025)

Release Date

2025-09-10

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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