SMTL ID : 8u6t.1

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-(2-(2-(3-acryloyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)ethoxy)phenoxy)-2-naphthonitrile (JLJ758), a non-nucleoside inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VO8: 5-(2-{2-[2-oxo-3-(prop-2-enoyl)-2,3-dihydro-1H-benzimidazol-1-yl]ethoxy}phenoxy)naphthalene-2-carbonitrile(Covalent)

VO8.1: 19 residues within 4Å: Chain A: P.97, L.102, K.103, K.104, K.105, K.106, 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 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.102, A:K.104, A:K.105, A:V.108, A:V.110, A:V.181, A:Y.183, A:Y.190, A:Y.190, A:L.236, A:L.236, A:P.238 Hydrogen bonds: A:K.105 pi-Stacking: A:Y.183, A:Y.190, A:W.231, A:W.231

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: K.355, Y.356, A.357, R.358, K.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.355, A:A.357 Salt bridges: A:K.376 PO4.3: 4 residues within 4Å: Chain A: R.450, T.475, N.476, Q.477 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.475, A:N.476, A:N.476, A:Q.477 Salt bridges: A:R.450 PO4.4: 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.279, A:M.359, A:R.360 Salt bridges: A:R.358

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.445, E.480, D.500 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.445, A:E.480, A:D.500, A:D.500 MG.6: 6 residues within 4Å: Chain B: Q.23, N.57, T.58, P.59, F.130, T.131 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.58, B:T.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prucha, G.R. et al., Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase. Eur.J.Med.Chem. (2023)

Release Date

2023-11-08

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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