SMTL ID : 8vu9.1

Crystal structure of wild-type HIV-1 reverse transcriptase in complex with non-nucleoside inhibitor 5i3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-mer

Ligands

1 x WB3: (2E)-3-[4-({2-[(1-{[4-(methanesulfonyl)phenyl]methyl}piperidin-4-yl)amino]pyrido[2,3-d]pyrimidin-4-yl}oxy)-3,5-dimethylphenyl]prop-2-enenitrile(Non-covalent)

WB3.1: 17 residues within 4Å: Chain A: P.97, L.102, K.103, K.105, K.106, S.107, V.108, V.181, Y.183, Y.190, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.138 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.97, A:L.102, A:L.102, A:K.105, A:V.108, A:V.181, A:V.181, A:V.181, A:Y.183, A:Y.183, A:Y.183, A:Y.190, A:Y.190, A:F.229, A:F.229, A:F.229, A:W.231, A:L.236, A:Y.320, B:E.138 Hydrogen bonds: A:K.103, A:K.103

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

SO4.2: 6 residues within 4Å: Chain A: M.43, K.75, F.118, Y.148, P.152, Q.153 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.148, A:Y.148, A:Q.153 Water bridges: A:K.75, A:K.75 Salt bridges: A:K.75 SO4.3: 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:G.337 Salt bridges: A:K.333, A:K.514 SO4.4: 5 residues within 4Å: Chain A: R.279, Q.280, K.283, Q.336, R.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.280 Water bridges: A:R.358 Salt bridges: A:R.279, A:K.283, A:R.358 SO4.5: 5 residues within 4Å: Chain A: K.478, E.516, S.517, E.518, L.519 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.516, A:E.518, A:L.519 Water bridges: A:S.517 Salt bridges: A:K.478 SO4.9: 3 residues within 4Å: Chain B: L.234, H.235, W.239 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.235, B:H.235 SO4.10: 8 residues within 4Å: Chain A: T.405, E.406, Y.407, W.408 Chain B: K.331, Q.332, G.333, K.424 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.406 Water bridges: A:E.406, B:K.424 Salt bridges: B:K.424

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: K.426, L.427, W.428, Y.429, Q.511, D.513 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.428, A:Y.429, A:Y.429, A:Q.511, A:D.513 EDO.7: 4 residues within 4Å: Chain A: E.8, V.10, S.165, K.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.8, A:E.8 Water bridges: A:E.8, A:S.165 EDO.11: 4 residues within 4Å: Chain B: W.24, E.399, W.402, T.403 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.399 Water bridges: B:E.399, B:T.403 EDO.12: 6 residues within 4Å: Chain B: I.31, V.35, I.132, P.133, S.134, I.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.132 Water bridges: B:I.135 EDO.13: 6 residues within 4Å: Chain B: K.65, V.108, L.109, D.110, D.186, Y.232 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.65, B:D.186 Water bridges: B:T.409

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: D.445, D.500, D.551 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.445, A:D.551, H2O.1, H2O.6, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Diarylpyrimidine-evolved HIV-1 non-nucleoside reverse transcriptase inhibitors show improved resistance and pharmacokinetic profiles against highly drug-resistant strains. To Be Published

Release Date

2025-05-07

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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