SMTL ID : 8vub.1

Crystal structure of wild-type HIV-1 reverse transcriptase in complex with non-nucleoside inhibitor 5e2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PKX: 4-[(4-{[4-(4-cyano-2,6-dimethylphenoxy)-6,7-dimethoxyquinazolin-2-yl]amino}piperidin-1-yl)methyl]benzamide(Non-covalent)

PKX.1: 18 residues within 4Å: Chain A: L.102, K.103, K.105, K.106, S.107, V.108, V.181, I.182, Y.183, Y.190, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.138, T.139 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.102, A:V.181, A:V.181, A:Y.183, A:Y.183, A:Y.190, A:F.229, A:P.238, A:Y.320 Hydrogen bonds: A:K.103, A:K.103, A:V.108 pi-Stacking: A:W.231 Water bridges: B:E.138

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

SO4.2: 5 residues within 4Å: Chain A: K.75, F.118, Y.148, P.152, Q.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.148, A:Y.148, A:Q.153 Salt bridges: A:K.75 SO4.3: 3 residues within 4Å: Chain A: K.333, G.335, Q.336 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.336 Water bridges: A:K.333, A:K.333, A:G.337 Salt bridges: A:K.333 SO4.4: 4 residues within 4Å: Chain A: R.279, Q.280, Q.336, R.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.280, A:Q.336 Water bridges: A:R.358 Salt bridges: A:R.279, A:R.358 SO4.5: 4 residues within 4Å: Chain A: K.478, S.517, E.518, L.519 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.517, 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 Water bridges: A:E.406, 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: 5 residues within 4Å: Chain A: E.8, V.10, S.165 Chain B: G.51, P.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.8 Water bridges: A:S.165 EDO.11: 4 residues within 4Å: Chain B: W.24, E.399, W.402, T.403 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: 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:T.139 EDO.13: 5 residues within 4Å: Chain B: V.108, D.110, D.186, Y.232, T.409 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.186

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: D.445, D.500, D.551 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.445, H2O.1, H2O.1, H2O.8, H2O.11

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

2025-04-30

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

Related Entries With Identical Sequence