SMTL ID : 6eli.1

Structure of HIV-1 reverse transcriptase (RT) in complex with rilpivirine and an RNase H inhibitor XZ462

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x T27: 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile(Non-covalent)

T27.1: 16 residues within 4Å: Chain A: P.97, L.102, K.103, K.105, V.108, V.181, Y.183, Y.190, P.227, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.138 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.97, A:L.102, A:L.102, A:K.105, A:V.108, A:V.181, A:V.181, A:Y.183, A:Y.183, A:Y.183, A:Y.183, A:Y.190, A:Y.190, A:Y.190, A:W.231, A:L.236, A:Y.320 Hydrogen bonds: A:K.103, A:K.103 Water bridges: A:I.182

1 x BA5: methyl 4-azanyl-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxylate(Non-covalent)

BA5.2: 9 residues within 4Å: Chain A: D.445, G.446, E.480, D.500, Q.502, H.541, D.551 Ligands: MG.3, MG.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.555 Salt bridges: A:H.541

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.445, D.551 Ligands: BA5.2, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.445, A:D.551, H2O.2, H2O.4 MG.4: 5 residues within 4Å: Chain A: D.445, E.480, D.500 Ligands: BA5.2, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.445, A:E.480, A:D.500

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

SO4.5: 5 residues within 4Å: Chain A: M.43, K.75, Y.148, P.152, Q.153 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.74, A:Y.148, A:Y.148, A:Q.153 Water bridges: A:K.75 Salt bridges: A:K.75 SO4.6: 5 residues within 4Å: Chain A: K.478, E.516, S.517, E.518, L.519 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.516, A:E.518, A:L.519 Salt bridges: A:K.478

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

EDO.7: 7 residues within 4Å: Chain B: V.75, D.76, F.77, N.81, G.152, W.410, I.411 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.75, B:F.77, B:I.411 Water bridges: B:N.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boyer, P.L. et al., Developing and Evaluating Inhibitors against the RNase H Active Site of HIV-1 Reverse Transcriptase. J. Virol. (2018)

Release Date

2018-04-11

Peptides

reverse transcriptase: A
Gag-Pol polyprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

reverse transcriptase

Gag-Pol polyprotein

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