SMTL ID : 8fe8.1

Crystal Structure of HIV-1 RT in Complex with the non-nucleoside inhibitor 18b1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x XRB: 5-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylphenoxy}pyrimidin-2-yl)amino]-2-[4-(methanesulfonyl)piperazin-1-yl]benzonitrile(Non-covalent)

XRB.1: 18 residues within 4Å: Chain A: P.97, L.102, K.103, K.104, K.105, V.108, V.181, Y.183, Y.190, P.227, P.228, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.139 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.97, A:K.105, A:V.181, A:Y.183, A:Y.183, A:Y.183, A:Y.183, A:Y.190, A:Y.190, A:W.231 Hydrogen bonds: A:K.103, A:K.103, A:F.229

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

SO4.2: 6 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.527, K.530, E.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.430, A:Q.430 SO4.3: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.336 Salt bridges: A:K.333 SO4.4: 4 residues within 4Å: Chain A: R.465, D.490, S.491, G.492 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.491 Salt bridges: A:R.465 SO4.6: 4 residues within 4Å: Chain B: W.25, E.400, W.403, T.404 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.400 SO4.7: 7 residues within 4Å: Chain A: I.382 Chain B: T.28, K.31, T.401, W.402, T.404, E.405 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.404, B:E.405 Water bridges: B:T.404 Salt bridges: B:K.31 SO4.8: 6 residues within 4Å: Chain A: K.13, Q.87 Chain B: E.54, P.56, Y.57, K.127 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.127, A:K.13

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

EDO.5: 4 residues within 4Å: Chain A: W.537 Chain B: N.266, W.267, W.427 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.502, B:N.266, B:W.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, X. et al., Discovery of diarylpyrimidine derivatives bearing piperazine sulfonyl as potent HIV-1 nonnucleoside reverse transcriptase inhibitors. Commun Chem (2023)

Release Date

2023-10-18

Peptides

Reverse transcriptase/ribonuclease H: A
Reverse transcriptase p51: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase/ribonuclease H

Reverse transcriptase p51

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