SMTL ID : 3lam.1

Crystal structure of HIV-1 reverse transcriptase in complex with N1-propyl pyrimidinedione non-nucleoside inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-dimer

Ligands

1 x KRP: 3-methyl-5-{[5-(1-methylethyl)-2,6-dioxo-3-propyl-1,2,3,6-tetrahydropyrimidin-4-yl]carbonyl}benzonitrile(Non-covalent)

KRP.1: 16 residues within 4Å: Chain A: P.95, L.100, K.101, K.102, K.103, V.106, V.179, Y.181, Y.188, V.189, G.190, F.227, W.229, L.234, H.235, Y.318 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.95, A:L.100, A:V.106, A:V.179, A:Y.181, A:Y.181, A:F.227, A:W.229, A:W.229, A:L.234 Hydrogen bonds: A:K.101, A:K.103 pi-Stacking: A:Y.188

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

SO4.2: 5 residues within 4Å: Chain A: G.436, A.437, N.460, R.461 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.436, A:N.460 Water bridges: A:T.439 Salt bridges: A:R.461 SO4.3: 2 residues within 4Å: Chain A: G.436, R.461 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.438, A:R.461 Salt bridges: A:R.461 SO4.4: 5 residues within 4Å: Chain A: N.460 Chain B: T.286, A.288, E.291 Ligands: SO4.2 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.288, A:N.460, A:N.460 SO4.5: 3 residues within 4Å: Chain A: S.515, E.516, L.517 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.516, A:L.517 SO4.6: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitchell, M.L. et al., N1-Alkyl pyrimidinediones as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg.Med.Chem.Lett. (2010)

Release Date

2010-02-23

Peptides

HIV Reverse transcriptase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV Reverse transcriptase

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