SMTL ID : 3lak.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x KR1: 3-({3-[(2-AMINO-6-FLUOROPYRIDIN-4-YL)METHYL]-5-(1-METHYLETHYL)-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL}CARBONYL)-5-METHYLBENZONITRILE(Non-covalent)

KR1.1: 16 residues within 4Å: Chain A: L.100, K.101, K.103, V.106, V.179, Y.181, Y.188, V.189, G.190, P.225, F.227, W.229, L.234, H.235, P.236, Y.318 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.100, A:V.106, A:V.179, A:Y.181, A:Y.188, A:Y.188, A:W.229, A:L.234, A:L.234 Hydrogen bonds: A:K.101, A:K.103 Water bridges: A:K.101, A:K.103, A:K.103 pi-Stacking: A:Y.188, A:W.229

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

SO4.2: 6 residues within 4Å: Chain A: G.436, A.437, E.438, N.460, R.461 Chain B: A.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.460, A:N.460 Water bridges: A:T.439 Salt bridges: A:R.461 SO4.3: 3 residues within 4Å: Chain A: G.436, R.461, G.490 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.438, A:R.461 Salt bridges: A:R.461 SO4.4: 4 residues within 4Å: Chain A: N.460 Chain B: T.286, A.288, E.291 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.460, B:A.288 SO4.5: 4 residues within 4Å: Chain A: K.476, S.515, E.516, L.517 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.516, A:L.517 Salt bridges: A:K.476

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain B: H.235, W.239 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitchell, M.L. et al., N1-Heterocyclic 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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