SMTL ID : 4i7f.2 (1 other biounit)

HIV-1 Reverse Transcriptase in complex with a phosphonate analog of nevirapine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NVE: diethyl ({4-[2-(11-ethyl-5-methyl-6-oxo-6,11-dihydro-5H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-8-yl)ethyl]phenoxy}methyl)phosphonate(Non-covalent)

NVE.1: 21 residues within 4Å: Chain A: P.95, L.100, K.101, K.103, K.104, S.105, V.106, T.107, V.179, Y.181, Y.188, V.189, G.190, R.199, P.225, F.227, W.229, L.234, H.235, P.236, Y.318 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.95, A:L.100, A:V.106, A:V.106, A:T.107, A:V.179, A:Y.181, A:F.227, A:Y.318, A:Y.318 Hydrogen bonds: A:V.106 pi-Stacking: A:W.229 NVE.9: 21 residues within 4Å: Chain C: P.95, L.100, K.101, K.103, K.104, S.105, V.106, T.107, V.179, Y.181, Y.188, V.189, G.190, R.199, P.225, F.227, W.229, L.234, H.235, P.236, Y.318 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:P.95, C:L.100, C:V.106, C:V.106, C:T.107, C:V.179, C:Y.181, C:F.227, C:Y.318, C:Y.318 Hydrogen bonds: C:V.106 pi-Stacking: C:W.229

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

SO4.2: 5 residues within 4Å: Chain A: G.436, A.437, N.460, R.461 Chain B: A.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.436, A:N.460 Salt bridges: A:R.461 SO4.3: 2 residues within 4Å: Chain A: G.436, R.461 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.461 Salt bridges: A:R.461 SO4.4: 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 SO4.5: 4 residues within 4Å: Chain A: Y.183, L.228, W.229, M.230 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:M.230 Water bridges: A:G.231, A:G.231 Salt bridges: C:K.249 SO4.10: 5 residues within 4Å: Chain C: G.436, A.437, N.460, R.461 Chain D: A.288 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.436, C:N.460 Salt bridges: C:R.461 SO4.11: 2 residues within 4Å: Chain C: G.436, R.461 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.461 Salt bridges: C:R.461 SO4.12: 3 residues within 4Å: Chain C: S.515, E.516, L.517 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.516, C:L.517 SO4.13: 4 residues within 4Å: Chain C: Y.183, L.228, W.229, M.230 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Salt bridges: A:K.249 Hydrogen bonds: C:Y.183, C:M.230 Water bridges: C:G.231, C:G.231

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: D.186 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: D.186 No protein-ligand interaction detected (PLIP)

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

CL.7: 1 residues within 4Å: Chain A: K.259 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: H.235, W.239 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain C: K.259 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain D: H.235, W.239 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parrish, J. et al., Synthesis and biological evaluation of phosphonate analogues of nevirapine. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-02-20

Peptides

Reverse transcriptase: AC
Reverse transcriptase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Reverse transcriptase

Reverse transcriptase

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