SMTL ID : 6ncj.1

Structure of HIV-1 Integrase with potent 5,6,7,8-Tetrahydro-1,6-naphthyridine Derivatives Allosteric Site Inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: G.77, R.78, W.79, P.80 Chain B: Y.54, N.155, H.156, G.168, V.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.77 EDO.2: 9 residues within 4Å: Chain A: L.34, C.36, L.45, E.63, T.86, D.87, N.88, N.91, F.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.86 EDO.3: 7 residues within 4Å: Chain A: E.56, A.57, F.71, K.74, L.75 Chain B: K.74, R.78 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.74, B:R.78, A:E.56, A:A.57 EDO.4: 4 residues within 4Å: Chain A: E.67, Y.70 Chain B: K.144 Ligands: KJJ.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.67, B:K.144 Hydrogen bonds: B:K.144 EDO.8: 9 residues within 4Å: Chain A: Y.54, N.155, H.156, G.168, V.172 Chain B: G.77, R.78, W.79, P.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.77 EDO.9: 9 residues within 4Å: Chain B: L.34, C.36, L.45, E.63, T.86, D.87, N.88, N.91, F.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.86 EDO.10: 7 residues within 4Å: Chain A: K.74, R.78 Chain B: E.56, A.57, F.71, K.74, L.75 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.57, A:K.74, A:R.78 EDO.11: 4 residues within 4Å: Chain A: K.144 Chain B: E.67, Y.70 Ligands: KJJ.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.144 Water bridges: A:K.144

2 x KJJ: (2~{S})-2-[4-(8-fluoranyl-5-methyl-3,4-dihydro-2~{H}-chromen-6-yl)-2-methyl-6-[[(1~{S},2~{R})-2-phenylcyclopropyl]methyl]-7,8-dihydro-5~{H}-1,6-naphthyridin-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid(Non-covalent)

KJJ.5: 16 residues within 4Å: Chain A: Q.66, A.69, T.95, T.96, K.98, A.99, A.100, W.102, W.103 Chain B: Q.139, A.140, E.141, H.142, T.145, M.149 Ligands: EDO.4 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.145, A:Q.66, A:T.96, A:A.99, A:W.102, A:W.103 Hydrogen bonds: B:E.141, B:H.142, B:T.145 Salt bridges: B:H.142 Water bridges: A:Q.66 KJJ.12: 16 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, T.145, M.149 Chain B: Q.66, A.69, T.95, T.96, K.98, A.99, A.100, W.102, W.103 Ligands: EDO.11 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.145, B:Q.66, B:T.96, B:A.99, B:W.102, B:W.103 Hydrogen bonds: A:E.141, A:H.142, A:T.145, A:T.145 Salt bridges: A:H.142 Water bridges: B:Q.66

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

SO4.6: 5 residues within 4Å: Chain A: K.42, R.137, E.141, H.142, L.143 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.141, A:L.143 Water bridges: A:K.42, A:K.144 Salt bridges: A:K.42, A:H.142 SO4.7: 2 residues within 4Å: Chain A: K.82, K.107 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.82, A:K.107 SO4.13: 5 residues within 4Å: Chain B: K.42, R.137, E.141, H.142, L.143 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.141, B:L.143 Water bridges: B:K.42, B:K.144 Salt bridges: B:K.42, B:H.142 SO4.14: 2 residues within 4Å: Chain B: K.82, K.107 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.82, B:K.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peese, K.M. et al., 5,6,7,8-Tetrahydro-1,6-naphthyridine Derivatives as Potent HIV-1-Integrase-Allosteric-Site Inhibitors. J. Med. Chem. (2019)

Release Date

2019-01-16

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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