SMTL ID : 7lqp.1

Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 1 residues within 4Å: Chain A: K.22 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: H.18, G.21 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: R.138, G.140 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: E.38, K.54 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: K.22, L.123, K.124 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain B: H.134 Ligand excluded by PLIP

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

SO4.5: 6 residues within 4Å: Chain A: L.19, E.20, I.113, G.114, R.117, L.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.117 Water bridges: A:G.114 SO4.6: 3 residues within 4Å: Chain A: C.16, T.17, H.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.18 Salt bridges: A:H.18, A:K.110 SO4.7: 1 residues within 4Å: Chain A: N.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.68 SO4.8: 5 residues within 4Å: Chain A: G.45, Q.46, S.74, T.75, T.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.76, A:T.76 SO4.9: 2 residues within 4Å: Chain A: P.60 Chain B: K.136 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.136 Water bridges: A:V.61, A:V.61, A:V.61 SO4.10: 7 residues within 4Å: Chain A: P.41, E.43, T.44, G.45, Q.46, E.47, T.48 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.45, A:Q.46, A:E.47, A:E.47, A:T.48 SO4.13: 4 residues within 4Å: Chain B: H.18, L.19, E.20, G.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.18, B:E.20, B:G.21 SO4.14: 6 residues within 4Å: Chain B: C.16, T.17, H.18, E.103, N.106, K.110 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.17, B:H.18, B:H.18, B:E.103, B:N.106 Salt bridges: B:K.110 SO4.15: 5 residues within 4Å: Chain B: L.19, E.20, I.113, G.114, R.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.20, B:I.113 SO4.16: 5 residues within 4Å: Chain B: G.45, Q.46, S.74, T.75, T.76 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.45, B:S.74, B:T.75, B:T.76, B:T.76, B:T.76, B:V.77 SO4.17: 5 residues within 4Å: Chain A: K.54 Chain B: E.38, Y.50, F.51, K.54 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.38 Water bridges: A:K.54 Salt bridges: A:K.54, B:K.54 SO4.18: 6 residues within 4Å: Chain B: I.11, Q.13, V.30, H.65, G.91, I.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.12, B:Q.13 Salt bridges: B:H.65

1 x YAV: 2-[2-[2-[3-[2-[2-[2-[[3-[2-[3-(2-hydroxy-2-oxoethyl)-5-methyl-1-benzofuran-2-yl]ethynyl]phenyl]carbonylamino]ethoxy]ethoxy]ethylcarbamoyl]phenyl]ethynyl]-5-methyl-1-benzofuran-3-yl]ethanoic acid(Non-covalent)

YAV.19: 24 residues within 4Å: Chain A: V.39, Q.46, E.47, A.49, Y.50, L.53, T.76, A.80, E.121, H.122, K.124, T.125, M.129 Chain B: Q.46, A.49, Y.50, T.76, A.80, A.120, E.121, H.122, K.124, T.125, M.129 26 PLIP interactions: 13 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:Q.46, A:E.47, A:A.49, A:Y.50, A:L.53, A:T.76, A:A.80, A:T.125, B:Q.46, B:A.49, B:Y.50, B:T.76, B:A.80, B:K.124, B:T.125 Hydrogen bonds: A:E.47, A:E.121, A:H.122, A:K.124, B:Q.46, B:E.121, B:H.122, B:K.124 pi-Stacking: A:H.122, B:H.122 Salt bridges: B:H.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening. To Be Published

Release Date

2022-02-23

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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