SMTL ID : 6lmi.1

Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-6-methanesulfonamido-2,3',4',5-tetramethyl-[1,1'-biphenyl]-4-yl]acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: E.23, K.25, R.120, E.124, H.125, L.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.124, A:L.126 Water bridges: A:K.127 Salt bridges: A:K.25, A:H.125 SO4.2: 2 residues within 4Å: Chain A: T.20, H.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.20, A:H.21 Salt bridges: A:H.21 SO4.6: 6 residues within 4Å: Chain B: E.23, K.25, R.120, E.124, H.125, L.126 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.124, B:L.126 Water bridges: B:K.127 Salt bridges: B:K.25, B:H.125 SO4.7: 2 residues within 4Å: Chain B: T.20, H.21 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.20, B:T.20, B:H.21 Salt bridges: B:H.21

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 6 residues within 4Å: Chain A: Q.49, E.50, Y.53 Chain B: H.125, K.127 Ligands: EJ9.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.125, B:K.127 PGE.8: 6 residues within 4Å: Chain A: H.125, K.127 Chain B: Q.49, E.50, Y.53 Ligands: EJ9.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.125, A:K.127

2 x EJ9: (2S)-2-[2-(3,4-dihydro-2H-chromen-6-yl)-4-(3,4-dimethylphenyl)-3,6-dimethyl-5-(methylsulfonylamino)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid(Non-covalent)

EJ9.4: 14 residues within 4Å: Chain A: Q.49, L.56, T.78, T.79, A.82, A.83, W.86 Chain B: Q.122, A.123, E.124, H.125, T.128, M.132 Ligands: PGE.3 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Q.49, A:T.78, A:T.79, A:A.82, A:W.86, B:T.128 Hydrogen bonds: B:E.124, B:E.124, B:H.125, B:T.128 Salt bridges: B:H.125 EJ9.9: 14 residues within 4Å: Chain A: Q.122, A.123, E.124, H.125, T.128, M.132 Chain B: Q.49, L.56, T.78, T.79, A.82, A.83, W.86 Ligands: PGE.8 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.128, B:Q.49, B:T.78, B:T.79, B:A.82, B:W.86 Hydrogen bonds: A:E.124, A:E.124, A:H.125, A:T.128, A:T.128 Water bridges: A:E.124 Salt bridges: A:H.125

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

EDO.5: 3 residues within 4Å: Chain A: S.77, T.78, T.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.78, A:T.78, A:T.79 EDO.10: 3 residues within 4Å: Chain B: S.77, T.78, T.79 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.78, B:T.78, B:T.78, B:T.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugiyama, S. et al., Discovery of novel integrase-LEDGF/p75 allosteric inhibitors based on a benzene scaffold. Bioorg.Med.Chem. (2020)

Release Date

2020-09-23

Peptides

Integrase catalytic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase catalytic

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