SMTL ID : 7d83.1

Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-(2-(3-cyclohexylureido)-3,6-dimethyl-5-(5-methylchroman-6-yl)pyridin-4-yl)acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: C.19, T.20, H.21, K.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.21 Salt bridges: A:H.21, A:K.113 SO4.2: 5 residues within 4Å: Chain A: K.25, R.120, E.124, H.125, L.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.120, A:L.126 Salt bridges: A:K.25, A:H.125 SO4.3: 6 residues within 4Å: Chain A: G.48, Q.49, S.77, T.78, T.79 Ligands: GZ9.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.49, A:S.77, A:S.77, A:T.78, A:T.78, A:T.79 SO4.5: 4 residues within 4Å: Chain B: C.19, T.20, H.21, K.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.21 Salt bridges: B:H.21, B:K.113 SO4.6: 5 residues within 4Å: Chain B: K.25, R.120, E.124, H.125, L.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.120, B:L.126 Salt bridges: B:K.25, B:H.125 SO4.7: 6 residues within 4Å: Chain B: G.48, Q.49, S.77, T.78, T.79 Ligands: GZ9.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.49, B:S.77, B:S.77, B:T.78, B:T.79

2 x GZ9: (2S)-2-[2-(cyclohexylcarbamoylamino)-3,6-dimethyl-5-(5-methyl-3,4-dihydro-2H-chromen-6-yl)pyridin-4-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid(Non-covalent)

GZ9.4: 13 residues within 4Å: Chain A: Q.49, L.56, T.79, A.82, A.83, W.86 Chain B: Q.122, A.123, E.124, H.125, T.128, M.132 Ligands: SO4.3 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.49, A:A.82, A:W.86, B:T.128 Hydrogen bonds: B:E.124, B:H.125, B:T.128 Salt bridges: B:H.125 GZ9.8: 13 residues within 4Å: Chain A: Q.122, A.123, E.124, H.125, T.128, M.132 Chain B: Q.49, L.56, T.79, A.82, A.83, W.86 Ligands: SO4.7 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.49, B:A.82, B:W.86, A:T.128 Hydrogen bonds: A:E.124, A:H.125 Salt bridges: A:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugiyama, S. et al., Discovery of novel HIV-1 integrase-LEDGF/p75 allosteric inhibitors based on a pyridine scaffold forming an intramolecular hydrogen bond. Bioorg.Med.Chem.Lett. (2020)

Release Date

2021-01-13

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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