SMTL ID : 7u2u.1

CRYSTAL STRUCTURE OF HIV-1 INTEGRASE COMPLEXED WITH Compound-2a AKA (2S)-2-(TERT-BUTOXY)-2-[7-(4,4-DIMETHYLPIPE RIDIN-1-YL)-8-{4-[2-(4-FLUOROPHENYL)ETHOXY]PHENYL}-2,5-DIM ETHYLIMIDAZO[1,2-A]PYRIDIN-6-YL]ACETIC ACID

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x KZD: (2S)-tert-butoxy[(4S)-7-(4,4-dimethylpiperidin-1-yl)-8-{4-[2-(4-fluorophenyl)ethoxy]phenyl}-2,5-dimethylimidazo[1,2-a]pyridin-6-yl]acetic acid(Non-covalent)

KZD.1: 14 residues within 4Å: Chain A: Q.66, 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 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:E.141, B:H.142, B:T.145, B:T.145 Salt bridges: B:H.142 Hydrophobic interactions: A:Q.66, A:T.95, A:T.96, A:A.99, A:W.102, A:W.103 KZD.5: 14 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, T.145, M.149 Chain B: Q.66, T.95, T.96, K.98, A.99, A.100, W.102, W.103 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.66, B:T.95, B:T.96, B:A.99, B:W.102, B:W.103 Hydrogen bonds: A:E.141, A:H.142, A:T.145 Salt bridges: A:H.142

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

SO4.2: 3 residues within 4Å: Chain A: T.37, H.38, K.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.37, A:H.38 Salt bridges: A:H.38, A:K.130 SO4.3: 4 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.94, A:T.95, A:T.96, A:T.96 Water bridges: A:G.65, A:G.65, A:Q.66 SO4.4: 4 residues within 4Å: Chain A: K.42, E.141, H.142, L.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.144 Salt bridges: A:H.142 SO4.6: 3 residues within 4Å: Chain B: T.37, H.38, K.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.37, B:T.37, B:H.38 Salt bridges: B:H.38, B:K.130 SO4.7: 4 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.94, B:T.95, B:T.96, B:T.96 Water bridges: B:G.65, B:G.65, B:Q.66, B:T.95 SO4.8: 4 residues within 4Å: Chain B: K.42, E.141, H.142, L.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.137, B:L.143 Water bridges: B:K.144 Salt bridges: B:H.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parcella, K. et al., Scaffold modifications to the 4-(4,4-dimethylpiperidinyl) 2,6-dimethylpyridinyl class of HIV-1 allosteric integrase inhibitors. Bioorg.Med.Chem. (2022)

Release Date

2022-06-08

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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