SMTL ID : 4o55.1

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

2 x LF9: (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid(Non-covalent)

LF9.1: 11 residues within 4Å: Chain A: Q.46, T.75, T.76, A.79, A.80 Chain B: Q.119, A.120, E.121, H.122, T.125, M.129 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.125, A:Q.46, A:T.76, A:A.79 Hydrogen bonds: B:E.121, B:H.122, B:H.122, B:T.125, A:T.76 Salt bridges: B:H.122 LF9.5: 11 residues within 4Å: Chain A: Q.119, A.120, E.121, H.122, T.125, M.129 Chain B: Q.46, T.75, T.76, A.79, A.80 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.125, B:Q.46, B:T.76, B:A.79 Hydrogen bonds: A:E.121, A:H.122, A:T.125, A:T.125, B:T.76 Salt bridges: A:H.122

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

SO4.2: 5 residues within 4Å: Chain A: G.45, Q.46, S.74, T.75, T.76 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.45, A:Q.46, A:S.74, A:T.75, A:T.76, A:T.76, A:T.76 SO4.3: 5 residues within 4Å: Chain A: K.22, R.117, E.121, H.122, L.123 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.117, A:L.123 Water bridges: A:K.22, A:K.22, A:E.121, A:E.121 Salt bridges: A:K.22, A:H.122 SO4.4: 3 residues within 4Å: Chain A: T.17, H.18, K.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.18 Salt bridges: A:H.18, A:K.110 SO4.6: 5 residues within 4Å: Chain B: G.45, Q.46, S.74, T.75, T.76 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.45, B:Q.46, B:S.74, B:T.75, B:T.75, B:T.76, B:T.76, B:T.76 SO4.7: 5 residues within 4Å: Chain B: K.22, R.117, E.121, H.122, L.123 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.20, B:R.117, B:L.123 Water bridges: B:K.22, B:K.22, B:E.121 Salt bridges: B:K.22, B:H.122 SO4.8: 3 residues within 4Å: Chain B: T.17, H.18, K.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.18 Salt bridges: B:H.18, B:K.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, A. et al., A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase. Plos Pathog. (2014)

Release Date

2014-07-02

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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