SMTL ID : 3nf6.1

Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.37, H.38, N.126, K.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.38, A:N.126 Salt bridges: A:H.38, A:K.130 SO4.2: 4 residues within 4Å: Chain A: K.42, R.137, H.142, L.143 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.144 Salt bridges: A:K.42, A:H.142 SO4.8: 4 residues within 4Å: Chain B: T.37, H.38, N.126, K.130 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.37, B:T.37, B:H.38, B:N.126 Salt bridges: B:H.38, B:K.130 SO4.9: 5 residues within 4Å: Chain B: K.42, R.137, E.141, H.142, L.143 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.137, B:E.141, B:L.143 Water bridges: B:K.42, B:K.42, B:K.144 Salt bridges: B:K.42, B:H.142

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

EDO.3: 8 residues within 4Å: Chain A: Y.54, N.155, H.156, G.168 Chain B: G.77, R.78, W.79, P.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.77 EDO.10: 10 residues within 4Å: Chain A: A.76, G.77, R.78, W.79, P.80 Chain B: Y.54, N.155, H.156, G.168 Ligands: EDO.12 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.77, B:N.155 Water bridges: B:N.155 EDO.11: 3 residues within 4Å: Chain B: E.63, T.64, G.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.65 Water bridges: B:T.64, B:Q.66 EDO.12: 8 residues within 4Å: Chain A: R.78, W.79, P.80 Chain B: W.79, G.168, E.169, V.172 Ligands: EDO.10 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: S.94, T.96 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: S.94, T.96 Ligand excluded by PLIP

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 5 residues within 4Å: Chain A: E.56, F.71, K.74, L.75, R.78 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Salt bridges: B:R.78, A:K.74 Hydrophobic interactions: A:F.71, A:K.74, A:L.75 Hydrogen bonds: A:E.56, A:R.78 ACY.14: 7 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, F.71, K.74, L.75, R.78 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.71, B:K.74, B:L.75 Hydrogen bonds: B:A.57 Salt bridges: B:K.74, A:R.78

4 x IMV: 5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid(Non-covalent)

IMV.6: 13 residues within 4Å: Chain A: A.140, E.141, H.142, K.144, T.145, M.149 Chain B: Q.66, Y.70, L.73, T.96, A.99, A.100, W.103 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.66, B:L.73, B:A.99, B:W.103, A:T.145 Hydrogen bonds: A:E.141, A:H.142, A:T.145 Salt bridges: A:H.142 IMV.7: 9 residues within 4Å: Chain A: V.48, V.50, G.53, I.55, V.121, M.125, E.128, L.129, H.154 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.48, A:V.50, A:I.55, A:V.121, A:M.125 Hydrogen bonds: A:V.121, A:H.154 Water bridges: A:R.170 IMV.15: 13 residues within 4Å: Chain A: Q.66, Y.70, L.73, T.96, A.99, A.100, W.103 Chain B: A.140, E.141, H.142, K.144, T.145, M.149 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.66, A:L.73, A:A.99, A:W.103, B:T.145 Hydrogen bonds: B:E.141, B:H.142, B:H.142 Salt bridges: B:H.142 IMV.16: 10 residues within 4Å: Chain B: V.48, V.50, G.53, I.55, V.121, I.122, M.125, E.128, L.129, H.154 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.48, B:I.55, B:V.121, B:I.122, B:M.125 Water bridges: B:R.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rhodes, D.I. et al., Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design. ANTIVIR.CHEM.CHEMOTHER. (2011)

Release Date

2011-04-27

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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