SMTL ID : 4ahr.1

Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: C.36, T.37, H.38, K.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.37, A:H.38, A:N.126 Salt bridges: A:H.38, A:K.130 SO4.2: 4 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.65, A:T.95, A:T.96, A:T.96 Water bridges: A:Q.66, A:T.95 SO4.3: 5 residues within 4Å: Chain A: K.42, R.137, E.141, H.142, L.143 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.144, A:K.144 Salt bridges: A:K.42, A:H.142 SO4.4: 4 residues within 4Å: Chain A: Y.70, K.74 Chain B: E.58, K.74 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Water bridges: B:E.58, B:V.59, B:K.74, B:K.74, B:K.74, B:Q.148, A:E.58 Salt bridges: B:K.74, B:K.144, A:K.74 Hydrogen bonds: A:Y.70, A:Y.70 SO4.9: 3 residues within 4Å: Chain B: T.37, H.38, K.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.38, B:N.126 Salt bridges: B:H.38, B:K.130 SO4.10: 5 residues within 4Å: Chain B: G.65, Q.66, S.94, T.95, T.96 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.65, B:T.95, B:T.96, B:T.96 Water bridges: B:Q.66 SO4.11: 5 residues within 4Å: Chain B: K.42, R.137, E.141, H.142, L.143 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.137, B:L.143 Water bridges: B:K.144 Salt bridges: B:K.42, B:H.142 SO4.12: 4 residues within 4Å: Chain B: H.38, V.43, A.62, E.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.63 Salt bridges: B:H.38

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

ACY.5: 8 residues within 4Å: Chain A: E.56, A.57, E.58, F.71, K.74, L.75 Chain B: R.78 Ligands: ACY.13 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:R.78, A:K.74 Hydrophobic interactions: A:F.71, A:K.74 Hydrogen bonds: A:A.57, A:E.58 ACY.6: 5 residues within 4Å: Chain A: A.140, E.141, H.142, T.145 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.141, A:H.142, A:T.145 Salt bridges: A:H.142 ACY.13: 8 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75 Ligands: ACY.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.71, B:K.74 Hydrogen bonds: B:E.56, B:A.57 Salt bridges: B:K.74, A:R.78

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: A.69, Y.70, L.73, A.100 Chain B: T.145, M.149 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.145, B:T.145, A:A.69 GOL.14: 7 residues within 4Å: Chain A: T.145, M.149 Chain B: A.69, Y.70, L.73, A.100 Ligands: ACY.6 No protein-ligand interaction detected (PLIP)

2 x I2E: 3-(1,3-benzodioxol-5-yl)propanoic acid(Non-covalent)

I2E.8: 13 residues within 4Å: Chain A: A.76, G.77, R.78, W.79, P.80, I.175, I.179 Chain B: Y.54, N.155, H.156, G.168, E.169, V.172 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.80, A:I.175, A:I.179, B:E.169, B:V.172 Salt bridges: A:K.82 I2E.15: 12 residues within 4Å: Chain A: Y.54, N.155, H.156, G.168, E.169, V.172 Chain B: G.77, R.78, W.79, P.80, I.175, I.179 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.80, B:I.175, B:I.179, A:E.169, A:V.172 Hydrogen bonds: A:E.169 Water bridges: A:S.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wielens, J. et al., Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification?. J.Biomol.Screen (2013)

Release Date

2012-12-19

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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