SMTL ID : 4ahv.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: 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: 5 residues within 4Å: Chain A: E.40, K.42, E.141, H.142, L.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.143 Water bridges: A:K.144 Salt bridges: A:K.42, A:H.142 SO4.3: 8 residues within 4Å: Chain A: E.56, A.57, E.58, F.71, K.74, L.75, R.78 Chain B: R.78 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.57, A:A.57, A:E.58 Salt bridges: A:K.74, B:R.78 SO4.11: 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 SO4.12: 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 SO4.13: 7 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:R.78, B:K.74 Hydrogen bonds: B:E.56, B:A.57, B:E.58, B:F.71

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

ACY.4: 4 residues within 4Å: Chain A: Y.70, K.74 Chain B: E.58 Ligands: ACY.5 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.70, B:E.58 Salt bridges: A:K.74, B:K.74, B:K.144 Water bridges: B:E.58 ACY.5: 4 residues within 4Å: Chain A: E.58 Chain B: Y.70, K.74 Ligands: ACY.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:V.59, A:Q.148 Salt bridges: A:K.74, A:K.144, B:K.74

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

EDO.6: 6 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, T.145 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.141, A:H.142, A:T.145 EDO.7: 5 residues within 4Å: Chain A: M.149 Chain B: L.73, A.100, W.103 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.99 Water bridges: B:A.100, B:A.100 EDO.8: 5 residues within 4Å: Chain A: S.28, I.31, T.83, K.107, E.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.28, A:T.83, A:K.107, A:E.109 EDO.14: 5 residues within 4Å: Chain B: Q.139, E.141, H.142, T.145 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.141, B:H.142 EDO.15: 5 residues within 4Å: Chain A: A.99, A.100 Chain B: T.145, M.149 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.99 Water bridges: A:A.100, A:A.100

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.9: 6 residues within 4Å: Chain A: T.64, G.65, Q.66, S.94, T.95, T.96 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.64, A:T.64, A:G.65, A:Q.66, A:T.95, A:T.95, A:T.95, A:T.96, A:T.96, A:T.96 TAM.16: 7 residues within 4Å: Chain B: T.64, G.65, Q.66, S.90, S.94, T.95, T.96 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.64, B:G.65, B:Q.66, B:T.95, B:T.95, B:T.96, B:T.96

2 x Z5P: 1-[2-(1H-pyrazol-1-yl)phenyl]methanamine(Non-covalent)

Z5P.10: 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: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.54, A:N.155, A:E.169, B:P.80, B:I.175, B:I.179 Hydrogen bonds: A:G.168 Z5P.17: 11 residues within 4Å: Chain A: G.77, R.78, W.79, P.80, I.179 Chain B: Y.54, N.155, H.156, G.168, E.169, V.172 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.54, B:N.155, B:E.169, A:P.80, A:I.179 Hydrogen bonds: B:G.168

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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