SMTL ID : 4ah9.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 0MB: 1-(3-PHENYL-1,2,4-THIADIAZOL-5-YL)-1,4-DIAZEPANE(Non-covalent)

0MB.1: 13 residues within 4Å: Chain A: G.77, R.78, W.79, P.80, I.175, I.179 Chain B: Y.54, N.155, H.156, R.158, G.168, E.169 Ligands: EDO.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.54, A:P.80 0MB.18: 13 residues within 4Å: Chain A: Y.54, H.156, R.158, G.168, E.169 Chain B: G.77, R.78, W.79, P.80, I.175, I.179 Ligands: EDO.24, EDO.25 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.54, B:P.80 Water bridges: A:S.166 pi-Stacking: A:H.156

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

SO4.2: 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:T.37, A:H.38, A:N.126 Salt bridges: A:K.130 SO4.3: 5 residues within 4Å: Chain A: H.38, V.43, A.62, E.63 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.63 Salt bridges: A:H.38 SO4.4: 5 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, T.145 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.141, A:H.142, A:T.145, A:T.145 Water bridges: A:H.142 Salt bridges: A:H.142 SO4.5: 8 residues within 4Å: Chain A: E.56, A.57, E.58, F.71, K.74, L.75, R.78 Chain B: R.78 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.57, A:E.58, A:E.58, A:F.71 Salt bridges: A:K.74, B:R.78 SO4.6: 3 residues within 4Å: Chain A: K.42, 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 SO4.19: 4 residues within 4Å: Chain B: T.37, H.38, N.126, K.130 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.38, B:N.126 Water bridges: B:T.37, B:T.37, B:K.130, B:K.130 Salt bridges: B:H.38, B:K.130 SO4.20: 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 SO4.21: 5 residues within 4Å: Chain B: Q.139, A.140, E.141, H.142, T.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.141, B:H.142, B:T.145 Salt bridges: B:H.142 SO4.22: 3 residues within 4Å: Chain B: K.42, H.142, L.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.143 Water bridges: B:K.144 Salt bridges: B:K.42, B:H.142 SO4.23: 8 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75, R.78 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.56, B:A.57, B:E.58, B:F.71 Salt bridges: B:K.74, A:R.78

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

EDO.7: 6 residues within 4Å: Chain A: P.29, G.30, P.80, I.175, D.178 Ligands: 0MB.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.80, A:I.175, A:D.178 EDO.8: 4 residues within 4Å: Chain A: A.99, A.100, W.103 Chain B: M.149 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: Y.70, K.74 Chain B: E.58, K.144 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.144, A:Y.70, A:K.74, A:K.74 Water bridges: B:E.58, B:E.58, B:V.59, B:Q.148 EDO.10: 4 residues within 4Å: Chain A: E.63, T.64 Ligands: SO4.3, CL.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.63 EDO.11: 4 residues within 4Å: Chain A: G.53, V.121, M.125, H.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.154 EDO.12: 4 residues within 4Å: Chain A: D.35, C.36, D.87, I.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.36, A:C.36 EDO.24: 7 residues within 4Å: Chain B: P.29, G.30, P.80, I.175, D.178 Ligands: 0MB.18, EDO.25 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.30, B:G.30 EDO.25: 3 residues within 4Å: Chain B: K.82 Ligands: 0MB.18, EDO.24 No protein-ligand interaction detected (PLIP) EDO.26: 3 residues within 4Å: Chain A: M.149 Chain B: A.99, A.100 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.100, B:W.103

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

CL.13: 4 residues within 4Å: Chain A: T.64, G.65 Ligands: EDO.10, TAM.17 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Ligands: TAM.17 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: K.144 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 6 residues within 4Å: Chain A: E.40, I.133, R.137, H.142, L.143, A.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.133, A:E.141 GOL.28: 6 residues within 4Å: Chain B: E.40, I.133, R.137, H.142, L.143, A.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.133, B:E.141

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

TAM.17: 9 residues within 4Å: Chain A: T.64, G.65, Q.66, S.90, S.94, T.95, T.96 Ligands: CL.13, CL.14 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.64, A:G.65, A:Q.66, A:Q.66, A:S.94, A:T.95, A:T.95, A:T.96, A:T.96 TAM.29: 6 residues within 4Å: Chain B: T.64, G.65, Q.66, S.94, T.95, T.96 8 PLIP interactions: 8 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 Water bridges: B:T.95

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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