SMTL ID : 4mk1.2 (1 other biounit)

5-bromopyridine-2,3-diol bound to influenza 2009 pH1N1 endonuclease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 8 residues within 4Å: Chain A: H.78, D.145, E.156, I.157, G.158, K.171 Ligands: MN.2, 27Y.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:D.145, A:E.156, A:I.157 MN.2: 5 residues within 4Å: Chain A: H.78, E.117, D.145 Ligands: MN.1, 27Y.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.117, A:D.145, H2O.2, H2O.4, H2O.6 MN.3: 5 residues within 4Å: Chain A: Y.61, E.117, G.118 Ligands: 27Y.8, 27Y.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.117, H2O.1 MN.4: 6 residues within 4Å: Chain A: F.90, H.111 Chain B: F.90, P.105, H.111 Ligands: MN.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.111 MN.10: 8 residues within 4Å: Chain B: H.78, D.145, E.156, I.157, G.158, K.171 Ligands: MN.11, 27Y.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.78, B:D.145, B:E.156, B:I.157 MN.11: 5 residues within 4Å: Chain B: H.78, E.117, D.145 Ligands: MN.10, 27Y.16 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.117, B:D.145, H2O.7, H2O.9, H2O.11 MN.12: 5 residues within 4Å: Chain B: Y.61, E.117, G.118 Ligands: 27Y.17, 27Y.18 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.117, H2O.6 MN.13: 6 residues within 4Å: Chain A: F.90, P.105, H.111 Chain B: F.90, H.111 Ligands: MN.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.111

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

SO4.5: 4 residues within 4Å: Chain A: I.67, E.68, T.69, N.70 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.69, A:T.69, A:N.70, A:N.70 Water bridges: A:E.68, A:E.68 SO4.14: 4 residues within 4Å: Chain B: I.67, E.68, T.69, N.70 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.69, B:T.69, B:N.70, B:N.70 Water bridges: B:E.68, B:E.68

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

EDO.6: 6 residues within 4Å: Chain A: N.70, K.71, A.74, R.161, S.231, E.232 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.161, A:R.161, A:S.231, A:S.231 EDO.15: 6 residues within 4Å: Chain B: N.70, K.71, A.74, R.161, S.231, E.232 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.161, B:R.161, B:S.231, B:S.231

6 x 27Y: 5-bromo-3-hydroxypyridin-2(1H)-one(Non-covalent)

27Y.7: 12 residues within 4Å: Chain A: K.71, I.75, H.78, E.117, D.145, E.156, I.157, G.158, K.171 Ligands: MN.1, MN.2, 27Y.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.117, A:K.171 pi-Stacking: A:H.78 27Y.8: 10 residues within 4Å: Chain A: A.57, M.58, Y.61, E.63, K.71, I.75, E.117 Ligands: MN.3, 27Y.7, 27Y.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.57, A:Y.61 Water bridges: A:Y.61 Halogen bonds: A:E.63 27Y.9: 10 residues within 4Å: Chain A: K.56, A.57, E.60, Y.61, E.117, G.118, R.119, D.120 Ligands: MN.3, 27Y.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.118, A:G.118 Water bridges: A:R.119 27Y.16: 12 residues within 4Å: Chain B: K.71, I.75, H.78, E.117, D.145, E.156, I.157, G.158, K.171 Ligands: MN.10, MN.11, 27Y.17 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.117, B:E.156, B:K.171 Water bridges: B:I.157, B:Y.167 pi-Stacking: B:H.78 27Y.17: 10 residues within 4Å: Chain B: A.57, M.58, Y.61, E.63, K.71, I.75, E.117 Ligands: MN.12, 27Y.16, 27Y.18 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.57, B:Y.61 Water bridges: B:Y.61 Halogen bonds: B:E.63 27Y.18: 10 residues within 4Å: Chain B: K.56, A.57, E.60, Y.61, E.117, G.118, R.119, D.120 Ligands: MN.12, 27Y.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.61, B:E.117, B:G.118, B:G.118 Water bridges: B:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauman, J.D. et al., Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors. Acs Chem.Biol. (2013)

Release Date

2013-09-25

Peptides

POLYMERASE PA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

POLYMERASE PA

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