SMTL ID : 4knx.1

Hin GlmU Bound to WG176

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x 1S9: [(4-{[4-(benzoylamino)phenyl]amino}-6-methoxyquinazolin-7-yl)oxy]acetic acid(Non-covalent)

1S9.1: 18 residues within 4Å: Chain A: L.11, A.12, A.13, G.14, V.26, Q.76, Q.79, T.82, A.85, Y.103, D.105, V.131, Y.139, N.169, T.170, V.223, E.224, G.225 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.103, A:Y.103, A:V.131, A:Y.139, A:V.223 Hydrogen bonds: A:A.13, A:G.14, A:Q.76, A:Q.79, A:D.105, A:V.223 Water bridges: A:K.25, A:G.81 1S9.10: 18 residues within 4Å: Chain B: L.11, A.12, A.13, G.14, V.26, Q.76, Q.79, T.82, A.85, Y.103, D.105, V.131, Y.139, N.169, T.170, V.223, E.224, G.225 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.103, B:Y.103, B:V.131, B:Y.139, B:V.223 Hydrogen bonds: B:A.13, B:G.14, B:Q.76, B:Q.79, B:D.105, B:V.223 Water bridges: B:K.25, B:G.81 1S9.19: 18 residues within 4Å: Chain C: L.11, A.12, A.13, G.14, V.26, Q.76, Q.79, T.82, A.85, Y.103, D.105, V.131, Y.139, N.169, T.170, V.223, E.224, G.225 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.103, C:Y.103, C:V.131, C:Y.139, C:V.223 Hydrogen bonds: C:A.13, C:G.14, C:Q.76, C:Q.79, C:D.105, C:V.223 Water bridges: C:K.25, C:G.81

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 8 residues within 4Å: Chain A: F.402, T.420, G.422, A.423 Chain C: N.386, Y.387, D.388, V.410 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.423, C:D.388 Water bridges: A:T.439, A:T.439, A:T.439 PG4.3: 6 residues within 4Å: Chain A: N.189, N.190, N.191, A.192, Q.193, G.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.189 PG4.11: 8 residues within 4Å: Chain A: N.386, Y.387, D.388, V.410 Chain B: F.402, T.420, G.422, A.423 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.423, A:D.388 Water bridges: B:T.439, B:T.439, B:T.439 PG4.12: 6 residues within 4Å: Chain B: N.189, N.190, N.191, A.192, Q.193, G.194 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.189 PG4.20: 8 residues within 4Å: Chain B: N.386, Y.387, D.388, V.410 Chain C: F.402, T.420, G.422, A.423 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.423, B:D.388 Water bridges: C:T.439, C:T.439, C:T.439 PG4.21: 6 residues within 4Å: Chain C: N.189, N.190, N.191, A.192, Q.193, G.194 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.189

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.13, MG.22 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.406, C:D.406, B:D.406, H2O.1, H2O.24, H2O.46 MG.5: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.14, MG.23 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.406, C:D.406, B:D.406, H2O.2, H2O.24, H2O.47 MG.13: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.4, MG.22 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.406, C:D.406, B:D.406, H2O.1, H2O.24, H2O.46 MG.14: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.5, MG.23 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.406, C:D.406, B:D.406, H2O.2, H2O.24, H2O.47 MG.22: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.4, MG.13 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.406, B:D.406, C:D.406, H2O.1, H2O.24, H2O.46 MG.23: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.5, MG.14 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.406, B:D.406, C:D.406, H2O.2, H2O.24, H2O.47

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

SO4.6: 5 residues within 4Å: Chain A: G.14, K.15, G.16, T.17, K.25 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.15, A:G.16, A:T.17 Water bridges: A:R.18, A:K.25, A:K.25, A:Q.79 Salt bridges: A:K.25 SO4.7: 3 residues within 4Å: Chain A: R.331, R.333, P.334 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.331 Water bridges: A:E.316, A:D.317, A:R.331, A:P.334, B:K.310, B:K.310 Salt bridges: A:R.333, B:K.310 SO4.8: 3 residues within 4Å: Chain B: K.360, N.362, H.363 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.362 Water bridges: B:N.377, B:N.377, B:N.377 Salt bridges: B:K.360, B:H.363, A:K.392 SO4.9: 3 residues within 4Å: Chain A: K.15, H.57, G.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.58 Water bridges: A:H.57, A:G.59 Salt bridges: A:H.57 SO4.15: 5 residues within 4Å: Chain B: G.14, K.15, G.16, T.17, K.25 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.15, B:G.16, B:T.17 Water bridges: B:R.18, B:K.25, B:K.25, B:Q.79 Salt bridges: B:K.25 SO4.16: 3 residues within 4Å: Chain B: R.331, R.333, P.334 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.331 Water bridges: B:E.316, B:D.317, B:R.331, B:P.334, C:K.310, C:K.310 Salt bridges: B:R.333, C:K.310 SO4.17: 3 residues within 4Å: Chain C: K.360, N.362, H.363 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.362 Water bridges: C:N.377, C:N.377, C:N.377 Salt bridges: C:K.360, C:H.363, B:K.392 SO4.18: 3 residues within 4Å: Chain B: K.15, H.57, G.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.58 Water bridges: B:H.57, B:G.59 Salt bridges: B:H.57 SO4.24: 5 residues within 4Å: Chain C: G.14, K.15, G.16, T.17, K.25 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:K.15, C:G.16, C:T.17 Water bridges: C:R.18, C:K.25, C:K.25, C:Q.79 Salt bridges: C:K.25 SO4.25: 3 residues within 4Å: Chain C: R.331, R.333, P.334 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.331 Water bridges: C:E.316, C:D.317, C:R.331, C:P.334, A:K.310, A:K.310 Salt bridges: C:R.333, A:K.310 SO4.26: 3 residues within 4Å: Chain A: K.360, N.362, H.363 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain A Salt bridges: C:K.392, A:K.360, A:H.363 Hydrogen bonds: A:N.362 Water bridges: A:N.377, A:N.377, A:N.377 SO4.27: 3 residues within 4Å: Chain C: K.15, H.57, G.58 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.58 Water bridges: C:H.57, C:G.59 Salt bridges: C:H.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doig, P. et al., Rational design of inhibitors of the bacterial cell wall synthetic enzyme GlmU using virtual screening and lead-hopping. Bioorg.Med.Chem. (2014)

Release Date

2014-10-15

Peptides

Bifunctional protein GlmU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bifunctional protein GlmU

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