SMTL ID : 4knr.1

Hin GlmU bound to WG188

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x 1S8: N-{4-[(2-benzyl-7-hydroxy-6-methoxyquinazolin-4-yl)amino]phenyl}benzamide(Non-covalent)

1S8.1: 16 residues within 4Å: Chain A: L.11, A.12, A.13, G.14, V.26, T.82, Y.103, D.105, V.131, Y.139, N.169, T.170, G.171, V.223, E.224, G.225 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.11, A:T.82, A:Y.103, A:Y.103, A:V.131, A:V.223 Hydrogen bonds: A:A.13, A:G.14, A:D.105, A:V.223 Water bridges: A:Q.76, A:Q.79 pi-Stacking: A:Y.139 1S8.11: 16 residues within 4Å: Chain B: L.11, A.12, A.13, G.14, V.26, T.82, Y.103, D.105, V.131, Y.139, N.169, T.170, G.171, V.223, E.224, G.225 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.11, B:T.82, B:Y.103, B:Y.103, B:V.131, B:V.223 Hydrogen bonds: B:A.13, B:G.14, B:D.105, B:V.223 Water bridges: B:Q.76, B:Q.79 pi-Stacking: B:Y.139 1S8.21: 16 residues within 4Å: Chain C: L.11, A.12, A.13, G.14, V.26, T.82, Y.103, D.105, V.131, Y.139, N.169, T.170, G.171, V.223, E.224, G.225 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.11, C:T.82, C:Y.103, C:Y.103, C:V.131, C:V.223 Hydrogen bonds: C:A.13, C:G.14, C:D.105, C:V.223 Water bridges: C:Q.76, C:Q.79 pi-Stacking: C:Y.139

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

PG4.2: 9 residues within 4Å: Chain A: F.402, T.420, G.422, A.423, I.438 Chain C: N.386, Y.387, D.388, V.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.423 Water bridges: 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 No protein-ligand interaction detected (PLIP) PG4.12: 9 residues within 4Å: Chain A: N.386, Y.387, D.388, V.410 Chain B: F.402, T.420, G.422, A.423, I.438 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.423 Water bridges: B:T.439, B:T.439 PG4.13: 6 residues within 4Å: Chain B: N.189, N.190, N.191, A.192, Q.193, G.194 No protein-ligand interaction detected (PLIP) PG4.22: 9 residues within 4Å: Chain B: N.386, Y.387, D.388, V.410 Chain C: F.402, T.420, G.422, A.423, I.438 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.423 Water bridges: C:T.439, C:T.439 PG4.23: 6 residues within 4Å: Chain C: N.189, N.190, N.191, A.192, Q.193, G.194 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406 Chain C: D.406, Q.408 Ligands: MG.14, MG.24 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.17, H2O.34 MG.5: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.15, MG.25 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.16, H2O.32, H2O.49 MG.14: 7 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406 Ligands: MG.4, MG.24 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.17, H2O.34 MG.15: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.5, MG.25 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.16, H2O.32, H2O.49 MG.24: 7 residues within 4Å: Chain A: D.406 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.4, MG.14 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:D.406, A:D.406, C:D.406, H2O.1, H2O.17, H2O.34 MG.25: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.5, MG.15 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.16, H2O.32, H2O.49

15 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.15, A:G.16, A:T.17, A:T.17 Water bridges: A:R.18, A:K.25 Salt bridges: A:K.25 SO4.7: 3 residues within 4Å: Chain A: R.331, R.333, P.334 7 PLIP interactions: 7 interactions with chain A Water bridges: A:E.316, A:R.331, A:R.331, A:R.331, A:R.333, A:P.334 Salt bridges: A:R.333 SO4.8: 3 residues within 4Å: Chain B: K.360, N.362, H.363 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.362 Water bridges: B:N.377, A:K.392 Salt bridges: B:K.360, B:H.363 SO4.9: 3 residues within 4Å: Chain A: K.15, H.57, G.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.58 Salt bridges: A:K.15, A:H.57 SO4.10: 3 residues within 4Å: Chain A: R.18, N.227, Q.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.227, A:Q.231 Water bridges: A:Q.231 Salt bridges: A:R.18 SO4.16: 5 residues within 4Å: Chain B: G.14, K.15, G.16, T.17, K.25 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.15, B:G.16, B:T.17, B:T.17 Water bridges: B:R.18, B:K.25 Salt bridges: B:K.25 SO4.17: 3 residues within 4Å: Chain B: R.331, R.333, P.334 7 PLIP interactions: 7 interactions with chain B Water bridges: B:E.316, B:R.331, B:R.331, B:R.331, B:R.333, B:P.334 Salt bridges: B:R.333 SO4.18: 3 residues within 4Å: Chain C: K.360, N.362, H.363 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.362 Water bridges: C:N.377, B:K.392 Salt bridges: C:K.360, C:H.363 SO4.19: 3 residues within 4Å: Chain B: K.15, H.57, G.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.58 Salt bridges: B:K.15, B:H.57 SO4.20: 3 residues within 4Å: Chain B: R.18, N.227, Q.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.227, B:Q.231 Water bridges: B:Q.231 Salt bridges: B:R.18 SO4.26: 5 residues within 4Å: Chain C: G.14, K.15, G.16, T.17, K.25 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.15, C:G.16, C:T.17, C:T.17 Water bridges: C:R.18, C:K.25 Salt bridges: C:K.25 SO4.27: 3 residues within 4Å: Chain C: R.331, R.333, P.334 7 PLIP interactions: 7 interactions with chain C Water bridges: C:E.316, C:R.331, C:R.331, C:R.331, C:R.333, C:P.334 Salt bridges: C:R.333 SO4.28: 3 residues within 4Å: Chain A: K.360, N.362, H.363 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.362 Water bridges: A:N.377, C:K.392 Salt bridges: A:K.360, A:H.363 SO4.29: 3 residues within 4Å: Chain C: K.15, H.57, G.58 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.58 Salt bridges: C:K.15, C:H.57 SO4.30: 3 residues within 4Å: Chain C: R.18, N.227, Q.231 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.227, C:Q.231 Water bridges: C:Q.231 Salt bridges: C:R.18

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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