SMTL ID : 4kpz.1

Hin GlmU bound to a small molecule fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-trimer

Ligands

3 x 1SF: 1-(3-nitrophenyl)dihydropyrimidine-2,4(1H,3H)-dione(Non-covalent)

1SF.1: 14 residues within 4Å: Chain A: L.11, A.12, A.13, G.14, V.26, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, G.104, D.105 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.11, A:T.82, A:Y.103 Hydrogen bonds: A:A.12, A:A.13, A:Q.76, A:Q.76, A:G.81 1SF.12: 14 residues within 4Å: Chain B: L.11, A.12, A.13, G.14, V.26, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, G.104, D.105 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.11, B:T.82, B:Y.103 Hydrogen bonds: B:A.12, B:A.13, B:Q.76, B:Q.76, B:G.81 1SF.23: 14 residues within 4Å: Chain C: L.11, A.12, A.13, G.14, V.26, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, G.104, D.105 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.11, C:T.82, C:Y.103 Hydrogen bonds: C:A.12, C:A.13, C:Q.76, C:Q.76, C:G.81

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

SO4.2: 3 residues within 4Å: Chain A: K.4, K.121, E.123 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: G.14, K.15, G.16, T.17, K.25 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.331, R.333, P.334 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: R.333, K.351, Y.366, K.392 Chain C: H.363 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: H.57, G.58 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: N.227, Q.231 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: K.4, K.121, E.123 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: G.14, K.15, G.16, T.17, K.25 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: R.331, R.333, P.334 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: H.363 Chain B: R.333, K.351, Y.366, K.392 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: H.57, G.58 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: N.227, Q.231 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: K.4, K.121, E.123 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain C: G.14, K.15, G.16, T.17, K.25 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: R.331, R.333, P.334 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: H.363 Chain C: R.333, K.351, Y.366, K.392 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain C: H.57, G.58 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain C: N.227, Q.231 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.19, MG.30 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.36, H2O.55 MG.9: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.20, MG.31 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.20, H2O.40 MG.19: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.8, MG.30 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.36, H2O.55 MG.20: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.9, MG.31 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.20, H2O.40 MG.30: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.8, MG.19 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.36, H2O.55 MG.31: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.9, MG.20 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.20, H2O.40

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

PG4.10: 8 residues within 4Å: Chain A: F.402, T.420, G.422, A.423 Chain B: N.386, Y.387, D.388, V.410 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.423, B:D.388 Water bridges: A:T.439, A:T.439, A:T.439 PG4.11: 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 PG4.21: 8 residues within 4Å: Chain B: 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 B, 1 interactions with chain C Hydrogen bonds: B:A.423, C:D.388 Water bridges: B:T.439, B:T.439, B:T.439 PG4.22: 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 PG4.32: 8 residues within 4Å: Chain A: 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 A Hydrogen bonds: C:A.423, A:D.388 Water bridges: C:T.439, C:T.439, C:T.439 PG4.33: 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

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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