SMTL ID : 6t37.1 (1 other biounit)

Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-tetramer

Ligands

4 x M9Z: ~{N}-[6-[3-[4-(aminomethyl)-1,2,3-triazol-1-yl]propylamino]-2,4-bis(oxidanylidene)-1-(phenylmethyl)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide(Non-covalent)

M9Z.1: 16 residues within 4Å: Chain A: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 Chain C: R.229 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.55, A:L.55, A:A.261, A:I.266, A:R.269 Hydrogen bonds: A:G.125, A:K.259, A:A.261 Water bridges: A:H.129, A:C.262, A:Q.270, A:Q.270 pi-Stacking: A:H.129 pi-Cation interactions: C:R.229 M9Z.4: 16 residues within 4Å: Chain B: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 Chain D: R.229 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.55, B:L.55, B:F.128, B:I.266, B:R.269 Hydrogen bonds: B:G.125, B:A.261 Water bridges: B:K.259, B:Q.270, D:R.229 pi-Stacking: B:H.129 pi-Cation interactions: D:R.229 M9Z.7: 16 residues within 4Å: Chain A: R.229 Chain C: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.55, C:L.55, C:A.261, C:I.266, C:R.269 Hydrogen bonds: C:G.125, C:K.259, C:A.261 Water bridges: C:H.129, C:C.262, C:Q.270, C:Q.270 pi-Stacking: C:H.129 pi-Cation interactions: A:R.229 M9Z.10: 16 residues within 4Å: Chain B: R.229 Chain D: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.55, D:L.55, D:F.128, D:I.266, D:R.269 Hydrogen bonds: D:G.125, D:A.261 Water bridges: D:K.259, D:Q.270, B:R.229 pi-Stacking: D:H.129 pi-Cation interactions: B:R.229

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 9 residues within 4Å: Chain A: F.160, G.164, K.165, A.166, L.222, S.223, V.224, I.226 Chain C: Y.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.166, A:V.224 Salt bridges: A:K.165 MES.8: 9 residues within 4Å: Chain A: Y.303 Chain C: F.160, G.164, K.165, A.166, L.222, S.223, V.224, I.226 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.166, C:V.224 Salt bridges: C:K.165

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

CL.3: 4 residues within 4Å: Chain A: H.126 Chain C: G.228, R.229, G.230 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: H.126 Chain D: G.228, R.229, G.230 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: Q.292, Y.293, R.296 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: G.228, R.229, G.230 Chain C: H.126 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: G.228, R.229, G.230 Chain D: H.126 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain D: Q.292, Y.293, R.296 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, G. et al., Next generation Glucose-1-phosphate thymidylyltransferase (RmlA) inhibitors: An extended SAR study to direct future design. Bioorg.Med.Chem. (2021)

Release Date

2020-08-19

Peptides

Glucose-1-phosphate thymidylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glucose-1-phosphate thymidylyltransferase

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