SMTL ID : 6t38.1

Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x MBK: ~{N}-[6-(4-azanylbutylamino)-1-[(4-bromophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide(Non-covalent)

MBK.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 D: R.229 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.55, A:L.55, A:A.261, A:I.266 Hydrogen bonds: A:G.125, A:A.261, D:R.229 Water bridges: A:C.262, A:E.265 pi-Cation interactions: D:R.229 MBK.8: 16 residues within 4Å: Chain B: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 Chain C: R.229 Ligands: CL.10 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.55, B:L.55, B:F.128, B:A.261, B:I.266 Hydrogen bonds: B:G.125, B:E.130, B:A.261, C:R.229 Water bridges: B:F.128, C:R.229, C:R.229 pi-Cation interactions: C:R.229 MBK.13: 16 residues within 4Å: Chain B: R.229 Chain C: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 Ligands: CL.12 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:R.229, B:R.229, C:G.125, C:A.261 Water bridges: B:R.229, B:R.229, C:H.129, C:Y.303 pi-Cation interactions: B:R.229 Hydrophobic interactions: C:L.55, C:L.55, C:V.260, C:A.261, C:R.269 MBK.17: 17 residues within 4Å: Chain A: R.229 Chain D: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, E.130, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 Ligands: CL.6 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain D Hydrogen bonds: A:R.229, D:G.125, D:K.259, D:A.261 pi-Cation interactions: A:R.229 Hydrophobic interactions: D:L.55, D:L.55, D:A.261, D:I.266 Water bridges: D:C.262

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

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

1 x BR: BROMIDE ION(Non-covalent)

BR.3: 3 residues within 4Å: Chain A: V.182, T.210, N.213 Ligand excluded by PLIP

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

CL.4: 5 residues within 4Å: Chain A: L.18, G.20, K.35, G.119, D.120 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: H.126 Chain D: G.228, R.229, G.230 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: G.228, R.229, G.230 Chain D: H.126 Ligands: MBK.17 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.269, E.300, T.301, V.302 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: H.126 Chain C: G.228, R.229, G.230 Ligands: MBK.8 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: V.182, T.210, N.213 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: G.228, R.229, G.230 Chain C: H.126 Ligands: MBK.13 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: V.182, T.210, N.213 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: K.259, G.289, Y.290 Chain D: H.239 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: T.238, H.239 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain D: G.21, G.23 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: R.255 Chain D: V.149, D.151, R.154 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: V.182, T.210, N.213 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain D: L.18, G.20, K.35, Q.36, G.119, D.120 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
C

D
D

Glucose-1-phosphate thymidylyltransferase

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