SMTL ID : 6ny0.1

Crystal structure of trimethoprim-resistant type II dihydrofolate reductase in complex with a bisbenzimidazole inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x LBA: 2-(4-{3-[4-(6-carboxy-1H-benzimidazol-2-yl)phenoxy]-2-hydroxypropoxy}phenyl)-1H-benzimidazole-5-carboxylic acid(Non-covalent)

LBA.1: 7 residues within 4Å: Chain A: V.49, Q.50, I.51 Chain C: V.49, Q.50, I.51 Ligands: LBA.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:I.51, C:I.51 LBA.6: 7 residues within 4Å: Chain B: V.49, Q.50, I.51 Chain D: V.49, Q.50, I.51 Ligands: LBA.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:I.51, B:I.51 LBA.11: 7 residues within 4Å: Chain A: V.49, Q.50, I.51 Chain C: V.49, Q.50, I.51 Ligands: LBA.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:I.51, C:I.51 LBA.16: 7 residues within 4Å: Chain B: V.49, Q.50, I.51 Chain D: V.49, Q.50, I.51 Ligands: LBA.6 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:I.51, B:I.51

8 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 7 residues within 4Å: Chain A: A.5, F.7, G.8, M.9, I.25, W.28, Y.38 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.5, A:I.25, A:W.28, A:Y.38 Water bridges: A:M.9 MRD.3: 3 residues within 4Å: Chain A: R.59, I.60, N.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.60 Water bridges: A:R.59 MRD.7: 7 residues within 4Å: Chain B: A.5, F.7, G.8, M.9, I.25, W.28, Y.38 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.5, B:I.25, B:W.28, B:Y.38 Water bridges: B:M.9 MRD.8: 3 residues within 4Å: Chain B: R.59, I.60, N.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.60 Water bridges: B:R.59 MRD.12: 7 residues within 4Å: Chain C: A.5, F.7, G.8, M.9, I.25, W.28, Y.38 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.5, C:I.25, C:W.28, C:Y.38 Water bridges: C:M.9 MRD.13: 3 residues within 4Å: Chain C: R.59, I.60, N.61 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.60 Water bridges: C:R.59 MRD.17: 7 residues within 4Å: Chain D: A.5, F.7, G.8, M.9, I.25, W.28, Y.38 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.5, D:I.25, D:W.28, D:Y.38 Water bridges: D:M.9 MRD.18: 3 residues within 4Å: Chain D: R.59, I.60, N.61 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.60 Water bridges: D:R.59

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: R.14, K.15, K.16, E.58 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.15, A:K.15, A:K.16, A:E.58 Salt bridges: A:R.14 PO4.5: 3 residues within 4Å: Chain A: N.32, L.33, P.35 No protein-ligand interaction detected (PLIP) PO4.9: 4 residues within 4Å: Chain B: R.14, K.15, K.16, E.58 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.58 Water bridges: B:K.15, B:K.15, B:K.16, B:E.58 Salt bridges: B:R.14 PO4.10: 3 residues within 4Å: Chain B: N.32, L.33, P.35 No protein-ligand interaction detected (PLIP) PO4.14: 4 residues within 4Å: Chain C: R.14, K.15, K.16, E.58 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.15, C:K.15, C:K.16, C:E.58 Salt bridges: C:R.14 PO4.15: 3 residues within 4Å: Chain C: N.32, L.33, P.35 No protein-ligand interaction detected (PLIP) PO4.19: 4 residues within 4Å: Chain D: R.14, K.15, K.16, E.58 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.58 Water bridges: D:K.15, D:K.15, D:K.16, D:E.58 Salt bridges: D:R.14 PO4.20: 3 residues within 4Å: Chain D: N.32, L.33, P.35 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toulouse, J.L. et al., Structure-Based Design of Dimeric Bisbenzimidazole Inhibitors to an Emergent Trimethoprim-Resistant Type II Dihydrofolate Reductase Guides the Design of Monomeric Analogues. Acs Omega (2019)

Release Date

2019-05-29

Peptides

Dihydrofolate reductase type 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Dihydrofolate reductase type 2