SMTL ID : 6nxz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x D49: 2-[4-[(2~{R})-4-[4-(6-carboxy-1~{H}-benzimidazol-2-yl)phenoxy]-2-oxidanyl-butoxy]phenyl]-1~{H}-benzimidazole-5-carboxylic acid(Non-covalent)

D49.1: 7 residues within 4Å: Chain A: V.50, Q.51, I.52, Y.53 Chain C: Q.51, I.52 Ligands: D49.9 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.51, C:I.52, A:I.52 Hydrophobic interactions: A:Q.51, A:I.52 D49.5: 7 residues within 4Å: Chain B: V.50, Q.51, I.52, Y.53 Chain D: Q.51, I.52 Ligands: D49.13 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Q.51, B:I.52 Hydrogen bonds: B:I.52, D:Q.51, D:I.52 D49.9: 7 residues within 4Å: Chain A: Q.51, I.52 Chain C: V.50, Q.51, I.52, Y.53 Ligands: D49.1 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Q.51, C:I.52 Hydrogen bonds: C:I.52, A:Q.51, A:I.52 D49.13: 7 residues within 4Å: Chain B: Q.51, I.52 Chain D: V.50, Q.51, I.52, Y.53 Ligands: D49.5 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Q.51, B:I.52, D:I.52 Hydrophobic interactions: D:Q.51, D:I.52

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

MRD.2: 2 residues within 4Å: Chain A: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.3: 4 residues within 4Å: Chain A: A.6, T.7, G.9, D.12 No protein-ligand interaction detected (PLIP) MRD.6: 2 residues within 4Å: Chain B: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.7: 4 residues within 4Å: Chain B: A.6, T.7, G.9, D.12 No protein-ligand interaction detected (PLIP) MRD.10: 2 residues within 4Å: Chain C: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.11: 4 residues within 4Å: Chain C: A.6, T.7, G.9, D.12 No protein-ligand interaction detected (PLIP) MRD.14: 2 residues within 4Å: Chain D: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.15: 4 residues within 4Å: Chain D: A.6, T.7, G.9, D.12 No protein-ligand interaction detected (PLIP)

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

PO4.4: 3 residues within 4Å: Chain A: C.31, T.32, N.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.32, A:N.33 Water bridges: A:N.33 PO4.8: 3 residues within 4Å: Chain B: C.31, T.32, N.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.32, B:N.33 Water bridges: B:N.33 PO4.12: 3 residues within 4Å: Chain C: C.31, T.32, N.33 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.32, C:N.33 Water bridges: C:N.33 PO4.16: 3 residues within 4Å: Chain D: C.31, T.32, N.33 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.32, D:N.33 Water bridges: D:N.33

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

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