SMTL ID : 6vv8.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB285

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: R.111 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.40, H2O.1, H2O.1, H2O.1 CO.2: 5 residues within 4Å: Chain A: H.159 Chain B: I.36, M.38, H.40, E.92 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.40, A:H.159

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.3: 29 residues within 4Å: Chain A: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, W.24, G.45, R.46, R.47, T.48, S.51, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: RPV.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.22 Hydrogen bonds: A:A.9, A:A.9, A:R.18, A:G.20, A:G.20, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:S.51, A:S.68, A:R.69, A:Q.70, A:Q.70, A:G.98, A:G.99, A:Q.100, A:V.101 Salt bridges: A:R.46, A:R.69 NAP.5: 27 residues within 4Å: Chain B: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, G.45, R.46, R.47, T.48, S.51, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, A.128 Ligands: RPV.6 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:A.9, B:A.9, B:R.18, B:G.20, B:R.46, B:R.46, B:R.47, B:R.47, B:R.47, B:T.48, B:T.48, B:S.51, B:S.68, B:R.69, B:R.69, B:Q.70, B:Q.70, B:G.98, B:G.99, B:Q.100, B:V.101, B:Y.102 Salt bridges: B:R.46 pi-Cation interactions: B:R.69, B:R.69

2 x RPV: 5-{[3-(1H-indol-3-yl)propanoyl]amino}-1-phenyl-1H-pyrazole-4-carboxylic acid(Non-covalent)

RPV.4: 9 residues within 4Å: Chain A: Q.30, F.33, R.34, L.52, V.56, L.59, R.62, I.96 Ligands: NAP.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.33, A:L.52, A:L.59, A:I.96 Salt bridges: A:R.62 pi-Stacking: A:F.33, A:F.33 RPV.6: 9 residues within 4Å: Chain B: R.25, Q.30, F.33, P.53, V.56, L.59, R.62, I.96 Ligands: NAP.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Q.30, B:P.53, B:V.56, B:L.59, B:I.96 Hydrogen bonds: B:Q.30, B:R.34 Salt bridges: B:R.62 pi-Stacking: B:F.33, B:F.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.A. et al., Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis. Acs Infect Dis. (2020)

Release Date

2020-07-15

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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