SMTL ID : 6vv6.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB113

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 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: H.159 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.40, B:H.159, H2O.1, H2O.3 CO.4: 2 residues within 4Å: Chain B: I.36, H.40 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.40, H2O.1, H2O.2, H2O.3

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

NAP.2: 28 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, 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: RPJ.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.9, A:G.20, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:T.48, A:S.68, A:R.69, A:R.69, A:Q.70, A:Q.70, A:G.98, A:G.99, A:Q.100, A:V.101, A:Y.102 Water bridges: A:S.51 Salt bridges: A:R.46 pi-Cation interactions: A:R.69 NAP.5: 25 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, L.67, S.68, R.69, Q.70, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.22 Hydrogen bonds: B:A.9, B:R.18, B:G.20, B:D.21, B:R.46, B:R.47, B:R.47, B:R.47, B:T.48, B:T.48, B:R.69, B:R.69, B:Q.70, B:G.98, B:G.98, B:G.99, B:Q.100, B:V.101, B:Y.102 Water bridges: B:G.19 Salt bridges: B:R.46

2 x RPJ: 1-(4-fluorophenyl)-5-[3-(1H-indol-3-yl)propoxy]-1H-pyrazole-4-carboxylic acid(Non-covalent)

RPJ.3: 13 residues within 4Å: Chain A: I.22, R.25, Q.30, F.33, T.48, L.52, P.53, V.56, L.59, P.60, R.62, I.96 Ligands: NAP.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.33, A:F.33, A:T.48, A:L.52, A:P.53, A:I.96 Salt bridges: A:R.62 RPJ.6: 9 residues within 4Å: Chain B: I.22, W.24, Q.30, A.31, F.33, R.34, L.52, P.53, V.56 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.22, B:Q.30, B:Q.30, B:F.33, B:V.56 Hydrogen bonds: B:Q.30 Water bridges: B:A.9, B:D.29 Salt bridges: B:R.34

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain B: R.46, R.47 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.47, B:R.47 Salt bridges: B:R.46, B:R.47

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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