SMTL ID : 6vv7.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB136

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 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: RPM.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48 Hydrogen bonds: A:A.9, A:I.16, A:R.18, A:G.20, A:G.20, A:G.45, A:R.46, A:R.47, A:T.48, A:T.48, A:R.69, A:R.69, A:Q.70, A:G.98, A:G.99, A:Q.100, A:Q.100, A:V.101 Water bridges: A:S.51, A:R.69, A:R.69 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NDP.7: 28 residues within 4Å: Chain B: 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: RPM.9 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, B:I.16, B:R.18, B:G.20, B:G.20, B:G.45, B:R.46, B:R.47, B:T.48, B:T.48, B:S.68, B:R.69, B:R.69, B:R.69, B:Q.70, B:Q.70, B:G.97, B:G.98, B:G.99, B:Q.100, B:Q.100, B:V.101 Water bridges: B:S.51 Salt bridges: B:R.46 pi-Cation interactions: B:R.69, B:R.69

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

CO.2: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: H.159 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:H.159, A:H.40, H2O.1, H2O.1, H2O.1, H2O.3 CO.8: 1 residues within 4Å: Chain B: H.40 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.40, H2O.3, H2O.3

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

RPM.3: 13 residues within 4Å: Chain A: R.25, D.29, Q.30, F.33, T.48, L.52, P.53, V.56, L.59, R.62, I.96 Ligands: NDP.1, PO4.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.33, A:F.33, A:T.48, A:L.52, A:L.59, A:I.96 Water bridges: A:D.29 Salt bridges: A:R.62 pi-Stacking: A:F.33, A:F.33 RPM.9: 15 residues within 4Å: Chain B: I.7, W.8, A.9, D.29, Q.30, F.33, R.34, L.52, P.53, V.56, L.59, R.62, I.96, Y.102 Ligands: NDP.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.33, B:F.33, B:L.52, B:L.59, B:I.96 Salt bridges: B:R.62 pi-Stacking: B:F.33, B:F.33

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

PO4.4: 2 residues within 4Å: Chain A: R.46, R.47 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.46, A:R.47 PO4.5: 4 residues within 4Å: Chain A: G.99, D.127, A.128, L.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.129 PO4.6: 3 residues within 4Å: Chain A: R.25, P.53 Ligands: RPM.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.25 PO4.10: 3 residues within 4Å: Chain B: Q.10, Y.156, Y.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.10, B:Q.10, B:Y.158, B:Y.158

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

SO4.11: 4 residues within 4Å: Chain B: G.99, D.127, A.128, L.129 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.127, B:L.129, B:L.129

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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