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

Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-((thiophen-2-ylthio)methyl)benzoic acid (fragment 13)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x JBB: 3-(thiophen-2-ylsulfanylmethyl)benzoic acid(Non-covalent)

JBB.1: 7 residues within 4Å: Chain A: R.25, F.33, T.48, L.52, V.56, I.96 Ligands: NAP.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.48, A:L.52 JBB.5: 8 residues within 4Å: Chain B: Q.30, F.33, R.34, L.52, L.59, R.62, I.96 Ligands: NAP.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Q.30, B:F.33, B:F.33, B:L.59, B:I.96 Salt bridges: B:R.34, B:R.62

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

NAP.2: 27 residues within 4Å: Chain A: 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, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: JBB.1 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48 Hydrogen bonds: A:A.9, A:R.18, A:G.20, A:G.20, A:G.45, A:G.45, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:T.48, A:R.69, A:R.69, A:R.69, A:Q.70, A:G.98, A:G.99, A:Q.100, A:V.101, A:Y.102 Water bridges: A:G.17, A:R.47, A:Y.102 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NAP.6: 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, 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: JBB.5 31 PLIP interactions: 31 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.46, B:R.47, 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.98, B:G.99, B:Q.100, B:Q.100, B:V.101 Water bridges: B:S.51, B:R.69 Salt bridges: B:R.46, B:R.47 pi-Cation interactions: B:R.69, B:R.69

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

CO.3: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: H.159 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.40, B:H.159, H2O.2, H2O.2, H2O.2, H2O.3 CO.7: 4 residues within 4Å: Chain A: H.159 Chain B: I.36, H.40, E.92 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.40, H2O.8, H2O.8, H2O.9, H2O.10

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

SO4.4: 2 residues within 4Å: Chain A: R.46, R.47 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.46, A:R.46, A:R.47 Salt bridges: A:R.46, A:R.47

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

PO4.8: 3 residues within 4Å: Chain B: R.34, M.38, P.60 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.34

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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