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

Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-(phenoxymethyl)benzoic acid(fragment 14)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 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 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.2, H2O.2, H2O.7 CO.3: 3 residues within 4Å: Chain B: I.36, H.40, E.92 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.40, H2O.4, H2O.5, H2O.6, H2O.6, H2O.6

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

NAP.2: 26 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 31 PLIP interactions: 31 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:T.48, A:T.48, A:R.69, 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:G.17, A:R.18, A:S.51, A:R.69 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NAP.4: 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: 4RG.5 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, B:R.18, B:G.20, B:G.20, B:R.46, B:R.46, B:R.47, B:T.48, B:T.48, 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, B:Y.102 Water bridges: B:R.18, B:S.51, B:R.69, B:L.84 Salt bridges: B:R.46, B:R.47 pi-Cation interactions: B:R.69, B:R.69

1 x 4RG: 3-(phenoxymethyl)benzoic acid(Non-covalent)

4RG.5: 8 residues within 4Å: Chain B: I.22, F.33, R.34, L.52, V.56, R.62, I.96 Ligands: NAP.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.22, B:F.33, B:L.52, B:V.56 Salt bridges: B:R.62

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

PO4.6: 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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