SMTL ID : 7k6c.2 (6 other biounits)

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium abscessus ATCC 19977 / DSM 44196 with NADP and inhibitor P218

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: W.17, A.18, I.25, G.26, A.27, G.29, A.30, I.31, G.54, R.55, K.56, T.57, S.60, L.76, T.77, R.78, D.79, G.91, I.107, G.108, G.109, G.110, E.111, I.112, Y.113, L.115, A.136 Ligands: MMV.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:I.31, A:T.57 Hydrogen bonds: A:A.18, A:I.25, A:A.27, A:G.29, A:G.29, A:G.54, A:R.55, A:R.55, A:K.56, A:T.57, A:T.57, A:S.60, A:R.78, A:R.78, A:R.78, A:D.79, A:G.108, A:G.109, A:G.110, A:E.111, A:E.111, A:I.112, A:Y.113 Water bridges: A:T.77, A:R.78, A:A.93, A:E.111 Salt bridges: A:R.55 pi-Cation interactions: A:R.78, A:R.78

1 x MMV: 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid(Non-covalent)

MMV.2: 18 residues within 4Å: Chain A: I.16, W.17, A.18, I.31, D.38, Q.39, F.42, K.43, L.61, P.62, L.68, P.69, R.71, I.107, Y.113, T.126 Ligands: NAP.1, EDO.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.31, A:Q.39, A:F.42, A:L.61, A:L.68 Hydrogen bonds: A:I.16, A:T.126, A:T.126 Salt bridges: A:D.38, A:K.43, A:R.71

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: I.31, W.33, R.34, L.35, Q.39 Ligands: MMV.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.33, A:L.35, A:Q.39

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: D.85 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.85, A:D.85, H2O.5 CA.5: 2 residues within 4Å: Chain A: G.63, R.66 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.63, A:R.66, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrade Meirelles, M. et al., Rational Exploration of 2,4-Diaminopyrimidines as DHFR Inhibitors Active against Mycobacterium abscessus and Mycobacterium avium , Two Emerging Human Pathogens. J.Med.Chem. (2024)

Release Date

2021-03-17

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dihydrofolate reductase

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