SMTL ID : 8ta1.1

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor MAM907

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x NA: SODIUM ION

NA.1: 2 residues within 4Å: Chain A: P.68, G.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.69 Water bridges: A:R.70

1 x ACT: ACETATE ION

ACT.2: 4 residues within 4Å: Chain A: A.111, Q.112, D.139 Ligands: NAP.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.111, A:Q.112

1 x EII: 3-(2-{3-[(2,4-diamino-6-cyclohexylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid

EII.3: 17 residues within 4Å: Chain A: I.15, W.16, A.17, I.30, D.37, L.38, F.41, K.42, L.60, P.61, H.64, L.67, R.70, I.108, Y.114, T.127 Ligands: NAP.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.30, A:L.38, A:L.60, A:P.61, A:L.67 Hydrogen bonds: A:Y.114, A:Y.114, A:T.127, A:T.127 Water bridges: A:K.42, A:K.42 Salt bridges: A:D.37, A:K.42, A:H.64, A:R.70

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

NAP.4: 28 residues within 4Å: Chain A: W.16, A.17, I.24, G.25, R.26, G.28, G.29, I.30, G.53, R.54, R.55, T.56, S.59, V.75, T.76, R.77, Q.78, G.90, I.108, G.109, G.110, A.111, Q.112, I.113, Y.114, L.116 Ligands: ACT.2, EII.3 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:I.30, A:T.56 Hydrogen bonds: A:A.17, A:R.26, A:G.28, A:G.53, A:R.54, A:R.54, A:R.55, A:T.56, A:S.59, A:T.76, A:T.76, A:R.77, A:R.77, A:R.77, A:Q.78, A:Q.78, A:G.109, A:G.110, A:A.111, A:Q.112, A:I.113, A:Y.114 Water bridges: A:G.28, A:R.55, A:R.55, A:Q.112, A:Q.112, A:Q.112, A:Q.112 Salt bridges: A:R.54, A:R.55 pi-Cation interactions: A:R.77

2 x PG4: TETRAETHYLENE GLYCOL

PG4.5: 8 residues within 4Å: Chain A: G.47, H.48, T.49, G.69, R.71, E.100, P.101, D.102 No protein-ligand interaction detected (PLIP) PG4.6: 6 residues within 4Å: Chain A: Q.18, E.128, V.144, L.145, H.168, Y.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.18, A:L.145

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

2024-08-28

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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