SMTL ID : 8f82.1

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor MAM845

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

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

XJT.1: 20 residues within 4Å: Chain A: I.15, W.16, A.17, I.30, W.32, L.34, D.37, L.38, F.41, K.42, L.60, P.61, H.64, L.67, P.68, R.70, I.108, Y.114, T.127 Ligands: NAP.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.30, A:L.38, A:P.61, A:H.64, A:L.67 Hydrogen bonds: A:Y.114, A:Y.114, A:T.127, A:T.127 Salt bridges: A:D.37, A:K.42, A:H.64, A:R.70 Halogen bonds: A:W.32, A:L.34

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 3 residues within 4Å: Chain A: D.130, W.156, R.164 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.156

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

NAP.3: 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, A.140 Ligands: XJT.1 41 PLIP interactions: 41 interactions with chain A Hydrophobic interactions: A:T.56 Hydrogen bonds: A:A.17, A:I.24, 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:Q.78, A:Q.78, A:G.109, A:G.110, A:A.111, A:Q.112, A:Q.112, A:I.113 Water bridges: A:R.26, A:G.28, A:I.30, A:R.55, A:R.55, A:R.55, A:R.77, A:R.77, A:R.77, A:R.77, A:L.92, 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

1 x BR: BROMIDE ION(Non-covalent)

BR.4: 2 residues within 4Å: Chain A: L.34, P.35 Ligand excluded by PLIP

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

2023-12-13

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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