SMTL ID : 6nd2.1

Staphylococcus aureus Dihydrofolate Reductase complexed with NADPH and 6-ETHYL-5-[(3R)-3-[2-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP1063)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.12, P.125, Y.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.126, A:Y.126 Water bridges: A:R.12

1 x G8J: 6-ethyl-5-{(3S)-3-[2-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine(Non-covalent)

G8J.2: 16 residues within 4Å: Chain A: L.5, V.6, A.7, N.18, Q.19, L.20, D.27, L.28, V.31, T.46, S.49, I.50, L.54, F.92, T.111 Ligands: XNP.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.20, A:T.46, A:I.50, A:I.50, A:L.54, A:F.92 Hydrogen bonds: A:L.5, A:T.111, A:T.111 Water bridges: A:A.7, A:A.7 Salt bridges: A:D.27

1 x XNP: Tricyclic NADPH(Non-covalent)

XNP.3: 25 residues within 4Å: Chain A: I.14, G.15, N.18, Q.19, L.20, G.43, R.44, K.45, T.46, S.49, L.62, T.63, S.64, D.65, H.77, I.79, F.92, G.93, G.94, Q.95, T.96, L.97, E.100, T.121 Ligands: G8J.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:I.14, A:N.18, A:N.18, A:R.44, A:R.44, A:K.45, A:T.46, A:T.46, A:S.49, A:T.63, A:S.64, A:D.65, A:G.94, A:Q.95, A:T.96, A:L.97, A:E.100 Water bridges: A:T.96, A:T.96, A:T.121, A:T.121 Salt bridges: A:R.44, A:K.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lombardo, M.N. et al., Structure-Guided In Vitro to In Vivo Pharmacokinetic Optimization of Propargyl-Linked Antifolates. Drug Metab.Dispos. (2019)

Release Date

2019-09-25

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

Dihydrofolate reductase

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