SMTL ID : 5ja3.1

Mycobacterium tuberculosis Dihydrofolate Reductase complexed with beta- NADPH and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-4'-methoxy-[1,1'-b iphenyl]-4-carboxylic acid (UCP1106)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 28 residues within 4Å: Chain A: W.6, A.7, I.14, G.15, R.16, G.18, D.19, I.20, G.43, R.44, R.45, T.46, S.49, L.65, S.66, R.67, Q.68, G.80, I.94, G.95, G.96, G.97, Q.98, V.99, Y.100, L.102, A.126 Ligands: U06.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.20, A:T.46 Hydrogen bonds: A:A.7, A:I.14, A:R.16, A:G.18, A:G.18, A:R.44, A:R.45, A:T.46, A:S.49, A:R.67, A:R.67, A:Q.68, A:Q.68, A:G.95, A:G.97, A:Q.98, A:V.99, A:Y.100 Water bridges: A:T.46 Salt bridges: A:R.44 pi-Cation interactions: A:R.67, A:R.67 NDP.3: 26 residues within 4Å: Chain B: W.6, A.7, I.14, G.15, R.16, G.18, D.19, I.20, G.43, R.44, R.45, T.46, S.49, L.65, S.66, R.67, Q.68, G.95, G.96, G.97, Q.98, V.99, Y.100, L.102, A.126 Ligands: U06.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.20, B:T.46 Hydrogen bonds: B:A.7, B:I.14, B:R.16, B:G.18, B:G.18, B:G.43, B:R.44, B:R.44, B:R.45, B:T.46, B:T.46, B:S.49, B:R.67, B:R.67, B:Q.68, B:Q.68, B:G.96, B:G.97, B:Q.98, B:Q.98, B:V.99, B:Y.100 Salt bridges: B:R.44 pi-Cation interactions: B:R.67 NDP.5: 28 residues within 4Å: Chain C: W.6, A.7, I.14, G.15, R.16, G.18, D.19, I.20, G.43, R.44, R.45, T.46, S.49, L.65, S.66, R.67, G.80, L.82, I.94, G.95, G.96, G.97, Q.98, V.99, Y.100, L.102, A.126 Ligands: U06.6 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:I.20, C:T.46 Hydrogen bonds: C:A.7, C:I.14, C:R.16, C:G.18, C:G.18, C:R.44, C:R.44, C:R.45, C:T.46, C:T.46, C:S.49, C:R.67, C:R.67, C:G.95, C:G.97, C:Q.98, C:Q.98, C:V.99 Salt bridges: C:R.44, C:R.67 pi-Cation interactions: C:R.67, C:R.67 NDP.7: 26 residues within 4Å: Chain D: W.6, A.7, I.14, G.15, G.18, D.19, I.20, G.43, R.44, R.45, T.46, S.49, L.65, S.66, R.67, Q.68, I.94, G.95, G.96, G.97, Q.98, V.99, Y.100, L.102, A.126 Ligands: U06.8 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.20, D:T.46 Hydrogen bonds: D:A.7, D:I.14, D:R.16, D:G.18, D:R.44, D:R.44, D:R.45, D:T.46, D:S.49, D:S.49, D:R.67, D:R.67, D:Q.68, D:G.97, D:Q.98, D:Q.98, D:V.99 Salt bridges: D:R.44

4 x U06: 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-4-methoxy-phenyl]benzoic acid(Non-covalent)

U06.2: 19 residues within 4Å: Chain A: I.5, W.6, A.7, D.19, I.20, D.27, Q.28, F.31, R.32, S.49, L.50, P.51, V.54, L.57, R.60, I.94, Y.100, T.113 Ligands: NDP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.20, A:Q.28, A:F.31, A:F.31, A:L.50, A:V.54, A:L.57 Hydrogen bonds: A:W.6, A:Y.100, A:T.113 Water bridges: A:H.30 Salt bridges: A:D.27, A:R.60 U06.4: 18 residues within 4Å: Chain B: I.5, W.6, A.7, D.19, I.20, D.27, Q.28, F.31, R.32, S.49, L.50, P.51, V.54, I.94, G.95, Y.100, T.113 Ligands: NDP.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.20, B:Q.28, B:F.31, B:L.50, B:P.51, B:V.54 Hydrogen bonds: B:W.6, B:Q.28, B:S.49, B:G.95, B:Y.100, B:T.113 Salt bridges: B:D.27, B:R.32 U06.6: 19 residues within 4Å: Chain C: I.5, W.6, A.7, D.19, I.20, D.27, Q.28, F.31, R.32, S.49, L.50, P.51, V.54, L.57, R.60, I.94, Y.100, T.113 Ligands: NDP.5 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.20, C:F.31, C:F.31, C:F.31, C:F.31, C:L.50, C:V.54, C:L.57 Hydrogen bonds: C:W.6, C:Q.28, C:I.94, C:Y.100, C:T.113 Salt bridges: C:D.27, C:R.32, C:R.60 U06.8: 19 residues within 4Å: Chain D: I.5, W.6, A.7, D.19, I.20, D.27, Q.28, F.31, R.32, S.49, L.50, P.51, V.54, L.57, R.60, I.94, Y.100, T.113 Ligands: NDP.7 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.20, D:F.31, D:F.31, D:L.50, D:V.54, D:L.57 Hydrogen bonds: D:W.6, D:Q.28, D:Y.100, D:Y.100, D:T.113 Water bridges: D:H.30 Salt bridges: D:D.27, D:R.32, D:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hajian, B. et al., Propargyl-Linked Antifolates Are Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis. Plos One (2016)

Release Date

2016-08-24

Peptides

Dihydrofolate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydrofolate reductase

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