SMTL ID : 5sd3.1

Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1088

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: W.26, A.27, I.34, G.35, R.36, G.38, D.39, I.40, G.63, R.64, R.65, T.66, S.69, L.85, S.86, R.87, Q.88, G.100, I.114, G.115, G.116, G.117, Q.118, V.119, Y.120, L.122, A.146 Ligands: H9I.2 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:I.40, A:T.66 Hydrogen bonds: A:A.27, A:I.34, A:R.36, A:G.38, A:G.38, A:G.63, A:R.64, A:R.64, A:R.65, A:R.65, A:R.65, A:T.66, A:S.69, A:R.87, A:R.87, A:Q.88, A:Q.88, A:G.115, A:G.116, A:G.117, A:Q.118, A:V.119 Water bridges: A:R.36, A:R.65, A:R.87, A:R.87, A:R.87, A:R.87, A:R.87, A:Q.118, A:Q.118 Salt bridges: A:R.64 pi-Cation interactions: A:R.87, A:R.87

1 x H9I: 3-{2-[(3-{[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]methyl}oxetan-3-yl)methoxy]phenyl}propanoic acid(Non-covalent)

H9I.2: 17 residues within 4Å: Chain A: I.25, W.26, A.27, I.40, D.47, Q.48, F.51, R.52, T.66, L.70, L.77, R.80, I.114, Y.120, T.133 Ligands: NAP.1, EDO.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.40, A:Q.48, A:F.51 Hydrogen bonds: A:W.26, A:Y.120, A:Y.120, A:T.133 Salt bridges: A:D.47, A:R.52, A:R.80

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

EDO.3: 7 residues within 4Å: Chain A: I.40, W.42, R.43, L.44, D.47, Q.48 Ligands: H9I.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.42, A:L.44, A:D.47, A:Q.48 EDO.4: 5 residues within 4Å: Chain A: P.76, R.80, R.81, N.82, G.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.82, A:N.82 Water bridges: A:E.97, A:E.97 EDO.5: 3 residues within 4Å: Chain A: A.121, P.149, V.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.150 Water bridges: A:A.121, A:A.148 EDO.6: 4 residues within 4Å: Chain A: W.26, Q.28, Y.174, Y.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.28 EDO.7: 4 residues within 4Å: Chain A: G.117, D.145, A.146, L.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.147 Water bridges: A:Q.118, A:D.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayclin, S.J. et al., Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1088. to be published

Release Date

2022-02-09

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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