SMTL ID : 6c9r.1

Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-(thiophen-3-yl)-9H-purin-9-yl)tetrahydrofuran-3,4-diol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x ERJ: 9-beta-D-ribofuranosyl-6-(thiophen-3-yl)-9H-purine(Non-covalent)

ERJ.1: 20 residues within 4Å: Chain A: S.21, A.23, D.25, G.60, G.61, V.62, N.65, F.115, F.129, M.134, A.159, Q.185, Q.186, R.189, T.266, G.267, D.270, T.306 Chain B: S.49, L.51 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.129, A:F.129, A:Q.185 Hydrogen bonds: A:S.21, A:D.25, A:G.61, A:N.65, A:G.267 pi-Stacking: A:F.129, A:F.129 ERJ.2: 12 residues within 4Å: Chain A: T.236, G.238, P.239, V.256, V.257, E.259, V.268, F.272, S.294, A.297, V.298, L.301 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.256 ERJ.4: 20 residues within 4Å: Chain A: S.49, L.51 Chain B: S.21, A.23, D.25, G.60, G.61, V.62, N.65, F.115, F.129, M.134, A.159, Q.185, Q.186, R.189, T.266, G.267, D.270, T.306 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.129, B:F.129, B:Q.185 Hydrogen bonds: B:S.21, B:D.25, B:G.61, B:N.65 pi-Stacking: B:F.129, B:F.129 ERJ.5: 10 residues within 4Å: Chain B: G.238, P.239, V.256, V.257, P.258, E.259, Q.262, V.268, V.298, L.301 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.239 Hydrogen bonds: B:E.259

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: D.264, T.266, V.300, S.303, G.305, T.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.264 NA.6: 7 residues within 4Å: Chain B: D.264, T.266, V.300, L.301, S.303, T.304, G.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.264, B:T.266

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 14 residues within 4Å: Chain A: M.28, T.116, C.117, T.118, I.126, A.127, S.128 Chain B: M.28, T.116, C.117, T.118, I.126, A.127, S.128 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.118, A:T.118, B:T.118, B:T.118, B:I.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crespo, R.A. et al., Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase. J.Med.Chem. (2019)

Release Date

2019-05-01

Peptides

Adenosine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosine kinase