SMTL ID : 6c9s.1

Mycobacterium tuberculosis adenosine kinase bound to (2R,3R,4S,5R)-2-(6-([1,1'-biphenyl]-4-ylethynyl)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x ERP: 6-[([1,1'-biphenyl]-4-yl)ethynyl]-9-beta-D-ribofuranosyl-9H-purine(Non-covalent)

ERP.1: 23 residues within 4Å: Chain A: S.8, A.10, D.12, G.47, G.48, V.49, N.52, F.102, F.116, M.121, A.146, Q.172, Q.173, A.175, R.176, T.253, G.254, D.257, T.293 Chain B: F.17, S.36, F.37, L.38 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.116, A:Q.172, A:A.175, A:R.176, B:F.17, B:L.38, B:L.38 Hydrogen bonds: A:D.12, A:G.48, A:N.52, A:Q.172, A:Q.173 Water bridges: A:G.254, A:G.254, A:G.254 pi-Stacking: A:F.116, A:F.116 ERP.4: 23 residues within 4Å: Chain A: F.17, S.36, F.37, L.38 Chain B: S.8, A.10, D.12, G.47, G.48, V.49, N.52, F.102, F.116, M.121, A.146, Q.172, Q.173, A.175, R.176, T.253, G.254, D.257, T.293 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.116, B:Q.172, B:A.175, B:R.176, A:F.17, A:L.38, A:L.38 Hydrogen bonds: B:D.12, B:G.48, B:N.52, B:Q.172, B:Q.173 Water bridges: B:G.254, B:G.254, B:G.254 pi-Stacking: B:F.116, B:F.116

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: N.195, T.223, V.255, G.256, R.260 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.195, A:G.256, A:R.260 Water bridges: A:S.171, A:N.195, A:T.223, A:T.223, A:G.254, A:G.254, A:D.257, A:R.260 SO4.5: 4 residues within 4Å: Chain B: N.195, T.223, G.256, R.260 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.195, B:T.223, B:G.256, B:R.260 Water bridges: B:T.223, B:P.252, B:G.254, B:G.254

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

NA.3: 6 residues within 4Å: Chain A: D.251, T.253, V.287, S.290, T.291, G.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.251, A:G.292 NA.6: 6 residues within 4Å: Chain B: D.251, T.253, V.287, S.290, T.291, G.292 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.251, B:T.253, B:G.292

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

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