SMTL ID : 6c9v.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ERS: (2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl]tetrahydrofuran-3,4-diol(Non-covalent)

ERS.1: 22 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: Q.24, S.36, L.38 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.175, A:R.176 Hydrogen bonds: A:S.8, A:D.12, A:G.48, A:N.52, A:Q.172 Water bridges: A:G.254, A:G.254, A:D.257 pi-Stacking: A:F.116, A:F.116 ERS.4: 22 residues within 4Å: Chain A: Q.24, S.36, 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.175, B:R.176 Hydrogen bonds: B:S.8, B:D.12, B:G.48, B:N.52, B:Q.172 Water bridges: B:G.254, B:G.254, B:D.257 pi-Stacking: B:F.116, B:F.116

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

SO4.2: 4 residues within 4Å: Chain A: N.195, T.223, G.256, R.260 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.195, A:G.256 Water bridges: A:T.223, A:G.254, A:G.254, 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:G.256 Water bridges: B:S.171, B:S.171, B:T.223, B:G.254, B:G.254, B:R.260

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.251 NA.6: 6 residues within 4Å: Chain B: D.251, T.253, V.287, S.290, T.291, G.292 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.251, B:V.287

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 14 residues within 4Å: Chain A: M.15, T.103, C.104, T.105, I.113, A.114, S.115 Chain B: M.15, T.103, C.104, T.105, I.113, A.114, S.115 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.105, B:T.105, A:T.105, A:T.105, A:T.105, A:I.113

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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