SMTL ID : 6c9p.1

Mycobacterium tuberculosis adenosine kinase bound to 6-methylmercaptopurine riboside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.195, V.255, G.256, R.260 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.195, A:G.256 Water bridges: A:E.198, A:T.223, A:T.223, A:T.223, A:D.257, A:R.260, A:R.260 SO4.5: 5 residues within 4Å: Chain B: S.171, N.195, T.223, G.256, R.260 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.195, B:G.256, B:R.260 Water bridges: B:N.195, B:T.223, B:T.223, B:G.254

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

NA.2: 7 residues within 4Å: Chain A: D.251, T.253, V.287, L.288, S.290, T.291, G.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.251, A:G.292 NA.7: 7 residues within 4Å: Chain B: D.251, T.253, V.287, L.288, S.290, T.291, G.292 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.251

4 x MTP: 2-HYDROXYMETHYL-5-(6-METHYLSULFANYL-PURIN-9-YL)-TETRAHYDRO-FURAN-3,4-DIOL(Non-covalent)

MTP.3: 20 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, R.176, T.253, G.254, D.257, T.293 Chain B: S.36, L.38 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.8, 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 MTP.4: 10 residues within 4Å: Chain A: G.225, P.226, V.243, V.244, E.246, Q.249, V.255, A.284, V.285, L.288 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.244, A:S.281 MTP.8: 20 residues within 4Å: Chain A: 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, R.176, T.253, G.254, D.257, T.293 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.8, 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 MTP.9: 10 residues within 4Å: Chain B: G.225, P.226, V.243, V.244, E.246, Q.249, V.255, A.284, V.285, L.288 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.225, B:S.281

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.103, A:T.105, A:T.105, B:T.105, B:T.105, B: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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