SMTL ID : 6c67.1

Mycobacterium tuberculosis adenosine kinase bound to iodotubercidin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

4 x 5ID: (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL(Non-covalent)

5ID.1: 19 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, T.253, G.254, D.257, T.293 Chain B: S.36, L.38 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.172 Hydrogen bonds: A:G.48, A:N.52, A:Q.172, A:Q.173, A:G.254 Water bridges: A:D.257, A:D.257 pi-Stacking: A:F.116, A:F.116 Halogen bonds: B:S.36 5ID.2: 13 residues within 4Å: Chain A: M.110, G.225, P.226, V.243, V.244, P.245, E.246, Q.249, P.252, V.255, A.284, V.285, L.288 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.288 Hydrogen bonds: A:V.244, A:E.246, A:Q.249 Water bridges: A:G.225, A:V.244 5ID.6: 19 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, T.253, G.254, D.257, T.293 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.172 Hydrogen bonds: B:G.48, B:N.52, B:Q.172, B:Q.173, B:G.254 Water bridges: B:D.257, B:D.257 pi-Stacking: B:F.116, B:F.116 Halogen bonds: A:S.36 5ID.7: 12 residues within 4Å: Chain B: M.110, G.225, P.226, V.243, V.244, P.245, E.246, P.252, V.255, A.284, V.285, L.288 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.288 Hydrogen bonds: B:V.244, B:E.246 Water bridges: B:V.244

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

NA.3: 7 residues within 4Å: Chain A: D.251, T.253, V.287, S.290, T.291, G.292, T.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.251, A:S.290 NA.8: 7 residues within 4Å: Chain B: D.251, T.253, V.287, S.290, T.291, G.292, T.293 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.253, B:S.290

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.103, B:T.105, B:T.105, A:T.103, A:T.105, A:T.105, A:T.105

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

SO4.5: 6 residues within 4Å: Chain A: S.171, N.195, T.223, V.255, G.256, R.260 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.195, A:T.223, A:G.256 Water bridges: A:T.223, A:P.252, A:G.254, A:G.254, A:R.260 SO4.9: 5 residues within 4Å: Chain B: N.195, T.223, V.255, G.256, R.260 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.195, B:T.223, B:G.256 Water bridges: B:Q.172, B:G.254, B:R.260, B:R.260

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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