SMTL ID : 2y71.1

Structure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-1,4,5-trihydroxy-3-((5-methylbenzo(b) thiophen-2-yl)methoxy)cyclohex-2-enecarboxylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x CB6: (1R,4S,5R)-1,4,5-trihydroxy-3-[(5-methyl-1-benzothiophen-2-yl)methoxy]cyclohex-2-ene-1-carboxylic acid(Non-covalent)

CB6.1: 15 residues within 4Å: Chain A: N.12, L.13, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain B: D.88, E.92 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.15, A:Y.24, A:V.105 Hydrogen bonds: A:N.75, A:N.75, A:N.75, A:G.77, A:H.81, A:I.102, A:S.103, A:R.112, B:D.88, B:D.88 Water bridges: A:N.12, A:G.78 Salt bridges: A:H.101 pi-Stacking: A:Y.24 CB6.9: 15 residues within 4Å: Chain B: N.12, L.13, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain C: D.88, E.92 16 PLIP interactions: 1 interactions with chain C, 15 interactions with chain B Hydrogen bonds: C:D.88, B:N.75, B:N.75, B:N.75, B:G.77, B:H.81, B:I.102, B:S.103, B:R.112 Hydrophobic interactions: B:R.15, B:Y.24, B:V.105 Water bridges: B:N.12, B:G.78 Salt bridges: B:H.101 pi-Stacking: B:Y.24 CB6.17: 15 residues within 4Å: Chain A: D.88, E.92 Chain C: N.12, L.13, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:R.15, C:Y.24, C:V.105 Hydrogen bonds: C:N.75, C:N.75, C:N.75, C:G.77, C:H.81, C:I.102, C:S.103, C:R.112, A:D.88 Water bridges: C:N.12, C:G.78 Salt bridges: C:H.101 pi-Stacking: C:Y.24

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

NA.2: 3 residues within 4Å: Chain A: I.4, N.6, E.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.6, A:E.70 NA.3: 4 residues within 4Å: Chain A: L.128, G.129, I.130, Q.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.128, A:I.130, A:Q.131 NA.10: 3 residues within 4Å: Chain B: I.4, N.6, E.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.6, B:E.70 NA.11: 4 residues within 4Å: Chain B: L.128, G.129, I.130, Q.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.128, B:I.130, B:Q.131 NA.18: 3 residues within 4Å: Chain C: I.4, N.6, E.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.6, C:E.70 NA.19: 4 residues within 4Å: Chain C: L.128, G.129, I.130, Q.131 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.128, C:I.130, C:Q.131

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

SO4.4: 6 residues within 4Å: Chain A: S.54 Chain B: S.54 Chain C: S.54, A.56 Ligands: SO4.12, SO4.20 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B Water bridges: A:S.54, A:A.56, C:S.54, C:Q.57, B:A.56, B:Q.57 Hydrogen bonds: C:S.54, B:S.54 SO4.5: 2 residues within 4Å: Chain A: K.46, R.50 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.37, A:A.47 Salt bridges: A:R.50 SO4.6: 2 residues within 4Å: Chain A: A.56, Q.57 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.57, A:Q.57 SO4.7: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.64 Water bridges: A:Q.57, A:Q.57, A:D.60 Salt bridges: A:R.50 SO4.8: 1 residues within 4Å: Chain A: R.113 No protein-ligand interaction detected (PLIP) SO4.12: 6 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54 Chain C: S.54 Ligands: SO4.4, SO4.20 8 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:S.54, A:S.54 Water bridges: C:A.56, C:Q.57, A:S.54, A:Q.57, B:S.54, B:A.56 SO4.13: 2 residues within 4Å: Chain B: K.46, R.50 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.37, B:A.47 Salt bridges: B:R.50 SO4.14: 2 residues within 4Å: Chain B: A.56, Q.57 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.57, B:Q.57 SO4.15: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.64 Water bridges: B:Q.57, B:Q.57, B:D.60 Salt bridges: B:R.50 SO4.16: 1 residues within 4Å: Chain B: R.113 No protein-ligand interaction detected (PLIP) SO4.20: 6 residues within 4Å: Chain A: S.54 Chain B: S.54, A.56 Chain C: S.54 Ligands: SO4.4, SO4.12 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A, 3 interactions with chain B Water bridges: C:S.54, C:A.56, A:A.56, A:Q.57, B:S.54, B:Q.57 Hydrogen bonds: A:S.54, B:S.54 SO4.21: 2 residues within 4Å: Chain C: K.46, R.50 3 PLIP interactions: 3 interactions with chain C Water bridges: C:E.37, C:A.47 Salt bridges: C:R.50 SO4.22: 2 residues within 4Å: Chain C: A.56, Q.57 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.57, C:D.60 SO4.23: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.64 Water bridges: C:Q.57, C:Q.57, C:D.60 Salt bridges: C:R.50 SO4.24: 1 residues within 4Å: Chain C: R.113 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tizon, L. et al., A prodrug approach for improving antituberculosis activity of potent Mycobacterium tuberculosis type II dehydroquinase inhibitors. J. Med. Chem. (2011)

Release Date

2011-08-17

Peptides

3-DEHYDROQUINATE DEHYDRATASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

3-DEHYDROQUINATE DEHYDRATASE

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