SMTL ID : 2y76.1

Structure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-3-(benzo(b)thiophen-5-ylmethoxy)-2-(benzo(b) thiophen-5-ylmethyl)-1,4,5-trihydroxycyclohex-2-enecarboxylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x CB7: (1R,4S,5R)-3-(BENZO[b]THIOPHEN-5-YL)METHOXY-2-(BENZO[b]THIOPHEN-5-YL)METHYL-1,4,5-TRIHYDROXYCYCLOHEX-2-ENE-1-CARBOXYLATE(Non-covalent)

CB7.1: 15 residues within 4Å: Chain A: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain C: D.88, E.92 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:N.12, A:L.13, A:V.105, C:D.88 Hydrogen bonds: A:N.75, A:N.75, A:N.75, A:G.77, A:I.102, A:S.103, A:R.112 Water bridges: A:N.12, A:G.78 Salt bridges: A:H.101 CB7.5: 15 residues within 4Å: Chain A: D.88, E.92 Chain B: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.12, B:L.13, B:V.105, A:D.88 Hydrogen bonds: B:N.75, B:N.75, B:N.75, B:G.77, B:I.102, B:S.103, B:R.112 Water bridges: B:N.12, B:G.78 Salt bridges: B:H.101 CB7.9: 15 residues within 4Å: Chain B: D.88, E.92 Chain C: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:N.12, C:L.13, C:V.105, B:D.88 Hydrogen bonds: C:N.75, C:N.75, C:N.75, C:G.77, C:I.102, C:S.103, C:R.112, B:D.88 Water bridges: C:N.12, C:G.78 Salt bridges: C:H.101

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

SO4.2: 4 residues within 4Å: Chain A: R.87, P.119 Chain B: E.109, F.111 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.87 SO4.3: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain C: S.54, A.56 Ligands: SO4.7, SO4.11 9 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:S.54, C:S.54, B:S.54 Water bridges: C:A.56, C:A.56, A:A.56, A:A.56, B:A.56, B:A.56 SO4.4: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.64 Water bridges: A:Q.57 Salt bridges: A:R.50 SO4.6: 4 residues within 4Å: Chain B: R.87, P.119 Chain C: E.109, F.111 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.87 SO4.7: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain C: S.54, A.56 Ligands: SO4.3, SO4.11 9 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:S.54, A:S.54, C:S.54 Water bridges: A:A.56, A:A.56, C:A.56, C:A.56, B:A.56, B:A.56 SO4.8: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.64 Water bridges: B:Q.57 Salt bridges: B:R.50 SO4.10: 4 residues within 4Å: Chain A: E.109, F.111 Chain C: R.87, P.119 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.87 SO4.11: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain C: S.54, A.56 Ligands: SO4.3, SO4.7 9 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: A:S.54, B:S.54, B:S.54 Water bridges: A:A.56, A:A.56, C:A.56, C:A.56, B:A.56, B:A.56 SO4.12: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.64 Water bridges: C:Q.57 Salt bridges: C:R.50

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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