SMTL ID : 2y77.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x CB8: (1R,4S,5R)-3-(BENZO[B]THIOPHEN-2-YL)METHOXY-1,4,5-TRIHYDROXY-2-(THIEN-2-YL)METHYLCYCLOHEX-2-EN-1-CARBOXYLATE(Non-covalent)

CB8.1: 14 residues within 4Å: Chain A: N.12, L.13, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain B: D.88 17 PLIP interactions: 2 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:D.88, B:D.88, A:N.75, A:N.75, A:G.77, A:H.81, A:H.101, A:I.102, A:S.103, A:R.112 Hydrophobic interactions: A:L.13, A:L.13, A:L.16, A:I.102, A:V.105 Water bridges: A:G.78 Salt bridges: A:H.101 CB8.6: 14 residues within 4Å: Chain B: N.12, L.13, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain C: D.88 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.13, B:L.13, B:L.16, B:I.102, B:V.105 Hydrogen bonds: B:N.75, B:N.75, B:G.77, B:H.81, B:H.101, B:I.102, B:S.103, B:R.112, C:D.88, C:D.88 Water bridges: B:G.78 Salt bridges: B:H.101 CB8.11: 14 residues within 4Å: Chain A: D.88 Chain C: N.12, L.13, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.13, C:L.13, C:L.16, C:I.102, C:V.105 Hydrogen bonds: C:N.75, C:N.75, C:G.77, C:H.81, C:H.101, C:I.102, C:S.103, C:R.112, A:D.88 Water bridges: C:G.78 Salt bridges: C:H.101

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

SO4.2: 4 residues within 4Å: Chain A: R.87, P.119 Chain C: E.109, F.111 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Salt bridges: A:R.87 Water bridges: C:E.110, C:E.110 SO4.3: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.61, A:Q.64 Water bridges: A:Q.57, A:Q.57, A:D.60 Salt bridges: A:R.50 SO4.4: 2 residues within 4Å: Chain A: A.56, Q.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.56 Water bridges: A:Q.57, A:D.60 SO4.5: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain C: S.54, A.56 Ligands: SO4.10, SO4.15 11 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:S.54, B:S.54 Water bridges: C:S.54, C:A.56, C:A.56, B:S.54, B:A.56, B:A.56, A:S.54, A:A.56, A:A.56 SO4.7: 4 residues within 4Å: Chain A: E.109, F.111 Chain B: R.87, P.119 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.87 Water bridges: A:E.110, A:E.110 SO4.8: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.61, B:Q.64 Water bridges: B:Q.57, B:Q.57 Salt bridges: B:R.50 SO4.9: 2 residues within 4Å: Chain B: A.56, Q.57 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.56 Water bridges: B:Q.57, B:Q.57 SO4.10: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain C: S.54, A.56 Ligands: SO4.5, SO4.15 11 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:S.54, A:S.54 Water bridges: C:S.54, C:A.56, C:A.56, B:S.54, B:A.56, B:A.56, A:S.54, A:A.56, A:A.56 SO4.12: 4 residues within 4Å: Chain B: E.109, F.111 Chain C: R.87, P.119 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:E.110, B:E.110 Salt bridges: C:R.87 SO4.13: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:W.61, C:Q.64 Water bridges: C:Q.57, C:Q.57, C:D.60 Salt bridges: C:R.50 SO4.14: 2 residues within 4Å: Chain C: A.56, Q.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.56 Water bridges: C:Q.57, C:D.60 SO4.15: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain C: S.54, A.56 Ligands: SO4.5, SO4.10 11 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B, 4 interactions with chain A Water bridges: C:S.54, C:A.56, C:A.56, B:S.54, B:A.56, B:A.56, A:S.54, A:A.56, A:A.56 Hydrogen bonds: B:S.54, A:S.54

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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