SMTL ID : 4cix.1

Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with(1R,4R,5R)-1,4,5-trihydroxy-3-((1S)-1-hydroxy-2-phenyl) ethylcyclohex-2-en-1-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-12-mer

Ligands

12 x W4N: (1R,4R,5R)-1,4,5-trihydroxy-3-[(1S)-1-hydroxy-2-phenyl]ethylcyclohex-2-ene-1-carboxylic acid(Non-covalent)

W4N.1: 15 residues within 4Å: Chain A: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain J: D.88 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain J Hydrophobic interactions: A:L.13, A:L.16, A:V.105 Hydrogen bonds: A:P.11, A:N.12, A:N.75, A:N.75, A:G.77, A:G.78, A:H.81, A:I.102, A:S.103, A:S.103, A:R.112, J:D.88, J:D.88 Salt bridges: A:H.101 W4N.4: 15 residues within 4Å: Chain B: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain F: D.88 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:L.13, B:L.16, B:V.105 Hydrogen bonds: B:P.11, B:N.12, B:N.75, B:N.75, B:G.77, B:G.78, B:H.81, B:H.101, B:I.102, B:S.103, B:S.103, B:R.112, F:D.88 Salt bridges: B:H.101 W4N.7: 15 residues within 4Å: Chain A: D.88 Chain C: P.11, N.12, L.13, L.16, R.18, 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:L.13, C:L.16, C:V.105 Hydrogen bonds: C:P.11, C:N.12, C:N.75, C:N.75, C:G.77, C:G.78, C:H.81, C:I.102, C:S.103, C:S.103, C:R.112, A:D.88 Salt bridges: C:H.101 W4N.10: 15 residues within 4Å: Chain D: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain E: D.88 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.13, D:L.16, D:V.105 Hydrogen bonds: D:P.11, D:N.12, D:N.75, D:N.75, D:G.77, D:G.78, D:H.81, D:H.101, D:I.102, D:S.103, D:S.103, D:R.112, E:D.88 Salt bridges: D:H.101 W4N.13: 15 residues within 4Å: Chain E: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain L: D.88 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain L Hydrophobic interactions: E:L.13, E:L.16, E:V.105 Hydrogen bonds: E:P.11, E:N.12, E:N.75, E:N.75, E:G.77, E:G.78, E:H.81, E:I.102, E:S.103, E:S.103, E:R.112, L:D.88, L:D.88 Salt bridges: E:H.101 W4N.16: 15 residues within 4Å: Chain F: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain K: D.88 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain K Hydrophobic interactions: F:L.13, F:L.16, F:V.105 Hydrogen bonds: F:P.11, F:N.12, F:N.75, F:N.75, F:G.77, F:G.78, F:H.81, F:I.102, F:S.103, F:S.103, F:R.112, K:D.88, K:D.88 Salt bridges: F:H.101 W4N.19: 15 residues within 4Å: Chain G: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain H: D.88 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:L.13, G:L.16, G:V.105 Hydrogen bonds: G:P.11, G:N.12, G:N.75, G:N.75, G:G.77, G:G.78, G:H.81, G:I.102, G:S.103, G:S.103, G:R.112, H:D.88 Salt bridges: G:H.101 W4N.22: 15 residues within 4Å: Chain H: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain I: D.88 17 PLIP interactions: 15 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:L.13, H:L.16, H:V.105 Hydrogen bonds: H:P.11, H:N.12, H:N.75, H:N.75, H:G.77, H:G.78, H:H.81, H:I.102, H:S.103, H:S.103, H:R.112, I:D.88, I:D.88 Salt bridges: H:H.101 W4N.25: 15 residues within 4Å: Chain G: D.88 Chain I: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 17 PLIP interactions: 16 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:L.13, I:L.16, I:V.105 Hydrogen bonds: I:P.11, I:N.12, I:N.75, I:N.75, I:G.77, I:G.78, I:H.81, I:H.101, I:I.102, I:S.103, I:S.103, I:R.112, G:D.88 Salt bridges: I:H.101 W4N.28: 15 residues within 4Å: Chain C: D.88 Chain J: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: J:L.13, J:L.16, J:V.105 Hydrogen bonds: J:P.11, J:N.12, J:N.75, J:N.75, J:G.77, J:G.78, J:H.81, J:H.101, J:I.102, J:S.103, J:S.103, J:R.112, C:D.88 Salt bridges: J:H.101 W4N.31: 15 residues within 4Å: Chain B: D.88 Chain K: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 18 PLIP interactions: 16 interactions with chain K, 2 interactions with chain B Hydrophobic interactions: K:L.13, K:L.16, K:V.105 Hydrogen bonds: K:P.11, K:N.12, K:N.75, K:N.75, K:G.77, K:G.78, K:H.81, K:H.101, K:I.102, K:S.103, K:S.103, K:R.112, B:D.88, B:D.88 Salt bridges: K:H.101 W4N.34: 15 residues within 4Å: Chain D: D.88 Chain L: P.11, N.12, L.13, L.16, R.18, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 18 PLIP interactions: 16 interactions with chain L, 2 interactions with chain D Hydrophobic interactions: L:L.13, L:L.16, L:V.105 Hydrogen bonds: L:P.11, L:N.12, L:N.75, L:N.75, L:G.77, L:G.78, L:H.81, L:H.101, L:I.102, L:S.103, L:S.103, L:R.112, D:D.88, D:D.88 Salt bridges: L:H.101

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

SO4.2: 5 residues within 4Å: Chain A: S.54 Chain C: S.54 Chain J: S.54 Ligands: SO4.8, SO4.29 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: R.87, H.114, S.115, Y.116, P.119 Chain B: R.113 Chain C: F.111 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain B: S.54 Chain F: S.54 Chain K: S.54 Ligands: SO4.17, SO4.32 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain A: R.113 Chain B: R.87, H.114, S.115, Y.116, P.119 Chain K: F.111 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: S.54 Chain C: S.54 Chain J: S.54 Ligands: SO4.2, SO4.29 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain C: R.87, H.114, S.115, Y.116, P.119 Chain J: F.111 Chain L: R.113 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain D: S.54 Chain E: S.54 Chain L: S.54 Ligands: SO4.14, SO4.35 Ligand excluded by PLIP SO4.12: 7 residues within 4Å: Chain D: R.87, H.114, S.115, Y.116, P.119 Chain H: R.113 Chain L: F.111 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain D: S.54 Chain E: S.54 Chain L: S.54 Ligands: SO4.11, SO4.35 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain D: F.111 Chain E: R.87, H.114, S.115, Y.116, P.119 Chain F: R.113 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain B: S.54 Chain F: S.54 Chain K: S.54 Ligands: SO4.5, SO4.32 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain B: F.111 Chain E: R.113 Chain F: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain G: S.54 Chain H: S.54 Chain I: S.54 Ligands: SO4.23, SO4.26 Ligand excluded by PLIP SO4.21: 7 residues within 4Å: Chain G: R.87, H.114, S.115, Y.116, P.119 Chain I: F.111 Chain K: R.113 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain G: S.54 Chain H: S.54 Chain I: S.54 Ligands: SO4.20, SO4.26 Ligand excluded by PLIP SO4.24: 7 residues within 4Å: Chain D: R.113 Chain G: F.111 Chain H: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain G: S.54 Chain H: S.54 Chain I: S.54 Ligands: SO4.20, SO4.23 Ligand excluded by PLIP SO4.27: 7 residues within 4Å: Chain H: F.111 Chain I: R.87, H.114, S.115, Y.116, P.119 Chain J: R.113 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain A: S.54 Chain C: S.54 Chain J: S.54 Ligands: SO4.2, SO4.8 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain A: F.111 Chain I: R.113 Chain J: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain B: S.54 Chain F: S.54 Chain K: S.54 Ligands: SO4.5, SO4.17 Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain F: F.111 Chain G: R.113 Chain K: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain D: S.54 Chain E: S.54 Chain L: S.54 Ligands: SO4.11, SO4.14 Ligand excluded by PLIP SO4.36: 7 residues within 4Å: Chain C: R.113 Chain E: F.111 Chain L: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blanco, B. et al., Exploring the water-binding pocket of the type II dehydroquinase enzyme in the structure-based design of inhibitors. J. Med. Chem. (2014)

Release Date

2014-04-16

Peptides

3-DEHYDROQUINATE DEHYDRATASE: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

3-DEHYDROQUINATE DEHYDRATASE

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