SMTL ID : 4kij.1

Design and structural analysis of aromatic inhibitors of type II dehydroquinase dehydratase from Mycobacterium tuberculosis - compound 35c [3,4-dihydroxy-5-(3-nitrophenoxy)benzoic acid]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-12-mer

Ligands

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: H.113 Chain J: H.113 Ligands: CL.19 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain B: H.113 Chain E: H.113 Ligands: CL.9 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain C: H.113 Chain I: H.113 Ligands: CL.17 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain D: H.113 Chain G: H.113 Ligands: CL.13 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: H.113 Chain E: H.113 Ligands: CL.3 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain F: H.113 Chain L: H.113 Ligands: CL.23 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain D: H.113 Chain G: H.113 Ligands: CL.7 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain H: H.113 Chain K: H.113 Ligands: CL.21 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain C: H.113 Chain I: H.113 Ligands: CL.5 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: H.113 Chain J: H.113 Ligands: CL.1 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain H: H.113 Chain K: H.113 Ligands: CL.15 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain F: H.113 Chain L: H.113 Ligands: CL.11 Ligand excluded by PLIP

12 x KIJ: 3,4-dihydroxy-5-(3-nitrophenoxy)benzoic acid(Non-covalent)

KIJ.2: 16 residues within 4Å: Chain A: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 Chain F: D.95 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:N.19, A:L.20, A:Y.31, A:Y.31, F:D.95 Hydrogen bonds: A:N.82, A:N.82, A:I.109, A:S.110, A:R.119, F:D.95 Salt bridges: A:H.108 KIJ.4: 16 residues within 4Å: Chain B: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 Chain G: D.95 12 PLIP interactions: 2 interactions with chain G, 10 interactions with chain B Hydrophobic interactions: G:D.95, B:N.19, B:L.20, B:Y.31, B:Y.31 Hydrogen bonds: G:D.95, B:N.82, B:N.82, B:I.109, B:S.110, B:R.119 Salt bridges: B:H.108 KIJ.6: 16 residues within 4Å: Chain C: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 Chain K: D.95 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain K Hydrophobic interactions: C:N.19, C:L.20, C:Y.31, C:Y.31, K:D.95 Hydrogen bonds: C:N.82, C:N.82, C:I.109, C:S.110, C:R.119 Salt bridges: C:H.108 KIJ.8: 16 residues within 4Å: Chain C: D.95 Chain D: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:N.19, D:L.20, D:Y.31, D:Y.31, C:D.95 Hydrogen bonds: D:N.82, D:N.82, D:I.109, D:S.110, D:R.119 Salt bridges: D:H.108 KIJ.10: 16 residues within 4Å: Chain E: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 Chain J: D.95 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: E:N.19, E:L.20, E:Y.31, E:Y.31, J:D.95 Hydrogen bonds: E:N.82, E:N.82, E:I.109, E:S.110, E:R.119 Salt bridges: E:H.108 KIJ.12: 16 residues within 4Å: Chain F: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 Chain H: D.95 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: F:N.19, F:L.20, F:Y.31, F:Y.31, H:D.95 Hydrogen bonds: F:N.82, F:N.82, F:I.109, F:S.110, F:R.119, H:D.95 Salt bridges: F:H.108 KIJ.14: 16 residues within 4Å: Chain G: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 Chain L: D.95 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain L Hydrophobic interactions: G:N.19, G:L.20, G:Y.31, G:Y.31, L:D.95 Hydrogen bonds: G:N.82, G:N.82, G:I.109, G:S.110, G:R.119 Salt bridges: G:H.108 KIJ.16: 16 residues within 4Å: Chain A: D.95 Chain H: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:N.19, H:L.20, H:Y.31, H:Y.31, A:D.95 Hydrogen bonds: H:N.82, H:N.82, H:I.109, H:S.110, H:R.119 Salt bridges: H:H.108 KIJ.18: 16 residues within 4Å: Chain E: D.95 Chain I: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 12 PLIP interactions: 10 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: I:N.19, I:L.20, I:Y.31, I:Y.31, E:D.95 Hydrogen bonds: I:N.82, I:N.82, I:I.109, I:S.110, I:R.119, E:D.95 Salt bridges: I:H.108 KIJ.20: 16 residues within 4Å: Chain I: D.95 Chain J: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 12 PLIP interactions: 2 interactions with chain I, 10 interactions with chain J Hydrophobic interactions: I:D.95, J:N.19, J:L.20, J:Y.31, J:Y.31 Hydrogen bonds: I:D.95, J:N.82, J:N.82, J:I.109, J:S.110, J:R.119 Salt bridges: J:H.108 KIJ.22: 16 residues within 4Å: Chain D: D.95 Chain K: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 12 PLIP interactions: 10 interactions with chain K, 2 interactions with chain D Hydrophobic interactions: K:N.19, K:L.20, K:Y.31, K:Y.31, D:D.95 Hydrogen bonds: K:N.82, K:N.82, K:I.109, K:S.110, K:R.119, D:D.95 Salt bridges: K:H.108 KIJ.24: 16 residues within 4Å: Chain B: D.95 Chain L: N.19, L.20, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain B Hydrophobic interactions: L:N.19, L:L.20, L:Y.31, L:Y.31, B:D.95 Hydrogen bonds: L:N.82, L:N.82, L:I.109, L:S.110, L:R.119 Salt bridges: L:H.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Howard, N.I. et al., Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase from Mycobacterium tuberculosis. Chemmedchem (2015)

Release Date

2014-05-14

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