SMTL ID : 4ki7.2 (2 other biounits)

Design and structural analysis of aromatic inhibitors of type II dehydroquinase from Mycobacterium tuberculosis - compound 41c [3-hydroxy-5-(3-nitrophenoxy)benzoic acid]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-12-mer

Ligands

10 x 1R2: 3-hydroxy-5-(3-nitrophenoxy)benzoic acid(Non-covalent)

1R2.1: 17 residues within 4Å: Chain B: P.18, N.19, L.20, R.22, L.23, E.27, Y.31, N.82, G.84, H.88, H.108, I.109, S.110, V.112, R.119 Chain E: D.95, E.99 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:L.20, B:Y.31, B:V.112, E:D.95 Hydrogen bonds: B:N.82, B:I.109, B:S.110, B:R.119 Salt bridges: B:H.108 1R2.2: 15 residues within 4Å: Chain B: D.95 Chain C: P.18, N.19, L.20, R.22, L.23, R.26, Y.31, N.82, G.84, H.88, H.108, I.109, S.110, R.119 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:N.19, C:Y.31, C:Y.31, B:D.95 Hydrogen bonds: C:L.20, C:N.82, C:N.82, C:I.109, C:S.110, C:R.119 1R2.3: 15 residues within 4Å: Chain D: P.18, N.19, L.20, R.22, L.23, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 Chain G: D.95 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:N.19, D:Y.31, G:D.95 Hydrogen bonds: D:N.82, D:N.82, D:I.109, D:S.110, D:R.119 Salt bridges: D:H.108 pi-Stacking: D:Y.31 1R2.4: 14 residues within 4Å: Chain D: D.95 Chain F: N.19, L.23, R.26, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.115, R.119 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain F Hydrophobic interactions: D:D.95, F:N.19, F:Y.31, F:Y.31 Hydrogen bonds: F:N.82, F:I.109, F:S.110, F:R.115, F:R.119 Salt bridges: F:H.108 1R2.5: 14 residues within 4Å: Chain F: D.95, E.99 Chain G: N.19, L.20, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 13 PLIP interactions: 1 interactions with chain F, 12 interactions with chain G Hydrophobic interactions: F:D.95, G:L.20, G:Y.31 Hydrogen bonds: G:Y.31, G:N.82, G:H.88, G:I.109, G:S.110, G:S.110, G:R.119 Salt bridges: G:H.108 pi-Stacking: G:Y.31 pi-Cation interactions: G:R.115 1R2.6: 16 residues within 4Å: Chain H: P.18, N.19, L.20, L.23, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, V.112, R.115, R.119 Chain J: D.95 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain J Hydrophobic interactions: H:Y.31, H:V.112, J:D.95 Hydrogen bonds: H:N.82, H:I.109, H:S.110, H:S.110, H:R.119 Salt bridges: H:H.108 pi-Stacking: H:Y.31 1R2.7: 15 residues within 4Å: Chain H: D.95 Chain I: P.18, N.19, L.20, L.23, R.26, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 10 PLIP interactions: 1 interactions with chain H, 9 interactions with chain I Hydrophobic interactions: H:D.95, I:N.19 Hydrogen bonds: I:L.20, I:N.82, I:N.82, I:I.109, I:S.110, I:R.115, I:R.119 Salt bridges: I:H.108 1R2.8: 17 residues within 4Å: Chain I: D.95, E.99 Chain J: P.18, N.19, L.20, R.22, R.26, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, V.112, R.119 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:N.19, J:L.20, J:Y.31, J:V.112 Hydrogen bonds: J:N.82, J:I.109, J:S.110, J:S.110, J:R.119 Salt bridges: J:H.108 pi-Stacking: J:Y.31 1R2.9: 16 residues within 4Å: Chain A: D.95 Chain K: P.18, N.19, L.20, R.22, L.23, R.26, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:L.20, K:L.23, K:Y.31 Hydrogen bonds: K:N.82, K:N.82, K:I.109, K:S.110, K:R.119 Salt bridges: K:H.108 1R2.10: 15 residues within 4Å: Chain K: D.95 Chain L: P.18, N.19, L.20, L.23, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.119 10 PLIP interactions: 9 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: L:N.19, L:Y.31, K:D.95 Hydrogen bonds: L:N.82, L:N.82, L:I.109, L:S.110, L:R.119 Salt bridges: L:H.108 pi-Stacking: L:Y.31

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
M

B
N

C
O

D
P

E
Q

F
R

G
S

H
T

I
U

J
V

K
W

L
X

3-dehydroquinate dehydratase

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