SMTL ID : 4ki7.1 (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

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-12-mer

Ligands

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

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

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

3-dehydroquinate dehydratase

Related Entries With Identical Sequence