SMTL ID : 4kiu.1 (1 other biounit)

Design and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from Mycobacterium tuberculosis - compound 49d [5-[(3-nitrobenzyl)oxy]benzene-1,3-dicarboxylic acid]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

12 x KIU: 5-[(3-nitrobenzyl)oxy]benzene-1,3-dicarboxylic acid(Non-covalent)(Covalent)

KIU.1: 17 residues within 4Å: Chain A: P.18, N.19, L.20, R.22, L.23, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, V.112, R.119 Chain L: D.95 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain L Hydrophobic interactions: A:N.19, A:V.112, L:D.95 Hydrogen bonds: A:N.82, A:N.82, A:G.85, A:I.109, A:S.110, L:D.95, L:D.95 Salt bridges: A:H.88, A:H.108, A:R.115, A:R.119 pi-Stacking: A:Y.31 KIU.2: 19 residues within 4Å: Chain B: P.18, N.19, R.22, L.23, R.26, E.27, 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, E.99 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:N.19, B:Y.31 Hydrogen bonds: B:R.22, B:N.82, B:I.109, B:S.110, B:S.110, E:D.95 Water bridges: B:N.19 Salt bridges: B:H.88, B:H.108, B:R.115, B:R.119 pi-Stacking: B:Y.31 KIU.3: 18 residues within 4Å: Chain B: D.95 Chain C: P.18, N.19, L.20, R.22, 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 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:N.19, C:L.20, C:Y.31, C:V.112, B:D.95 Hydrogen bonds: C:E.27, C:N.82, C:G.85, C:I.109, C:S.110, C:S.110 Water bridges: C:N.19 Salt bridges: C:H.88, C:H.108, C:R.115, C:R.119 pi-Stacking: C:Y.31 KIU.4: 18 residues within 4Å: Chain D: P.18, N.19, L.20, R.22, L.23, G.24, R.26, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, R.115, R.119 Chain G: D.95 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:N.19, D:Y.31 Hydrogen bonds: D:R.26, D:N.82, D:G.84, D:G.85, D:I.109, D:S.110, D:S.110 Salt bridges: D:H.88, D:H.108, D:R.115, D:R.119 pi-Stacking: D:Y.31 KIU.5: 17 residues within 4Å: Chain C: D.95 Chain E: 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 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:N.19, E:Y.31, C:D.95 Hydrogen bonds: E:N.82, E:N.82, E:G.85, E:I.109, E:S.110 Salt bridges: E:H.88, E:H.108, E:H.108, E:R.115, E:R.119 pi-Stacking: E:Y.31 Water bridges: C:D.95 KIU.6: 19 residues within 4Å: Chain D: V.91, 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.115, R.119 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:N.19, F:L.20, F:Y.31, F:Y.31, F:V.112, D:D.95 Hydrogen bonds: F:N.82, F:N.82, F:G.85, F:I.109, F:S.110 Salt bridges: F:H.88, F:H.108, F:R.115, F:R.119 KIU.7: 18 residues within 4Å: Chain F: V.91, D.95, E.99 Chain G: 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 14 PLIP interactions: 13 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:N.19, G:L.20, G:Y.31 Hydrogen bonds: G:R.22, G:N.82, G:N.82, G:I.109, G:S.110, F:D.95 Salt bridges: G:H.88, G:H.108, G:R.115, G:R.119 pi-Stacking: G:Y.31 KIU.8: 18 residues within 4Å: Chain H: P.18, N.19, L.20, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, V.112, R.119 Chain J: D.95, E.99 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:N.19, H:L.20, H:L.23, H:Y.31 Hydrogen bonds: H:R.26, H:N.82, H:I.109, H:S.110, H:S.110 Salt bridges: H:H.88, H:H.108, H:R.115, H:R.119 pi-Stacking: H:Y.31 KIU.9: 18 residues within 4Å: Chain H: D.95 Chain I: 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 17 PLIP interactions: 15 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: I:N.19, I:L.20, I:Y.31, I:V.112, H:D.95 Hydrogen bonds: I:N.82, I:G.85, I:I.109, I:S.110, I:S.110, H:D.95 Water bridges: I:N.19 Salt bridges: I:H.88, I:H.108, I:R.115, I:R.119 pi-Stacking: I:Y.31 KIU.10: 19 residues within 4Å: Chain I: V.91, D.95, E.99 Chain J: P.18, N.19, R.22, L.23, R.26, E.27, Y.31, N.82, G.84, G.85, H.88, H.108, I.109, S.110, V.112, R.119 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:N.19, J:L.23, J:Y.31 Hydrogen bonds: J:R.22, J:N.82, J:N.82, J:I.109, J:S.110 Water bridges: J:N.19 Salt bridges: J:H.88, J:H.108, J:R.115, J:R.119 pi-Stacking: J:Y.31 KIU.11: 17 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.119 15 PLIP interactions: 14 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: K:N.19, K:L.20, K:Y.31, K:V.112, A:D.95 Hydrogen bonds: K:N.82, K:N.82, K:G.85, K:I.109, K:S.110 Salt bridges: K:H.88, K:H.108, K:R.115, K:R.119 pi-Stacking: K:Y.31 KIU.12: 18 residues within 4Å: Chain K: D.95 Chain L: 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 15 PLIP interactions: 13 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:N.19, L:Y.31, L:V.112, K:D.95 Hydrogen bonds: L:N.82, L:I.109, L:S.110, L:S.110, K:D.95 Water bridges: L:G.85 Salt bridges: L:H.88, L:H.108, 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

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