SMTL ID : 4ki7.3 (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-24-mer

Ligands

22 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: 8 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: A:V.112, L:D.95 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: 1 interactions with chain E, 10 interactions with chain B Hydrophobic interactions: E:D.95, B:Y.31, B:Y.31, B:V.112 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: 11 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:N.19, F:Y.31, F:Y.31, F:V.112, D:D.95 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: 11 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: K:N.19, K:L.20, K:Y.31, K:Y.31, K:V.112, A:D.95 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 1R2.13: 17 residues within 4Å: Chain N: 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 Q: D.95, E.99 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain Q Hydrophobic interactions: N:L.20, N:Y.31, N:V.112, Q:D.95 Hydrogen bonds: N:N.82, N:I.109, N:S.110, N:R.119 Salt bridges: N:H.108 1R2.14: 15 residues within 4Å: Chain N: D.95 Chain O: 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 O, 1 interactions with chain N Hydrophobic interactions: O:N.19, O:Y.31, O:Y.31, N:D.95 Hydrogen bonds: O:L.20, O:N.82, O:N.82, O:I.109, O:S.110, O:R.119 1R2.15: 15 residues within 4Å: Chain P: 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 S: D.95 10 PLIP interactions: 9 interactions with chain P, 1 interactions with chain S Hydrophobic interactions: P:N.19, P:Y.31, S:D.95 Hydrogen bonds: P:N.82, P:N.82, P:I.109, P:S.110, P:R.119 Salt bridges: P:H.108 pi-Stacking: P:Y.31 1R2.16: 14 residues within 4Å: Chain P: D.95 Chain R: 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: 9 interactions with chain R, 1 interactions with chain P Hydrophobic interactions: R:N.19, R:Y.31, R:Y.31, P:D.95 Hydrogen bonds: R:N.82, R:I.109, R:S.110, R:R.115, R:R.119 Salt bridges: R:H.108 1R2.17: 14 residues within 4Å: Chain R: D.95, E.99 Chain S: 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: 12 interactions with chain S, 1 interactions with chain R Hydrophobic interactions: S:L.20, S:Y.31, R:D.95 Hydrogen bonds: S:Y.31, S:N.82, S:H.88, S:I.109, S:S.110, S:S.110, S:R.119 Salt bridges: S:H.108 pi-Stacking: S:Y.31 pi-Cation interactions: S:R.115 1R2.18: 16 residues within 4Å: Chain T: 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 V: D.95 10 PLIP interactions: 9 interactions with chain T, 1 interactions with chain V Hydrophobic interactions: T:Y.31, T:V.112, V:D.95 Hydrogen bonds: T:N.82, T:I.109, T:S.110, T:S.110, T:R.119 Salt bridges: T:H.108 pi-Stacking: T:Y.31 1R2.19: 15 residues within 4Å: Chain T: D.95 Chain U: 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: 9 interactions with chain U, 1 interactions with chain T Hydrophobic interactions: U:N.19, T:D.95 Hydrogen bonds: U:L.20, U:N.82, U:N.82, U:I.109, U:S.110, U:R.115, U:R.119 Salt bridges: U:H.108 1R2.20: 17 residues within 4Å: Chain U: D.95, E.99 Chain V: 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 V Hydrophobic interactions: V:N.19, V:L.20, V:Y.31, V:V.112 Hydrogen bonds: V:N.82, V:I.109, V:S.110, V:S.110, V:R.119 Salt bridges: V:H.108 pi-Stacking: V:Y.31 1R2.21: 16 residues within 4Å: Chain M: D.95 Chain W: 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 W Hydrophobic interactions: W:L.20, W:L.23, W:Y.31 Hydrogen bonds: W:N.82, W:N.82, W:I.109, W:S.110, W:R.119 Salt bridges: W:H.108 1R2.22: 15 residues within 4Å: Chain W: D.95 Chain X: 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 X, 1 interactions with chain W Hydrophobic interactions: X:N.19, X:Y.31, W:D.95 Hydrogen bonds: X:N.82, X:N.82, X:I.109, X:S.110, X:R.119 Salt bridges: X:H.108 pi-Stacking: X: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: ABCDEFGHIJKLMNOPQRSTUVWX

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

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

3-dehydroquinate dehydratase

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