SMTL ID : 2bt4.1

Type II Dehydroquinase inhibitor complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-12-mer

Ligands

12 x CA2: (1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID(Non-covalent)

CA2.1: 17 residues within 4Å: Chain A: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, R.118 Chain B: D.93, T.97 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.18, A:L.20, A:L.21, A:R.24, B:T.97 Hydrogen bonds: A:N.80, A:N.80, A:A.82, A:H.86, A:I.108, A:S.109, A:S.109, A:R.118, B:D.93 Salt bridges: A:H.107 pi-Stacking: A:Y.29 Water bridges: B:D.93 CA2.5: 17 residues within 4Å: Chain B: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain C: D.93 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.18, B:L.20, B:L.21, B:R.24, B:Y.29, B:Y.29, B:I.111 Hydrogen bonds: B:N.80, B:N.80, B:A.82, B:H.107, B:I.108, B:S.109, B:S.109, B:R.118, C:D.93 Water bridges: B:A.83 Salt bridges: B:H.107 CA2.7: 17 residues within 4Å: Chain A: D.93 Chain C: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.18, C:L.20, C:L.21, C:R.24, C:Y.29, C:Y.29, C:I.111 Hydrogen bonds: C:N.80, C:N.80, C:A.82, C:I.108, C:S.109, C:S.109, C:R.118, A:D.93 Water bridges: C:A.83 Salt bridges: C:H.107 pi-Stacking: C:Y.29 CA2.9: 17 residues within 4Å: Chain D: P.16, N.17, L.20, L.21, G.22, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain E: D.93 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.20, D:L.21, D:R.24, D:Y.29, D:I.111 Hydrogen bonds: D:N.80, D:N.80, D:A.82, D:H.86, D:H.107, D:I.108, D:S.109, D:S.109, D:R.118, E:D.93 Water bridges: D:A.83 pi-Stacking: D:Y.29 CA2.12: 18 residues within 4Å: Chain E: P.16, N.17, L.18, L.20, L.21, G.22, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain F: D.93 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.18, E:L.20, E:L.21, E:R.24, E:Y.29, E:I.111 Hydrogen bonds: E:N.80, E:N.80, E:A.82, E:I.108, E:S.109, E:S.109, E:R.118, F:D.93 Salt bridges: E:H.107 Water bridges: F:D.93 CA2.15: 18 residues within 4Å: Chain D: D.93 Chain F: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.114, R.118 19 PLIP interactions: 17 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.18, F:L.20, F:L.21, F:R.24, F:Y.29, F:I.111 Hydrogen bonds: F:N.80, F:N.80, F:A.82, F:H.86, F:H.107, F:I.108, F:S.109, F:S.109, F:R.114, F:R.118, D:D.93 pi-Stacking: F:Y.29 Water bridges: D:D.93 CA2.18: 17 residues within 4Å: Chain G: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain H: D.93 19 PLIP interactions: 18 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:L.18, G:L.20, G:L.21, G:R.24, G:Y.29, G:I.111 Hydrogen bonds: G:N.80, G:N.80, G:A.82, G:H.86, G:H.107, G:I.108, G:S.109, G:S.109, G:R.118, H:D.93 Water bridges: G:A.83 Salt bridges: G:H.107 pi-Stacking: G:Y.29 CA2.20: 17 residues within 4Å: Chain H: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain I: D.93 16 PLIP interactions: 15 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:L.20, H:L.21, H:R.24, H:I.111 Hydrogen bonds: H:N.80, H:N.80, H:A.82, H:H.86, H:I.108, H:S.109, H:S.109, H:R.114, H:R.118, I:D.93 Water bridges: H:A.83 pi-Stacking: H:Y.29 CA2.23: 18 residues within 4Å: Chain G: D.93 Chain I: P.16, N.17, L.18, L.20, L.21, G.22, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 18 PLIP interactions: 17 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:L.20, I:L.21, I:R.24, I:Y.29, I:Y.29, I:I.111 Hydrogen bonds: I:N.80, I:N.80, I:A.82, I:I.108, I:S.109, I:S.109, I:R.118, I:R.118, G:D.93 Water bridges: I:A.83 Salt bridges: I:H.107 pi-Stacking: I:Y.29 CA2.26: 17 residues within 4Å: Chain J: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain K: D.93 18 PLIP interactions: 17 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:L.18, J:L.20, J:L.21, J:R.24, J:Y.29, J:Y.29, J:I.111 Hydrogen bonds: J:N.80, J:N.80, J:A.82, J:H.107, J:I.108, J:S.109, J:S.109, J:R.118, K:D.93 Water bridges: J:A.83 Salt bridges: J:H.107 CA2.28: 17 residues within 4Å: Chain K: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain L: D.93 19 PLIP interactions: 18 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:L.18, K:L.20, K:L.21, K:R.24, K:Y.29, K:I.111 Hydrogen bonds: K:N.80, K:N.80, K:A.82, K:H.86, K:H.107, K:I.108, K:S.109, K:S.109, K:R.118, L:D.93 Water bridges: K:A.83 Salt bridges: K:H.107 pi-Stacking: K:Y.29 CA2.30: 17 residues within 4Å: Chain J: D.93 Chain L: P.16, N.17, L.18, L.20, L.21, R.24, Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 18 PLIP interactions: 16 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:L.18, L:L.20, L:L.21, L:R.24, L:Y.29, L:I.111 Hydrogen bonds: L:N.80, L:N.80, L:A.82, L:H.86, L:I.108, L:S.109, L:S.109, L:R.118, J:D.93 Salt bridges: L:H.107 pi-Stacking: L:Y.29 Water bridges: J:D.93

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: H.59, E.60, G.61 Chain B: H.59, G.61 Chain C: H.59, E.60, G.61 10 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:G.61, B:G.61, C:G.61 Water bridges: A:E.60, B:H.59, B:E.60, C:E.60 Salt bridges: A:H.59, B:H.59, C:H.59 PO4.10: 8 residues within 4Å: Chain D: H.59, E.60, G.61 Chain E: H.59, G.61 Chain F: H.59, E.60, G.61 10 PLIP interactions: 4 interactions with chain F, 3 interactions with chain E, 3 interactions with chain D Hydrogen bonds: F:G.61, E:G.61, D:G.61 Water bridges: F:E.60, F:E.60, E:E.60, D:E.60 Salt bridges: F:H.59, E:H.59, D:H.59 PO4.24: 8 residues within 4Å: Chain G: H.59, E.60, G.61 Chain H: H.59, E.60, G.61 Chain I: H.59, G.61 12 PLIP interactions: 3 interactions with chain G, 3 interactions with chain I, 6 interactions with chain H Hydrogen bonds: G:G.61, I:G.61, H:G.61 Water bridges: G:E.60, I:E.60, H:H.59, H:H.59, H:E.60, H:E.60 Salt bridges: G:H.59, I:H.59, H:H.59 PO4.31: 9 residues within 4Å: Chain J: H.59, E.60, G.61 Chain K: H.59, E.60, G.61 Chain L: H.59, E.60, G.61 10 PLIP interactions: 3 interactions with chain J, 4 interactions with chain K, 3 interactions with chain L Hydrogen bonds: J:G.61, K:G.61, L:E.60, L:G.61 Water bridges: J:E.60, K:E.60, K:E.60 Salt bridges: J:H.59, K:H.59, L:H.59

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 10 residues within 4Å: Chain A: E.60, Y.84, T.87, S.88 Chain B: E.60, T.87, S.88 Chain C: E.60, T.87, S.88 10 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: C:E.60, C:T.87, C:S.88, A:T.87, B:T.87, B:T.87 Water bridges: C:V.89, A:V.89, B:E.60, B:V.89 TRS.16: 10 residues within 4Å: Chain D: E.60, T.87, S.88 Chain E: E.60, T.87, S.88 Chain F: E.60, Y.84, T.87, S.88 8 PLIP interactions: 2 interactions with chain E, 5 interactions with chain D, 1 interactions with chain F Hydrogen bonds: E:T.87, D:E.60, D:T.87, D:T.87, F:T.87 Water bridges: E:V.89, D:E.60, D:V.89 TRS.21: 9 residues within 4Å: Chain G: E.60, T.87, S.88 Chain H: E.60, T.87, S.88 Chain I: E.60, T.87, S.88 10 PLIP interactions: 3 interactions with chain I, 4 interactions with chain G, 3 interactions with chain H Hydrogen bonds: I:E.60, I:T.87, G:T.87, G:S.88, H:T.87, H:T.87 Water bridges: I:V.89, G:E.60, G:V.89, H:V.89 TRS.32: 10 residues within 4Å: Chain J: E.60, T.87, S.88 Chain K: E.60, T.87, S.88 Chain L: E.60, Y.84, T.87, S.88 9 PLIP interactions: 4 interactions with chain K, 3 interactions with chain J, 2 interactions with chain L Hydrogen bonds: K:T.87, K:T.87, J:E.60, J:T.87, L:T.87 Water bridges: K:E.60, K:V.89, J:V.89, L:V.89

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.119, H.120, S.121 Chain D: H.112, H.119 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Water bridges: D:H.112, D:H.119, A:S.124 Hydrogen bonds: A:S.121, A:S.121 GOL.6: 6 residues within 4Å: Chain B: H.119, H.120, S.121 Chain G: H.112, H.119, H.120 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:H.112, B:S.121, B:S.121 Water bridges: G:H.119, G:H.120 GOL.8: 5 residues within 4Å: Chain C: H.119, H.120, S.121 Chain J: H.112, H.119 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain J Hydrogen bonds: C:H.120, C:S.121, J:H.112 Water bridges: C:S.124, C:Q.125, J:H.112 GOL.11: 5 residues within 4Å: Chain A: H.112, H.119 Chain D: H.119, H.120, S.121 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:H.112, A:H.119, D:H.120, D:S.121 Water bridges: D:S.124 GOL.13: 5 residues within 4Å: Chain E: H.119, H.120, S.121 Chain L: H.112, H.119 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.121, E:S.121 Water bridges: E:S.124 GOL.14: 4 residues within 4Å: Chain E: H.112, H.119 Chain L: H.120, S.121 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:H.120, L:S.121, L:S.121 Water bridges: L:S.124 GOL.17: 5 residues within 4Å: Chain F: H.119, H.120, S.121 Chain H: H.112, H.119 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:S.121, H:H.112, H:H.119 Water bridges: F:H.112, F:S.124, F:S.124 GOL.19: 6 residues within 4Å: Chain B: H.112, H.119 Chain G: H.112, H.119, H.120, S.121 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:S.121, B:H.112 Water bridges: G:H.112, G:S.124, B:H.112 GOL.22: 5 residues within 4Å: Chain F: H.112, H.119 Chain H: H.119, H.120, S.121 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain H Hydrogen bonds: F:H.112, H:S.121, H:S.121 Water bridges: H:S.124 GOL.25: 5 residues within 4Å: Chain I: H.119, H.120, S.121 Chain K: H.112, H.119 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K Hydrogen bonds: I:H.119, I:S.121, K:H.112 GOL.27: 5 residues within 4Å: Chain C: H.112, H.119 Chain J: H.119, H.120, S.121 7 PLIP interactions: 4 interactions with chain J, 3 interactions with chain C Hydrogen bonds: J:S.121, C:H.112, C:H.119 Water bridges: J:H.119, J:Q.125, J:Q.125, C:H.112 GOL.29: 6 residues within 4Å: Chain I: H.112, H.119 Chain K: H.119, H.120, S.121, S.124 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain K Hydrogen bonds: I:H.112, I:H.119, K:S.121, K:S.124, K:S.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toscano, M.D. et al., Rational Design of New Bifunctional Inhibitors of Type II Dehydroquinase. Org.Biomol.Chem. (2005)

Release Date

2006-02-13

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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