SMTL ID : 2cjf.1

TYPE II DEHYDROQUINASE INHIBITOR COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-12-mer

Ligands

12 x RP4: (1S,4S,5S)-1,4,5-TRIHYDROXY-3-[3-(PHENYLTHIO)PHENYL]CYCLOHEX-2-ENE-1-CARBOXYLIC ACID(Non-covalent)

RP4.1: 17 residues within 4Å: Chain A: 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 B: D.93, T.97 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:N.17, A:L.20, A:L.21, A:R.24, A:Y.29, A:A.82, A:I.111, B:D.93, B:T.97 Hydrogen bonds: A:N.80, A:N.80, A:H.86, A:H.107, A:I.108, A:S.109, A:R.118, B:D.93, B:D.93 Water bridges: A:A.83 Salt bridges: A:H.107 pi-Stacking: A:Y.29 RP4.3: 18 residues within 4Å: Chain B: 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 C: D.93, T.97 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.21, B:R.24, B:Y.29, B:I.111, C:D.93, C:T.97 Hydrogen bonds: B:N.80, B:N.80, B:A.82, B:H.86, B:H.107, B:I.108, B:S.109, B:R.118 Water bridges: B:A.83 RP4.7: 16 residues within 4Å: Chain A: D.93, T.97 Chain C: 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 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:N.17, C:L.21, C:R.24, C:Y.29, C:Y.29, C:Y.29, A:D.93, A:T.97 Hydrogen bonds: C:N.80, C:N.80, C:A.82, C:H.107, C:I.108, C:S.109, C:R.118 Water bridges: A:D.93 RP4.8: 16 residues within 4Å: Chain D: 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 E: D.93 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:N.17, D:L.20, D:R.24, D:Y.29, D:I.111, E:D.93 Hydrogen bonds: D:N.80, D:N.80, D:A.82, D:H.86, D:H.107, D:I.108, D:S.109, D:R.118 Water bridges: D:A.83 RP4.11: 19 residues within 4Å: Chain E: 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.114, R.118 Chain F: D.93, T.97 17 PLIP interactions: 14 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:L.20, E:L.21, E:R.24, E:I.111, F:D.93, F:T.97 Hydrogen bonds: E:N.80, E:N.80, E:A.82, E:H.86, E:H.107, E:I.108, E:S.109, E:R.114, E:R.118, F:D.93 Water bridges: E:A.83 RP4.13: 19 residues within 4Å: Chain D: D.93, T.97 Chain F: N.17, L.18, L.20, L.21, G.22, Q.23, 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 F, 1 interactions with chain D Hydrophobic interactions: F:N.17, F:L.20, F:L.21, F:R.24, F:Y.29, F:Y.29, F:Y.29, F:I.111, D:T.97 Hydrogen bonds: F:N.80, F:N.80, F:H.86, F:H.107, F:I.108, F:S.109, F:R.118 Water bridges: F:A.83 Salt bridges: F:H.107 RP4.16: 17 residues within 4Å: Chain G: 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, T.97 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:L.20, G:L.21, G:R.24, G:Y.29, G:I.111, H:D.93, H:T.97 Hydrogen bonds: G:N.80, G:N.80, G:A.82, G:H.86, G:H.107, G:I.108, G:S.109, G:R.118 Water bridges: G:A.83 Salt bridges: G:H.107 RP4.19: 17 residues within 4Å: Chain H: 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 I: D.93 17 PLIP interactions: 16 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:N.17, H:L.21, H:R.24, H:Y.29, H:Y.29, H:A.82, H:I.111, I:D.93 Hydrogen bonds: H:Y.29, H:N.80, H:N.80, H:H.86, H:H.107, H:I.108, H:S.109, H:R.118 Water bridges: H:A.83 RP4.21: 16 residues within 4Å: Chain G: D.93 Chain I: 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 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:N.17, I:L.20, I:L.21, I:R.24, I:Y.29, I:I.111, G:D.93 Hydrogen bonds: I:N.80, I:A.82, I:H.86, I:H.107, I:I.108, I:S.109, I:S.109, I:R.118 Water bridges: I:A.83 RP4.23: 17 residues within 4Å: Chain J: 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, T.97 18 PLIP interactions: 15 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: J:N.17, J:L.20, J:L.21, J:R.24, J:Y.29, J:I.111, K:D.93, K:T.97 Hydrogen bonds: J:N.80, J:N.80, J:A.82, J:H.86, J:H.107, J:I.108, J:S.109, J:R.118 Salt bridges: J:H.107 Water bridges: K:D.93 RP4.28: 17 residues within 4Å: Chain K: 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 L: D.93 19 PLIP interactions: 18 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:N.17, K:L.20, K:L.21, K:R.24, K:Y.29, K:Y.29, K:Y.29, K:I.111, L:D.93 Hydrogen bonds: K:N.80, K:N.80, K:A.82, K:H.86, K:H.107, K:I.108, K:S.109, K:R.118 Water bridges: K:A.83 Salt bridges: K:H.107 RP4.31: 17 residues within 4Å: Chain J: D.93 Chain L: 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 17 PLIP interactions: 16 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: L:L.20, L:L.21, L:R.24, L:Y.29, L:A.82, L:I.111, J:D.93 Hydrogen bonds: L:N.80, L:N.80, L:A.82, L:H.86, L:H.107, L:I.108, L:S.109, L:R.114, L:R.118 Water bridges: L:A.83

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: H.112, H.119 Chain D: H.119, H.120, S.121 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.120, D:S.121, A:H.112 Water bridges: D:S.124, A:H.112 GOL.6: 6 residues within 4Å: Chain B: H.112, H.119 Chain G: H.120, S.121, S.124 Ligands: GOL.18 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B Hydrogen bonds: G:S.121, B:H.112 GOL.10: 5 residues within 4Å: Chain A: H.119, H.120, S.121 Chain D: H.112, H.119 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.121, A:S.121, D:H.112, D:H.119 Water bridges: A:S.124 GOL.12: 5 residues within 4Å: Chain E: H.112, H.119 Chain L: H.120, S.121, S.124 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain L Water bridges: E:H.112 Hydrogen bonds: L:S.121, L:S.121 GOL.15: 5 residues within 4Å: Chain F: H.112, H.119 Chain H: H.120, S.121 Ligands: GOL.20 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:S.121, H:S.121, F:H.112, F:H.119 GOL.18: 7 residues within 4Å: Chain B: H.119, H.120, S.121, S.124 Chain G: H.112, H.119 Ligands: GOL.6 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain B Water bridges: G:H.112, G:H.119, B:S.124 Hydrogen bonds: B:S.121, B:S.121 GOL.20: 6 residues within 4Å: Chain F: H.119, H.120, S.121 Chain H: H.112, H.119 Ligands: GOL.15 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:S.121, F:S.121, H:H.112 Water bridges: F:S.124, H:H.119 GOL.26: 8 residues within 4Å: Chain C: H.112, H.119, H.120 Chain J: H.119, H.120, S.121, S.124 Ligands: GOL.27 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain J Water bridges: C:H.112, C:H.112, C:H.119, J:H.119, J:H.120 Hydrogen bonds: J:S.121 GOL.27: 6 residues within 4Å: Chain C: H.119, H.120, S.121 Chain J: H.112, H.119 Ligands: GOL.26 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain J Hydrogen bonds: C:H.119, C:H.120, C:S.121, C:S.121, J:H.119 GOL.29: 6 residues within 4Å: Chain I: H.120, S.121, S.124, Q.125 Chain K: H.112, H.119 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain K Hydrogen bonds: I:S.121, I:S.121, I:Q.125, K:H.112 Water bridges: K:H.119 GOL.30: 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, K:S.121, K:S.121 Water bridges: I:H.119, K:S.124 GOL.32: 5 residues within 4Å: Chain E: H.120, S.121, S.124 Chain L: H.112, H.119 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain E Hydrogen bonds: L:H.112, E:S.121, E:S.121, E:S.124 Water bridges: L:H.119

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

PO4.4: 9 residues within 4Å: Chain A: H.59, E.60, G.61 Chain B: H.59, E.60, G.61 Chain C: H.59, E.60, G.61 13 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C, 6 interactions with chain B Hydrogen bonds: A:E.60, A:G.61, C:E.60, C:G.61, B:G.61 Water bridges: A:E.60, B:E.60, B:E.60, B:E.60, B:E.60 Salt bridges: A:H.59, C:H.59, B:H.59 PO4.14: 8 residues within 4Å: Chain D: H.59, G.61 Chain E: H.59, E.60, G.61 Chain F: H.59, E.60, G.61 12 PLIP interactions: 3 interactions with chain E, 5 interactions with chain F, 4 interactions with chain D Hydrogen bonds: E:G.61, F:E.60, F:G.61, D:H.59, D:G.61 Water bridges: E:E.60, F:E.60, F:E.60, D:E.60, D:E.60 Salt bridges: E:H.59, F:H.59 PO4.17: 9 residues within 4Å: Chain G: H.59, E.60, G.61 Chain H: H.59, E.60, G.61 Chain I: H.59, E.60, G.61 12 PLIP interactions: 3 interactions with chain G, 5 interactions with chain H, 4 interactions with chain I Hydrogen bonds: G:E.60, G:G.61, H:E.60, H:G.61, I:G.61 Salt bridges: G:H.59, H:H.59, I:H.59 Water bridges: H:E.60, H:E.60, I:E.60, I:E.60 PO4.24: 8 residues within 4Å: Chain J: H.59, E.60, G.61 Chain K: H.59, E.60, G.61 Chain L: H.59, G.61 12 PLIP interactions: 3 interactions with chain J, 5 interactions with chain L, 4 interactions with chain K Hydrogen bonds: J:E.60, J:G.61, L:G.61, K:E.60, K:G.61 Salt bridges: J:H.59, L:H.59, K:H.59 Water bridges: L:E.60, L:E.60, L:E.60, K:E.60

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

TRS.5: 11 residues within 4Å: Chain A: E.60, Y.84, T.87, S.88 Chain B: E.60, Y.84, T.87, S.88 Chain C: E.60, T.87, S.88 8 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:T.87, B:T.87, C:E.60, C:T.87, A:T.87 Water bridges: B:E.60, C:V.89, A:T.87 TRS.9: 11 residues within 4Å: Chain D: E.60, Y.84, T.87, S.88 Chain E: E.60, T.87, S.88 Chain F: E.60, Y.84, T.87, S.88 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: D:E.60, D:T.87, D:S.88, E:S.88, F:T.87, F:T.87 TRS.22: 10 residues within 4Å: Chain G: E.60, T.87, S.88 Chain H: E.60, T.87, S.88 Chain I: E.60, Y.84, T.87, S.88 7 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G, 2 interactions with chain I Hydrogen bonds: H:E.60, H:T.87, H:T.87, G:T.87, I:T.87, I:S.88 Water bridges: H:V.89 TRS.25: 11 residues within 4Å: Chain J: E.60, Y.84, T.87, S.88 Chain K: E.60, Y.84, T.87, S.88 Chain L: E.60, T.87, S.88 8 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L, 3 interactions with chain J Hydrogen bonds: K:T.87, L:E.60, L:T.87, L:T.87, J:T.87 Water bridges: K:V.89, J:Y.84, J:V.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Payne, R.J. et al., Design, synthesis, and structural studies on potent biaryl inhibitors of type II dehydroquinases. Chemmedchem (2007)

Release Date

2007-04-10

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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