SMTL ID : 3sz9.5 (5 other biounits)

Crystal structure of human ALDH2 modified with the beta-elimination product of Aldi-3; 1-(4-ethylbenzene)prop-2-en-1-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.40, A:D.109 NA.7: 4 residues within 4Å: Chain B: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.40, B:D.109 NA.13: 4 residues within 4Å: Chain C: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.40, C:V.40 NA.23: 4 residues within 4Å: Chain D: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.40, D:Q.196

9 x GAI: GUANIDINE(Non-covalent)

GAI.2: 6 residues within 4Å: Chain A: F.70, E.157, P.158, V.159 Chain B: Q.447, Y.468 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.158, A:P.158, B:Y.468 Water bridges: A:R.77 Salt bridges: A:E.157 GAI.3: 5 residues within 4Å: Chain A: I.146, D.147, F.150 Chain B: V.458, F.459 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.459, B:F.459, A:D.147 Water bridges: A:D.147 GAI.8: 6 residues within 4Å: Chain A: Q.447, Y.468 Chain B: F.70, E.157, P.158, V.159 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.158, A:Y.468 Water bridges: B:R.77, B:E.157, B:V.159, B:V.159 Salt bridges: B:E.157 GAI.9: 5 residues within 4Å: Chain A: V.458, F.459 Chain B: I.146, D.147, F.150 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.147, B:D.147, B:D.147, A:F.459 Water bridges: A:F.459 GAI.14: 4 residues within 4Å: Chain C: E.157, P.158, V.159 Chain D: Y.468 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Water bridges: D:Q.447, C:R.77, C:E.157, C:E.487 Hydrogen bonds: C:P.158, C:P.158 Salt bridges: C:E.157 GAI.15: 5 residues within 4Å: Chain C: I.146, D.147, F.150 Chain D: V.458, F.459 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.147, C:D.147, D:F.459, D:F.459 Water bridges: C:D.147 GAI.16: 6 residues within 4Å: Chain C: F.350, I.373, A.375, D.376, G.378 Ligands: EDO.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.378, C:G.378 Water bridges: C:A.375, C:G.378 GAI.22: 5 residues within 4Å: Chain C: V.458, F.459 Chain D: I.146, D.147, F.150 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.147, D:D.147, C:F.459 Water bridges: D:D.147, D:D.147, D:D.147 GAI.24: 4 residues within 4Å: Chain C: Y.468 Chain D: E.157, P.158, V.159 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Y.468, D:P.158, D:P.158 Water bridges: D:R.77, D:E.157 Salt bridges: D:E.157

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443 Chain D: F.151 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.155, B:S.443 Water bridges: B:S.443 EDO.5: 4 residues within 4Å: Chain A: F.18, D.98, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.98, A:Y.203 EDO.10: 7 residues within 4Å: Chain B: Q.14, N.41, T.44, E.46, V.47, I.48, L.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.41 EDO.12: 5 residues within 4Å: Chain A: N.440, S.443 Chain B: Y.153, R.155 Chain C: F.151 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.153, B:R.155, A:S.443 EDO.17: 5 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.443, C:R.155 EDO.18: 6 residues within 4Å: Chain C: N.41, T.44, E.46, V.47, I.48, L.108 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.41 EDO.19: 3 residues within 4Å: Chain C: F.18, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.97, C:Y.101 EDO.20: 3 residues within 4Å: Chain C: E.347, F.350 Ligands: GAI.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.347 EDO.25: 4 residues within 4Å: Chain A: F.151 Chain C: S.443 Chain D: Y.153, R.155 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.443, D:R.155 Water bridges: D:Y.153

4 x I3E: 1-(4-ethylphenyl)propan-1-one(Covalent)

I3E.6: 11 residues within 4Å: Chain A: M.124, N.169, F.170, L.173, W.177, F.296, C.301, C.302, D.457, F.459, F.465 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.173, A:W.177, A:F.296, A:D.457, A:F.459, A:F.459, A:F.459, A:F.465 Hydrogen bonds: A:N.169, A:C.302 pi-Stacking: A:F.170 I3E.11: 10 residues within 4Å: Chain B: M.124, N.169, F.170, F.296, C.301, C.302, C.303, D.457, F.459, F.465 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.296, B:D.457, B:F.459, B:F.459, B:F.465 Hydrogen bonds: B:N.169, B:C.302 pi-Stacking: B:F.170 I3E.21: 12 residues within 4Å: Chain C: M.124, N.169, F.170, L.173, W.177, F.296, C.301, C.302, C.303, D.457, F.459, F.465 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.173, C:W.177, C:F.296, C:D.457, C:F.459, C:F.459, C:F.465 Hydrogen bonds: C:N.169, C:C.302, C:C.303 pi-Stacking: C:F.170 I3E.26: 12 residues within 4Å: Chain D: M.124, N.169, F.170, L.173, W.177, F.296, C.301, C.302, C.303, D.457, F.459, F.465 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.173, D:W.177, D:F.296, D:F.459, D:F.459, D:F.465 Hydrogen bonds: D:N.169, D:C.302 pi-Stacking: D:F.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khanna, M. et al., Discovery of a novel class of covalent inhibitor for aldehyde dehydrogenases. J.Biol.Chem. (2011)

Release Date

2011-11-02

Peptides

Aldehyde dehydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aldehyde dehydrogenase, mitochondrial

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