SMTL ID : 3sz9.6 (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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.40, A:Q.196 Water bridges: A:T.39 NA.8: 4 residues within 4Å: Chain B: T.39, V.40, D.109, Q.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.40, B:D.109 Water bridges: B:T.39 NA.18: 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:D.109

9 x GAI: GUANIDINE(Non-covalent)

GAI.2: 6 residues within 4Å: Chain A: F.70, E.157, P.158, V.159, G.160 Chain B: Y.468 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.158, B:Y.468 Water bridges: A:R.77, A:E.157, A:V.159, B:Y.468 Salt bridges: A:E.157 GAI.6: 6 residues within 4Å: Chain A: V.458, F.459 Chain B: I.146, D.147, G.148, F.150 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.147, B:D.147, A:F.459, A:F.459, A:F.459 GAI.7: 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.9: 6 residues within 4Å: Chain A: Q.447, Y.468 Chain B: F.70, E.157, P.158, V.159 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:Q.447, B:R.77, B:E.157, B:V.159 Hydrogen bonds: B:P.158, B:P.158 Salt bridges: B:E.157 GAI.10: 5 residues within 4Å: Chain B: F.350, A.375, D.376, G.378 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.375, B:G.378 GAI.19: 6 residues within 4Å: Chain C: F.70, E.157, P.158, V.159 Chain D: Q.447, Y.468 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.158, C:P.158 Water bridges: C:R.77, C:E.157 Salt bridges: C:E.157 GAI.20: 6 residues within 4Å: Chain C: I.146, D.147, G.148, 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.24: 6 residues within 4Å: Chain C: Q.447, Y.468 Chain D: F.70, E.157, P.158, V.159 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.158, D:P.158 Water bridges: D:R.77, D:E.157 Salt bridges: D:E.157 GAI.25: 5 residues within 4Å: Chain C: V.458, F.459 Chain D: I.146, D.147, F.150 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:F.459, C:F.459, D:D.147, D:D.147 Water bridges: D:D.147

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

EDO.3: 7 residues within 4Å: Chain A: Y.153, R.155, V.491 Chain B: N.440, S.443, Q.444 Chain D: F.151 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.153, A:R.155, B:S.443 EDO.4: 4 residues within 4Å: Chain A: F.18, D.98, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.98, A:D.98 EDO.11: 5 residues within 4Å: Chain A: N.440, S.443 Chain B: Y.153, R.155 Chain C: F.151 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.443, B:Y.153, B:R.155 EDO.12: 6 residues within 4Å: Chain B: N.41, T.44, E.46, V.47, I.48, L.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.41, B:T.44 EDO.13: 3 residues within 4Å: Chain B: F.18, Y.101, Y.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.203 EDO.14: 3 residues within 4Å: Chain B: A.68, Q.71, S.74 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain B: E.347, F.350 Ligands: GAI.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.347 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.21: 4 residues within 4Å: Chain C: F.18, D.98, Y.101, Y.203 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.98 Water bridges: C:Y.101, C:Y.203 EDO.26: 6 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443, Q.444 Chain D: Y.153, R.155 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.153, D:R.155, C:S.443 EDO.27: 7 residues within 4Å: Chain C: K.469, M.470 Chain D: D.239, N.261, L.262, K.263, R.264 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.239, D:N.261, C:K.469 Water bridges: D:V.159, D:N.261, D:R.264 EDO.28: 3 residues within 4Å: Chain D: F.18, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.98, D:Y.203

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

I3E.5: 11 residues within 4Å: Chain A: M.124, N.169, F.170, L.173, F.296, C.301, C.302, C.303, D.457, F.459, F.465 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.173, A:F.296, A:F.459, A:F.459, A:F.465 Hydrogen bonds: A:N.169, A:C.302 pi-Stacking: A:F.170 I3E.16: 11 residues within 4Å: Chain B: M.124, N.169, F.170, L.173, F.296, C.301, C.302, C.303, D.457, F.459, F.465 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.173, 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.22: 11 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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.173, C:W.177, C:F.296, C:F.459, C:F.459, C:F.459 Hydrogen bonds: C:N.169, C:C.302 pi-Stacking: C:F.170 I3E.29: 12 residues within 4Å: Chain D: M.124, N.169, F.170, L.173, M.174, W.177, F.296, C.301, C.302, C.303, D.457, F.459 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.173, D:W.177, D:F.296, D:F.459, D:F.459, D:F.459 Hydrogen bonds: D:N.169, D:C.302, D:C.303 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
E

B
F

C
G

D
H

Aldehyde dehydrogenase, mitochondrial

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