SMTL ID : 3sz9.2 (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

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 1 residues within 4Å: Chain A: F.151 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.443, A:R.155 EDO.7: 6 residues within 4Å: Chain A: N.41, T.44, E.46, V.47, I.48, L.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.41 EDO.8: 3 residues within 4Å: Chain A: F.18, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.97, A:Y.101 EDO.9: 3 residues within 4Å: Chain A: E.347, F.350 Ligands: GAI.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.347 EDO.14: 3 residues within 4Å: Chain A: S.443 Chain B: Y.153, R.155 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.155, A:S.443 Water bridges: B:Y.153

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

NA.2: 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:T.39, A:V.40 NA.12: 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:Q.196

5 x GAI: GUANIDINE(Non-covalent)

GAI.3: 4 residues within 4Å: Chain A: E.157, P.158, V.159 Chain B: Y.468 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.158, A:P.158 Water bridges: A:R.77, A:E.157, A:E.487, B:Q.447 Salt bridges: A:E.157 GAI.4: 5 residues within 4Å: Chain A: I.146, D.147, F.150 Chain B: V.458, F.459 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.147, A:D.147, B:F.459, B:F.459 Water bridges: A:D.147 GAI.5: 6 residues within 4Å: Chain A: F.350, I.373, A.375, D.376, G.378 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.378, A:G.378 Water bridges: A:A.375, A:G.378 GAI.11: 5 residues within 4Å: Chain A: V.458, F.459 Chain B: I.146, D.147, F.150 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:F.459, B:D.147, B:D.147 Water bridges: B:D.147, B:D.147, B:D.147 GAI.13: 4 residues within 4Å: Chain A: Y.468 Chain B: E.157, P.158, V.159 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.158, B:P.158, A:Y.468 Water bridges: B:R.77, B:E.157 Salt bridges: B:E.157

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

I3E.10: 12 residues within 4Å: Chain A: 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 A Hydrophobic interactions: A:L.173, A:W.177, A:F.296, A:D.457, A:F.459, A:F.459, A:F.465 Hydrogen bonds: A:N.169, A:C.302, A:C.303 pi-Stacking: A:F.170 I3E.15: 12 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:L.173, B:W.177, B:F.296, B:F.459, B:F.459, B:F.465 Hydrogen bonds: B:N.169, B:C.302 pi-Stacking: B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Aldehyde dehydrogenase, mitochondrial

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