SMTL ID : 4kwf.2 (1 other biounit)

Crystal Structure Analysis of ALDH2+ALDiB33

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

2 x 3AK: 1-benzyl-1H-indole-2,3-dione(Non-covalent)

3AK.1: 12 residues within 4Å: Chain A: F.164, L.167, M.168, W.171, E.262, F.290, C.295, C.296, C.297, D.451, F.453, F.459 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.167, A:W.171, A:F.290, A:F.453, A:F.459 Hydrogen bonds: A:C.296, A:C.297 pi-Stacking: A:F.164 3AK.10: 12 residues within 4Å: Chain D: F.164, L.167, M.168, W.171, E.262, F.290, C.295, C.296, C.297, D.451, F.453, F.459 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.167, D:W.171, D:W.171, D:F.290, D:F.453, D:F.459 Hydrogen bonds: D:C.296, D:C.297 pi-Stacking: D:F.164, D:F.164

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

NA.2: 4 residues within 4Å: Chain A: V.34, D.103, Q.190, V.339 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.34, A:V.339 NA.5: 5 residues within 4Å: Chain B: V.34, P.36, D.103, Q.190, V.339 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.339 NA.8: 4 residues within 4Å: Chain C: T.33, V.34, D.103, Q.190 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.34, C:D.103, C:D.103 NA.11: 4 residues within 4Å: Chain D: T.33, V.34, D.103, Q.190 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.34, D:D.103, D:Q.190

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

EDO.3: 6 residues within 4Å: Chain A: N.434, S.437, Q.438 Chain B: Y.147, R.149 Chain C: F.145 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.434, B:Y.147, B:R.149 EDO.4: 7 residues within 4Å: Chain A: F.145 Chain C: N.434, S.437, Q.438 Chain D: Y.147, R.149, V.485 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.147 EDO.6: 5 residues within 4Å: Chain B: F.145 Chain C: Y.147, R.149 Chain D: S.437, Q.438 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.437, C:R.149 EDO.12: 6 residues within 4Å: Chain A: Y.147, R.149 Chain B: N.434, S.437, Q.438 Chain D: F.145 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.434

3 x GAI: GUANIDINE(Non-covalent)

GAI.7: 5 residues within 4Å: Chain A: Q.441, Y.462 Chain B: F.64, P.152, V.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.152, B:P.152 GAI.9: 5 residues within 4Å: Chain C: F.64, E.151, P.152, V.153 Chain D: Y.462 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:P.152, C:P.152 Salt bridges: C:E.151 GAI.13: 5 residues within 4Å: Chain C: Y.462 Chain D: F.64, E.151, P.152, V.153 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.71, D:V.153, C:Y.462, C:Y.462 Salt bridges: D:E.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimble-Hill, A.C. et al., Development of selective inhibitors for aldehyde dehydrogenases based on substituted indole-2,3-diones. J.Med.Chem. (2014)

Release Date

2014-04-09

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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