SMTL ID : 5l13.2 (1 other biounit)

Structure of ALDH2 in complex with 2P3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: T.56, V.57, D.126, Q.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.56, A:V.57 Water bridges: A:T.56 NA.8: 4 residues within 4Å: Chain B: T.56, V.57, D.126, Q.213 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.57, B:Q.213 NA.13: 4 residues within 4Å: Chain C: T.56, V.57, D.126, Q.213 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.57, C:D.126, C:Q.213 NA.21: 4 residues within 4Å: Chain D: T.56, V.57, D.126, Q.213 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.57, D:Q.213

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

EDO.2: 6 residues within 4Å: Chain A: Y.170, R.172 Chain B: N.457, S.460, Q.461 Chain D: F.168 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.460, A:R.172 EDO.3: 4 residues within 4Å: Chain A: P.513 Chain C: I.430, D.454, Y.458 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: N.457, S.460 Chain B: Y.170, R.172 Chain C: F.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.170, B:Y.170 EDO.10: 4 residues within 4Å: Chain B: F.35, D.115, Y.118, Y.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.115, B:Y.220 EDO.14: 6 residues within 4Å: Chain B: F.168 Chain C: Y.170, R.172, V.508 Chain D: N.457, S.460 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.460, C:R.172 EDO.15: 5 residues within 4Å: Chain A: Q.514 Chain C: Y.458, Q.461, A.462 Chain D: L.89 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.458, C:Q.461, A:Q.514 EDO.16: 6 residues within 4Å: Chain C: N.58, T.61, E.63, V.64, I.65, L.125 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.58, C:E.63

8 x GAI: GUANIDINE(Non-covalent)

GAI.4: 5 residues within 4Å: Chain A: F.87, E.174, P.175, V.176 Chain B: Y.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.175 Water bridges: A:E.174, A:V.176 Salt bridges: A:E.174 GAI.5: 5 residues within 4Å: Chain A: I.163, D.164, F.167 Chain B: V.475, F.476 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.164, A:D.164, B:F.476 Water bridges: B:F.476 GAI.6: 5 residues within 4Å: Chain A: G.242, P.243, G.246, A.247, I.266 No protein-ligand interaction detected (PLIP) GAI.11: 5 residues within 4Å: Chain A: Y.485 Chain B: F.87, E.174, P.175, V.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.175, B:P.175 Salt bridges: B:E.174 GAI.17: 6 residues within 4Å: Chain C: F.87, E.174, P.175, V.176 Chain D: Q.464, Y.485 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.175, C:V.176 Water bridges: C:R.94, C:R.94 Salt bridges: C:E.174 GAI.18: 5 residues within 4Å: Chain C: I.163, D.164, F.167 Chain D: V.475, F.476 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.164, C:D.164, D:F.476, D:F.476, D:F.476 GAI.19: 4 residues within 4Å: Chain C: F.35, D.115, Y.118, Y.220 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.220 Salt bridges: C:D.115 pi-Cation interactions: C:Y.118 GAI.22: 6 residues within 4Å: Chain C: Q.464, Y.485 Chain D: F.87, E.174, P.175, V.176 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Water bridges: C:Q.464, D:E.174, D:V.176 Hydrogen bonds: D:P.175 Salt bridges: D:E.174

4 x 6ZE: 2,3,5-trimethyl-6-propyl-7H-furo[3,2-g][1]benzopyran-7-one(Non-covalent)

6ZE.7: 14 residues within 4Å: Chain A: V.137, M.141, F.187, L.190, M.191, W.194, T.261, F.313, C.318, C.319, C.320, D.474, F.476, F.482 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.137, A:F.187, A:W.194, A:T.261, A:F.476, A:F.482 Hydrogen bonds: A:C.319, A:C.320 pi-Stacking: A:F.187, A:F.187, A:F.476 6ZE.12: 13 residues within 4Å: Chain B: M.141, N.186, F.187, M.191, W.194, F.309, F.313, C.318, C.319, C.320, D.474, F.476, F.482 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.194, B:F.309, B:F.313, B:F.476, B:F.476, B:F.482 Hydrogen bonds: B:N.186, B:C.319, B:C.320 pi-Stacking: B:F.187, B:F.187 6ZE.20: 15 residues within 4Å: Chain C: V.137, M.141, F.187, L.190, M.191, W.194, E.285, F.309, F.313, C.318, C.319, C.320, D.474, F.476, F.482 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.190, C:W.194, C:E.285, C:F.309, C:F.313, C:F.476, C:F.482 Hydrogen bonds: C:C.319, C:C.320 pi-Stacking: C:F.187, C:F.476 6ZE.23: 14 residues within 4Å: Chain D: V.137, M.141, F.187, L.190, M.191, W.194, F.309, F.313, C.318, C.319, C.320, D.474, F.476, F.482 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.137, D:F.187, D:F.187, D:W.194, D:W.194, D:F.309, D:F.476, D:F.482 Hydrogen bonds: D:N.186, D:C.319, D:C.320 pi-Stacking: D:F.187, D:F.476

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buchman, C.D. et al., Inhibition of the Aldehyde Dehydrogenase 1/2 Family by Psoralen and Coumarin Derivatives. J. Med. Chem. (2017)

Release Date

2017-03-08

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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