SMTL ID : 4l1o.1

Crystal structure of human ALDH3A1 with inhibitor 1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-1H-indole-2,3-dione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x 1VL: (3S)-1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-3-hydroxy-1,3-dihydro-2H-indol-2-one(Covalent)

1VL.1: 17 residues within 4Å: Chain A: E.78, Y.82, N.131, Y.132, N.135, L.136, T.203, E.226, M.254, T.259, C.260, I.408, I.411, T.412, F.418, Y.429, H.430 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.136, A:I.411, A:F.418 Hydrogen bonds: A:E.78, A:N.131, A:C.260 1VL.5: 16 residues within 4Å: Chain B: E.78, Y.82, N.131, Y.132, N.135, L.136, E.226, M.254, T.259, C.260, I.408, I.411, T.412, F.418, Y.429, H.430 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.136, B:F.418 Hydrogen bonds: B:E.78, B:N.131, B:C.260

4 x K: POTASSIUM ION(Non-covalent)

K.2: 2 residues within 4Å: Chain A: T.338, D.339 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.339, H2O.1 K.3: 3 residues within 4Å: Chain A: K.456, Y.459, P.461 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.459 K.6: 3 residues within 4Å: Chain B: E.96, W.97, A.99 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.96, B:A.99, H2O.21, H2O.25 K.7: 3 residues within 4Å: Chain B: K.456, Y.459, P.461 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.456, B:Y.459, H2O.19, H2O.20

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: M.450, N.451, D.452, K.456, Y.459 Chain B: R.247 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.456, A:Y.459 Hydrogen bonds: A:N.451, A:D.452, A:D.452, A:Y.459 Salt bridges: B:R.247 ACT.8: 7 residues within 4Å: Chain A: R.247 Chain B: M.450, N.451, D.452, L.455, K.456, Y.459 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.456, B:Y.459 Hydrogen bonds: B:D.452, B:Y.459 Salt bridges: A:R.247

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

2014-04-16

Peptides

Aldehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aldehyde dehydrogenase

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