SMTL ID : 4l2o.1 (1 other biounit)

Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4-fluorophenyl)sulfonyl-2-methylbenzimidazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 1 residues within 4Å: Chain A: D.339 No protein-ligand interaction detected (PLIP) K.2: 3 residues within 4Å: Chain A: K.456, Y.459, P.461 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.459, H2O.6 K.7: 3 residues within 4Å: Chain B: E.96, W.97, A.99 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.96, H2O.14, H2O.18 K.8: 3 residues within 4Å: Chain B: K.456, Y.459, P.461 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Y.459

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

ACT.3: 6 residues within 4Å: Chain A: M.450, N.451, D.452, K.456, Y.459 Chain B: R.247 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.459 Hydrogen bonds: A:N.451, A:D.452 Salt bridges: B:R.247 ACT.4: 6 residues within 4Å: Chain A: R.247 Chain B: M.450, N.451, D.452, 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

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.5: 24 residues within 4Å: Chain A: T.129, W.130, N.131, L.136, E.157, L.158, V.186, T.189, T.203, G.204, S.205, V.208, I.211, E.226, L.227, G.228, C.260, R.305, H.306, E.350, F.352, L.378, F.418 Ligands: 1DD.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.129, A:L.136, A:T.203 Hydrogen bonds: A:T.129, A:E.157, A:S.205, A:S.205, A:L.227, A:R.305, A:E.350 Water bridges: A:W.130, A:K.154, A:K.154, A:S.156, A:T.190, A:G.229 Salt bridges: A:H.306 NAD.9: 21 residues within 4Å: Chain B: T.129, W.130, N.131, L.136, E.157, L.158, V.186, T.203, G.204, S.205, V.208, I.211, E.226, L.227, G.228, C.260, H.306, E.350, F.352, L.378, F.418 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.129, B:L.136, B:T.203 Hydrogen bonds: B:T.129, B:E.157, B:S.205, B:E.226, B:L.227, B:E.350 Water bridges: B:W.130, B:K.154, B:S.156, B:T.190, B:Y.202, B:Y.202, B:Y.202, B:Y.202, B:E.350, B:E.350, B:E.350 Salt bridges: B:H.306

2 x 1DD: 1-[(4-fluorophenyl)sulfonyl]-2-methyl-1H-benzimidazole(Non-covalent)

1DD.6: 15 residues within 4Å: Chain A: E.78, E.79, Y.82, Y.132, N.135, L.136, Q.139, M.254, C.260, I.408, I.411, T.412, F.418, H.430 Ligands: NAD.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.82, A:Y.82, A:Y.82, A:Y.132, A:Y.132, A:L.136, A:L.136, A:I.408, A:I.411, A:T.412, A:F.418, A:F.418 Hydrogen bonds: A:N.135 1DD.10: 14 residues within 4Å: Chain B: E.78, E.79, Y.82, Y.132, N.135, L.136, Q.139, M.254, C.260, I.408, I.411, T.412, F.418, H.430 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.82, B:Y.82, B:Y.132, B:Y.132, B:L.136, B:L.136, B:I.411, B:T.412, B:F.418, B:F.418 Hydrogen bonds: B:N.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parajuli, B. et al., Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4-fluorophenyl)sulfonyl-2-methylbenzimidazole. J.Med.Chem. (2014)

Release Date

2014-01-29

Peptides

Aldehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aldehyde dehydrogenase

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