SMTL ID : 7rad.1

Crystal Structure Analysis of ALDH1B1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: I.158, I.159, P.160, W.161, N.162, M.167, K.185, V.186, A.187, E.188, G.218, P.219, G.222, A.223, F.236, T.237, G.238, S.239, V.242, I.246, E.261, L.262, G.263, C.295, E.392, F.394, L.420, F.458 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.160, A:T.237 Hydrogen bonds: A:I.159, A:K.185, A:E.188, A:S.239, A:L.262, A:E.392 Water bridges: A:S.239 NAD.8: 28 residues within 4Å: Chain B: I.158, I.159, P.160, W.161, N.162, M.167, K.185, A.187, E.188, G.218, P.219, G.222, A.223, F.236, T.237, G.238, S.239, V.242, L.245, I.246, E.261, L.262, G.263, C.295, E.392, F.394, L.420, F.458 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.160, B:T.237 Hydrogen bonds: B:I.159, B:K.185, B:E.188, B:S.239, B:E.261, B:L.262, B:E.392 Water bridges: B:E.392 NAD.15: 28 residues within 4Å: Chain C: I.158, I.159, P.160, W.161, N.162, M.167, K.185, V.186, A.187, E.188, G.218, P.219, G.222, A.223, F.236, T.237, G.238, S.239, V.242, I.246, E.261, L.262, G.263, C.295, E.392, F.394, L.420, F.458 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:P.160, C:T.237 Hydrogen bonds: C:I.159, C:K.185, C:E.188, C:S.239, C:E.261, C:L.262, C:E.392 Water bridges: C:S.239 NAD.22: 28 residues within 4Å: Chain D: I.158, I.159, P.160, W.161, N.162, M.167, K.185, A.187, E.188, G.218, P.219, G.222, A.223, F.236, T.237, G.238, S.239, V.242, L.245, I.246, E.261, L.262, G.263, C.295, E.392, F.394, L.420, F.458 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:P.160, D:T.237 Hydrogen bonds: D:I.159, D:K.185, D:E.188, D:S.239, D:L.262, D:E.392 Water bridges: D:E.392, D:E.392

4 x ZGJ: 3-(2-methoxyphenyl)-1-(4-phenylphenyl)-6,7,8,9-tetrahydro-5~{H}-imidazo[1,2-a][1,3]diazepine(Non-covalent)

ZGJ.2: 11 residues within 4Å: Chain A: L.113, D.114, E.117, F.163, Q.282, E.285, F.289, C.294, Y.449, N.450, V.452 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.113, A:L.113, A:E.117, A:F.163, A:F.163, A:E.285, A:F.289 pi-Stacking: A:F.289 ZGJ.9: 12 residues within 4Å: Chain B: L.113, E.117, F.163, E.281, Q.282, E.285, F.289, C.294, Y.449, N.450, I.451, V.452 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.113, B:F.163, B:F.163, B:E.285, B:E.285, B:F.289, B:F.289, B:I.451 ZGJ.16: 11 residues within 4Å: Chain C: L.113, D.114, E.117, F.163, Q.282, E.285, F.289, C.294, Y.449, N.450, V.452 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.113, C:L.113, C:E.117, C:F.163, C:F.163, C:E.285, C:F.289 pi-Stacking: C:F.289 ZGJ.23: 12 residues within 4Å: Chain D: L.113, E.117, F.163, E.281, Q.282, E.285, F.289, C.294, Y.449, N.450, I.451, V.452 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.113, D:F.163, D:F.163, D:E.285, D:E.285, D:F.289, D:F.289, D:I.451

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

NA.3: 4 residues within 4Å: Chain A: T.32, V.33, D.102, Q.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.32, A:V.33, A:D.102 NA.10: 4 residues within 4Å: Chain B: T.32, V.33, D.102, Q.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.32, B:V.33, B:D.102 NA.17: 4 residues within 4Å: Chain C: T.32, V.33, D.102, Q.189 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.33, C:D.102, C:D.102 NA.24: 4 residues within 4Å: Chain D: T.32, V.33, D.102, Q.189 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.33, D:D.102, D:D.102

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

EDO.4: 5 residues within 4Å: Chain A: E.89, R.90, D.91, R.92, V.93 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: E.317, K.320 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: K.320, L.361 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: C.362, G.363 Ligands: EDO.6 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: F.146, R.148 Chain B: M.433, T.436, Q.437 Chain D: F.144 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: T.136 Chain C: R.148, H.149 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: Q.490 Chain C: L.65, G.66 Chain D: Y.434 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain B: K.487, P.489 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: E.89, R.90, D.91, R.92, V.93 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain C: E.317, K.320 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain C: K.320, L.361 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: C.362, G.363 Ligands: EDO.20 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: F.144 Chain C: F.146, R.148 Chain D: M.433, T.436, Q.437 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: R.148, H.149 Chain D: T.136 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: L.65, G.66 Chain B: Y.434 Chain D: Q.490 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain D: K.487, P.489 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, D., Inhibitors targeted to aldehyde dehydrogenase. Nat.Chem.Biol. (2022)

Release Date

2022-06-08

Peptides

Aldehyde dehydrogenase X, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Aldehyde dehydrogenase X, mitochondrial