SMTL ID : 7mjd.1

Crystal Structure Analysis of ALDH1B1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: T.37, V.38, D.107, Q.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.38, A:V.38 NA.15: 4 residues within 4Å: Chain B: T.37, V.38, D.107, Q.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.38, B:D.107

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

NAD.2: 32 residues within 4Å: Chain A: I.163, I.164, P.165, W.166, N.167, M.172, W.175, K.190, V.191, A.192, E.193, G.223, P.224, G.227, A.228, F.241, T.242, G.243, S.244, V.247, I.251, E.266, L.267, G.268, C.300, E.397, F.399, L.425, F.463 Ligands: 1PE.7, 1PE.9, 1PE.12 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.165, A:T.242 Hydrogen bonds: A:I.164, A:K.190, A:E.193, A:S.244, A:L.267, A:E.397 Water bridges: A:Q.194, A:S.244, A:T.245 NAD.16: 28 residues within 4Å: Chain B: I.163, I.164, P.165, W.166, N.167, M.172, K.190, V.191, A.192, E.193, G.223, P.224, G.227, A.228, F.241, T.242, G.243, S.244, V.247, I.251, E.266, L.267, G.268, C.300, E.397, F.399, L.425, F.463 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.165, B:T.242 Hydrogen bonds: B:I.164, B:K.190, B:E.193, B:S.244, B:E.266, B:L.267, B:E.397 Water bridges: B:Q.194, B:Q.194, B:T.245

2 x ZGG: 8-(2-methoxyphenyl)-10-(4-phenylphenyl)-1$l^{4},8-diazabicyclo[5.3.0]deca-1(7),9-diene(Non-covalent)

ZGG.3: 12 residues within 4Å: Chain A: L.118, D.119, E.122, F.168, E.286, Q.287, E.290, F.294, C.299, N.455, I.456, V.457 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.118, A:E.286, A:E.290, A:I.456 pi-Stacking: A:F.168, A:F.294 ZGG.17: 12 residues within 4Å: Chain B: L.118, D.119, E.122, F.168, E.286, Q.287, E.290, F.294, C.299, Y.454, N.455, V.457 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.118, B:F.168, B:F.168, B:E.290 pi-Stacking: B:F.294

18 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 4 residues within 4Å: Chain A: E.370, R.371, G.373, E.374 Ligand excluded by PLIP 1PE.5: 5 residues within 4Å: Chain A: F.151, R.153 Chain B: M.438, T.441, Q.442 Ligand excluded by PLIP 1PE.6: 15 residues within 4Å: Chain A: G.269, K.270, S.271, P.272, R.305, A.418, N.419, T.421, Y.423, G.424, L.425, A.426, A.427, L.444, Q.445 Ligand excluded by PLIP 1PE.7: 7 residues within 4Å: Chain A: W.166, Q.194, D.344, E.346, Q.347 Ligands: NAD.2, 1PE.12 Ligand excluded by PLIP 1PE.8: 1 residues within 4Å: Chain A: Y.129 Ligand excluded by PLIP 1PE.9: 7 residues within 4Å: Chain A: A.228, A.231, Q.232, L.250, I.251, A.254 Ligands: NAD.2 Ligand excluded by PLIP 1PE.10: 3 residues within 4Å: Chain A: K.136, W.137, H.138 Ligand excluded by PLIP 1PE.11: 5 residues within 4Å: Chain A: Q.445, F.466 Chain B: E.155, P.156, V.157 Ligand excluded by PLIP 1PE.12: 6 residues within 4Å: Chain A: Q.347, R.350, E.397, F.399 Ligands: NAD.2, 1PE.7 Ligand excluded by PLIP 1PE.13: 4 residues within 4Å: Chain A: E.94, D.121, I.124, K.125 Ligand excluded by PLIP 1PE.14: 4 residues within 4Å: Chain A: M.234, D.237, N.259 Chain B: K.467 Ligand excluded by PLIP 1PE.20: 1 residues within 4Å: Chain B: T.141 Ligand excluded by PLIP 1PE.21: 4 residues within 4Å: Chain B: R.350, G.353, Y.354, R.392 Ligand excluded by PLIP 1PE.22: 3 residues within 4Å: Chain B: W.137, G.139, H.154 Ligand excluded by PLIP 1PE.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP 1PE.24: 5 residues within 4Å: Chain B: Y.17, R.95, Y.201, S.204, E.208 Ligand excluded by PLIP 1PE.25: 4 residues within 4Å: Chain B: K.136, W.137, H.138, E.477 Ligand excluded by PLIP 1PE.26: 3 residues within 4Å: Chain B: R.128, Y.129, G.132 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 5 residues within 4Å: Chain A: M.438, T.441, Q.442 Chain B: F.151, R.153 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.441, B:R.153 GOL.19: 12 residues within 4Å: Chain B: P.272, R.305, A.418, N.419, T.421, Y.423, G.424, L.425, A.426, L.444, Q.445, K.467 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.423, B:L.425, B:A.426, B:Q.445, B:K.467 Water bridges: B:K.270, B:S.271

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aldehyde dehydrogenase X, mitochondrial

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