SMTL ID : 6b5g.1

ALDH1A2 liganded with NAD and (3-ethoxythiophen-2-yl){4-[4-nitro-3-(pyrrolidin-1-yl)phenyl]piperazin-1-yl}methanone (compound 6-118)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 29 residues within 4Å: Chain A: I.158, I.159, P.160, W.161, N.162, M.167, K.185, A.187, E.188, G.218, G.222, A.223, F.236, T.237, G.238, S.239, V.242, I.246, E.261, L.262, G.263, G.264, C.295, Q.342, E.392, F.394, L.420, F.458 Ligands: CQY.2 13 PLIP interactions: 13 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:E.261, A:E.261, A:G.264, A:E.392 Water bridges: A:Q.189, A:G.263, A:K.345 NAD.3: 25 residues within 4Å: Chain B: I.158, I.159, P.160, W.161, N.162, K.185, A.187, E.188, G.218, 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, L.420, F.458 Ligands: CQY.4 13 PLIP interactions: 13 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:S.239, B:E.261, B:E.261, B:G.264, B:E.392 Water bridges: B:W.161, B:T.240 NAD.5: 30 residues within 4Å: Chain C: I.158, I.159, P.160, W.161, N.162, M.167, K.185, A.187, E.188, Y.217, 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 Ligands: CQY.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:P.160, C:T.237 Hydrogen bonds: C:I.159, C:E.188, C:S.239, C:S.239, C:E.261, C:E.261, C:G.264, C:E.392 Water bridges: C:Q.189 NAD.7: 28 residues within 4Å: Chain D: I.158, I.159, P.160, W.161, N.162, M.167, K.185, A.187, E.188, Y.217, G.218, 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 Ligands: CQY.8 14 PLIP interactions: 14 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:S.239, D:E.261, D:G.263, D:G.264, D:E.392 Water bridges: D:W.161, D:E.392, D:E.392

4 x CQY: (3-ethoxythiophen-2-yl){4-[4-nitro-3-(pyrrolidin-1-yl)phenyl]piperazin-1-yl}methanone(Non-covalent)

CQY.2: 14 residues within 4Å: Chain A: V.113, N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, T.296, N.450, L.452 Chain C: Y.143 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.170, A:W.170, A:F.289, A:F.289, A:L.452 Hydrogen bonds: A:T.296 pi-Stacking: A:F.163 CQY.4: 15 residues within 4Å: Chain B: N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, T.296, N.450, A.451, L.452, N.453 Chain D: Y.143 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.170, B:W.170, B:F.289, B:L.452 pi-Stacking: B:F.163 CQY.6: 15 residues within 4Å: Chain A: Y.143 Chain C: V.113, N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, T.296, N.450, A.451, L.452 Ligands: NAD.5 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.170, C:W.170, C:F.289, C:L.452 Hydrogen bonds: C:T.296 pi-Stacking: C:F.163 CQY.8: 15 residues within 4Å: Chain D: V.113, N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, T.296, N.450, A.451, L.452, N.453 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.170, D:W.170, D:F.289, D:L.452 Hydrogen bonds: D:N.162 pi-Stacking: D:F.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Structural Basis of ALDH1A2 Inhibition by Irreversible and Reversible Small Molecule Inhibitors. ACS Chem. Biol. (2018)

Release Date

2018-01-10

Peptides

Retinal dehydrogenase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Retinal dehydrogenase 2

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