SMTL ID : 6b5h.1

ALDH1A2 liganded with NAD and 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3-[4-(methylsulfonyl)phenyl]-1H-pyrazole-4-carboxamide (compound CM121)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: 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, F.394, F.458 Ligands: CU4.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.237 Hydrogen bonds: A:I.159, A:K.185, A:E.188, A:S.239, A:E.261, A:G.263, A:E.392 Water bridges: A:W.161, A:Q.189, A:G.218 NAD.3: 27 residues within 4Å: Chain B: I.158, I.159, P.160, W.161, N.162, 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, I.246, E.261, L.262, G.263, C.295, F.394, L.420, F.458 Ligands: CU4.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.160, B:T.237 Hydrogen bonds: B:I.159, B:E.188, B:S.239, B:E.261, B:E.261, B:G.263 Water bridges: B:Q.189 NAD.5: 29 residues within 4Å: Chain C: 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 Ligands: CU4.6 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.237 Hydrogen bonds: C:I.159, C:S.239, C:S.239, C:E.261, C:E.392 NAD.7: 22 residues within 4Å: Chain D: I.158, I.159, P.160, W.161, N.162, K.185, A.187, 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 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.160, D:T.237 Hydrogen bonds: D:I.159, D:K.185, D:S.239, D:L.262, D:E.392 Water bridges: D:Q.189

4 x CU4: 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3-[4-(methylsulfonyl)phenyl]-1H-pyrazole-4-carboxamide(Non-covalent)

CU4.2: 19 residues within 4Å: Chain A: V.113, G.117, T.121, N.162, F.163, L.166, W.170, Q.285, F.289, C.294, C.295, T.296, N.450, L.452, N.453, A.454, F.458, M.470 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.163, A:F.163, A:L.166, A:W.170, A:L.452 pi-Stacking: A:F.289 CU4.4: 18 residues within 4Å: Chain B: G.117, T.121, N.162, F.163, L.166, W.170, Q.282, Q.285, F.289, C.294, C.295, T.296, Y.449, N.450, L.452, A.454, F.458 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.163, B:W.170, B:W.170, B:T.296, B:L.452 Hydrogen bonds: B:Q.282, B:L.452 pi-Stacking: B:F.289 CU4.6: 19 residues within 4Å: Chain C: V.113, G.117, T.121, N.162, F.163, L.166, M.167, W.170, Q.285, F.289, C.294, C.295, T.296, N.450, L.452, N.453, A.454, F.458 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.113, C:W.170, C:W.170, C:N.450, C:L.452 pi-Stacking: C:F.163, C:F.289 CU4.8: 19 residues within 4Å: Chain D: V.113, G.117, T.121, N.162, F.163, L.166, W.170, Q.285, F.289, C.294, C.295, T.296, N.450, A.451, L.452, N.453, A.454, F.458, M.470 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.113, D:L.166, D:W.170, D:T.296, D:N.450, D:L.452, D:L.452 pi-Stacking: D:F.163, D:F.289

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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