SMTL ID : 7a6q.1

Crystal structure of human aldehyde dehydrogenase 1A3 in complex with selective NR6 inhibitor compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: I.177, T.178, P.179, W.180, K.204, P.205, A.206, E.207, G.237, G.241, A.242, F.255, S.258, V.261, L.264, K.360, Q.361, K.364 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.360 Hydrogen bonds: A:T.178, A:K.204, A:E.207, A:S.258 NAD.10: 17 residues within 4Å: Chain B: I.177, T.178, W.180, K.204, P.205, A.206, E.207, F.236, G.237, G.241, A.242, F.255, G.257, S.258, V.261, K.360, Q.361 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.360 Hydrogen bonds: B:T.178, B:K.204, B:E.207, B:S.258 Water bridges: B:S.245

2 x R2Q: 3-(2-phenylimidazo[1,2-a]pyridin-6-yl)benzenecarbonitrile(Non-covalent)

R2Q.2: 12 residues within 4Å: Chain A: I.132, G.136, R.139, T.140, L.185, N.469, A.470, L.471, Y.472, A.473 Chain B: D.159, N.161 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.471 Hydrogen bonds: A:A.473 R2Q.11: 12 residues within 4Å: Chain A: D.159, N.161 Chain B: I.132, G.136, R.139, T.140, L.185, N.469, A.470, L.471, Y.472, A.473 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.140, B:A.473

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

NA.3: 4 residues within 4Å: Chain A: T.51, C.52, D.121, Q.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.51, A:C.52, A:C.52 NA.7: 1 residues within 4Å: Chain A: E.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.169 NA.15: 2 residues within 4Å: Chain B: R.96, H.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.96, B:H.168 NA.16: 1 residues within 4Å: Chain B: I.425 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.453, B:K.453

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: W.147, K.150, I.151, Q.152, H.168, E.491, L.494 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.150, A:Q.152, A:H.168 Water bridges: A:T.498 GOL.5: 7 residues within 4Å: Chain A: P.238, A.242, S.245, L.264, V.265, A.268 Ligands: NAD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.245 GOL.6: 8 residues within 4Å: Chain A: L.94, G.97, R.98, H.101, A.145, G.146, D.149, K.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.98, A:K.150, A:K.150 GOL.8: 7 residues within 4Å: Chain A: K.266, R.276, V.277 Chain B: K.266, V.277, N.485 Ligands: GOL.9 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.266, A:K.266, A:K.266, A:V.277, A:V.277 GOL.9: 9 residues within 4Å: Chain A: V.277, T.278, N.485, G.486, E.496 Chain B: R.276, V.277 Ligands: GOL.8, GOL.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.277, A:E.496, B:V.277 GOL.12: 9 residues within 4Å: Chain A: N.485, R.487 Chain B: I.171, R.276, A.495, T.498, E.499, V.500 Ligands: GOL.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.499, B:V.500, A:N.485 GOL.14: 6 residues within 4Å: Chain B: I.156, P.157, T.158, D.159, D.160, V.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.158, B:D.159, B:V.162

1 x R2K: (3-oxidanylidene-3-sodiooxy-propanoyl)oxysodium(Non-covalent)

R2K.13: 9 residues within 4Å: Chain B: A.50, T.51, C.52, P.54, D.121, Q.208, T.209, I.357, D.358 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.51, B:C.52, B:Q.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gelardi, E.L.M. et al., A Selective Competitive Inhibitor of Aldehyde Dehydrogenase 1A3 Hinders Cancer Cell Growth, Invasiveness and Stemness In Vitro. Cancers (Basel) (2021)

Release Date

2021-02-17

Peptides

Aldehyde dehydrogenase family 1 member A3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aldehyde dehydrogenase family 1 member A3

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