SMTL ID : 7jwu.1

Crystal structure of human ALDH1A1 bound to compound (R)-28

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

8 x YB: YTTERBIUM (III) ION(Non-functional Binders)

YB.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.2: 2 residues within 4Å: Ligands: CL.4, NAD.5 No protein-ligand interaction detected (PLIP) YB.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.8: 2 residues within 4Å: Ligands: CL.10, NAD.11 No protein-ligand interaction detected (PLIP) YB.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.14: 2 residues within 4Å: Ligands: CL.16, NAD.17 No protein-ligand interaction detected (PLIP) YB.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.20: 2 residues within 4Å: Ligands: CL.22, NAD.23 No protein-ligand interaction detected (PLIP)

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: R.143, T.155, H.157 Chain B: Y.481 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: E.349 Ligands: YB.2 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: Y.481 Chain B: R.143, T.155, H.157 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: E.349 Ligands: YB.8 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: R.143, T.155, H.157 Chain D: Y.481 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: E.349 Ligands: YB.14 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain C: Y.481 Chain D: R.143, T.155, H.157 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: E.349 Ligands: YB.20 Ligand excluded by PLIP

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

NAD.5: 27 residues within 4Å: Chain A: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.168 Hydrogen bonds: A:I.167, A:I.167, A:N.170, A:E.196, A:G.246, A:S.247, A:S.247, A:E.269, A:C.303, A:Q.350, A:Q.350, A:K.353, A:K.353, A:E.400 Water bridges: A:Q.197, A:T.248 pi-Stacking: A:F.402 NAD.11: 27 residues within 4Å: Chain B: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.8 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:P.168 Hydrogen bonds: B:I.167, B:I.167, B:N.170, B:E.196, B:G.246, B:S.247, B:S.247, B:E.269, B:C.303, B:Q.350, B:Q.350, B:K.353, B:K.353, B:E.400 Water bridges: B:Q.197, B:T.248 pi-Stacking: B:F.402 NAD.17: 27 residues within 4Å: Chain C: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.14 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:P.168 Hydrogen bonds: C:I.167, C:I.167, C:N.170, C:E.196, C:G.246, C:S.247, C:S.247, C:E.269, C:C.303, C:Q.350, C:Q.350, C:K.353, C:K.353 Water bridges: C:Q.197, C:T.248, C:E.249 pi-Stacking: C:F.402 NAD.23: 27 residues within 4Å: Chain D: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.20 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:P.168 Hydrogen bonds: D:I.167, D:I.167, D:N.170, D:E.196, D:G.246, D:S.247, D:S.247, D:E.269, D:C.303, D:Q.350, D:Q.350, D:K.353, D:K.353 Water bridges: D:Q.197, D:T.248, D:E.249 pi-Stacking: D:F.402

4 x VMA: 1-methyl-5-phenyl-6-{[(1R)-1-(pyridin-2-yl)ethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

VMA.6: 14 residues within 4Å: Chain A: S.121, G.125, T.129, F.171, M.175, W.178, Y.297, C.302, I.304, G.458, V.460, S.461, A.462, F.466 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.178, A:I.304, A:F.466 Water bridges: A:C.303 pi-Stacking: A:F.171, A:Y.297 VMA.12: 14 residues within 4Å: Chain B: S.121, G.125, T.129, F.171, M.175, W.178, Y.297, C.302, I.304, G.458, V.460, S.461, A.462, F.466 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.178, B:I.304, B:F.466 Water bridges: B:C.303 pi-Stacking: B:F.171, B:Y.297 VMA.18: 14 residues within 4Å: Chain C: S.121, G.125, T.129, F.171, M.175, W.178, Y.297, C.302, I.304, G.458, V.460, S.461, A.462, F.466 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.178, C:I.304, C:F.466 Water bridges: C:C.303 pi-Stacking: C:F.171, C:Y.297 VMA.24: 14 residues within 4Å: Chain D: S.121, G.125, T.129, F.171, M.175, W.178, Y.297, C.302, I.304, G.458, V.460, S.461, A.462, F.466 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.178, D:I.304, D:F.466 Water bridges: D:C.303 pi-Stacking: D:F.171, D:Y.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huddle, B.C. et al., Development of 2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one inhibitors of aldehyde dehydrogenase 1A (ALDH1A) as potential adjuncts to ovarian cancer chemotherapy. Eur.J.Med.Chem. (2020)

Release Date

2020-12-30

Peptides

Retinal dehydrogenase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Retinal dehydrogenase 1

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