SMTL ID : 4wpn.1

Structure of human ALDH1A1 with inhibitor CM053

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x 3ST: 1-{[1,3-dimethyl-7-(3-methylbutyl)-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl]methyl}piperidine-4-carboxamide(Non-covalent)

3ST.1: 13 residues within 4Å: Chain A: N.121, G.125, T.129, F.171, V.174, W.178, H.293, G.294, Y.297, C.302, I.304, G.458, V.460 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.171 Hydrogen bonds: A:T.129, A:T.129 Water bridges: A:A.462 pi-Stacking: A:Y.297, A:Y.297 3ST.7: 13 residues within 4Å: Chain B: N.121, G.125, T.129, F.171, V.174, W.178, H.293, G.294, Y.297, C.302, I.304, G.458, V.460 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.171 Hydrogen bonds: B:T.129, B:T.129 Water bridges: B:A.462 pi-Stacking: B:Y.297, B:Y.297 3ST.13: 13 residues within 4Å: Chain C: N.121, G.125, T.129, F.171, V.174, W.178, H.293, G.294, Y.297, C.302, I.304, G.458, V.460 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.171 Hydrogen bonds: C:T.129, C:T.129 Water bridges: C:A.462 pi-Stacking: C:Y.297, C:Y.297 3ST.19: 13 residues within 4Å: Chain D: N.121, G.125, T.129, F.171, V.174, W.178, H.293, G.294, Y.297, C.302, I.304, G.458, V.460 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.171 Hydrogen bonds: D:T.129, D:T.129 Water bridges: D:A.462 pi-Stacking: D:Y.297, D:Y.297

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

CL.2: 5 residues within 4Å: Chain A: E.46, G.379 Ligands: CL.3, CL.4, YB.6 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Ligands: CL.2, CL.4, YB.6 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Y.351 Ligands: CL.2, CL.3, YB.6 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: E.46, G.379 Ligands: CL.9, CL.10, YB.12 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Ligands: CL.8, CL.10, YB.12 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: Y.351 Ligands: CL.8, CL.9, YB.12 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: E.46, G.379 Ligands: CL.15, CL.16, YB.18 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Ligands: CL.14, CL.16, YB.18 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: Y.351 Ligands: CL.14, CL.15, YB.18 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain D: E.46, G.379 Ligands: CL.21, CL.22, YB.24 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Ligands: CL.20, CL.22, YB.24 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain D: Y.351 Ligands: CL.20, CL.21, YB.24 Ligand excluded by PLIP

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

YB.5: 1 residues within 4Å: Chain A: E.58 No protein-ligand interaction detected (PLIP) YB.6: 3 residues within 4Å: Ligands: CL.2, CL.3, CL.4 No protein-ligand interaction detected (PLIP) YB.11: 1 residues within 4Å: Chain B: E.58 No protein-ligand interaction detected (PLIP) YB.12: 3 residues within 4Å: Ligands: CL.8, CL.9, CL.10 No protein-ligand interaction detected (PLIP) YB.17: 1 residues within 4Å: Chain C: E.58 No protein-ligand interaction detected (PLIP) YB.18: 3 residues within 4Å: Ligands: CL.14, CL.15, CL.16 No protein-ligand interaction detected (PLIP) YB.23: 1 residues within 4Å: Chain D: E.58 No protein-ligand interaction detected (PLIP) YB.24: 3 residues within 4Å: Ligands: CL.20, CL.21, CL.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, C.A. et al., Characterization of Two Distinct Structural Classes of Selective Aldehyde Dehydrogenase 1A1 Inhibitors. J.Med.Chem. (2015)

Release Date

2015-02-11

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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