SMTL ID : 8t0n.1

Structure of Compound 4 bound to human ALDH1A1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

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

YB.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.2: 2 residues within 4Å: Chain A: E.349 Ligands: NAD.4 No protein-ligand interaction detected (PLIP) YB.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.7: 2 residues within 4Å: Chain B: E.349 Ligands: NAD.9 No protein-ligand interaction detected (PLIP) YB.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.12: 2 residues within 4Å: Chain C: E.349 Ligands: NAD.14 No protein-ligand interaction detected (PLIP) YB.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.17: 2 residues within 4Å: Chain D: E.349 Ligands: NAD.19 No protein-ligand interaction detected (PLIP)

4 x Y0B: 2-methoxy-6-{[(1-propyl-1H-benzimidazol-2-yl)amino]methyl}phenol

Y0B.3: 18 residues within 4Å: Chain A: S.121, D.122, G.125, T.129, F.171, V.174, M.175, W.178, Y.297, C.302, C.303, I.304, G.458, V.460, S.461, A.462, F.466, L.478 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.178 Hydrogen bonds: A:S.121, A:W.178 Water bridges: A:S.121 pi-Stacking: A:F.171, A:F.171 Y0B.8: 18 residues within 4Å: Chain B: S.121, D.122, G.125, T.129, F.171, V.174, M.175, W.178, Y.297, C.302, C.303, I.304, G.458, V.460, S.461, A.462, F.466, L.478 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.178 Hydrogen bonds: B:S.121, B:W.178 Water bridges: B:S.121 pi-Stacking: B:F.171, B:F.171 Y0B.13: 18 residues within 4Å: Chain C: S.121, D.122, G.125, T.129, F.171, V.174, M.175, W.178, Y.297, C.302, C.303, I.304, G.458, V.460, S.461, A.462, F.466, L.478 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.178 Hydrogen bonds: C:S.121, C:W.178 Water bridges: C:S.121 pi-Stacking: C:F.171, C:F.171 Y0B.18: 18 residues within 4Å: Chain D: S.121, D.122, G.125, T.129, F.171, V.174, M.175, W.178, Y.297, C.302, C.303, I.304, G.458, V.460, S.461, A.462, F.466, L.478 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.178 Hydrogen bonds: D:S.121, D:W.178 Water bridges: D:S.121 pi-Stacking: D:F.171, D:F.171

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

NAD.4: 34 residues within 4Å: Chain A: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, S.234, F.244, T.245, G.246, S.247, T.248, V.250, L.253, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.168, A:F.402, A:F.402 Hydrogen bonds: A:I.167, A:W.169, A:N.170, A:K.193, A:E.196, A:Q.197, A:G.246, A:S.247, A:S.247, A:E.269, A:C.303, A:Q.350, A:K.353, A:E.400 NAD.9: 34 residues within 4Å: Chain B: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, S.234, F.244, T.245, G.246, S.247, T.248, V.250, L.253, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.168, B:F.402, B:F.402 Hydrogen bonds: B:I.167, B:W.169, B:N.170, B:K.193, B:E.196, B:Q.197, B:G.246, B:S.247, B:S.247, B:E.269, B:C.303, B:Q.350, B:K.353, B:E.400 NAD.14: 34 residues within 4Å: Chain C: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, S.234, F.244, T.245, G.246, S.247, T.248, V.250, L.253, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.12 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:P.168, C:F.402, C:F.402 Hydrogen bonds: C:I.167, C:W.169, C:N.170, C:K.193, C:E.196, C:Q.197, C:G.246, C:S.247, C:S.247, C:E.269, C:C.303, C:Q.350, C:K.353 NAD.19: 34 residues within 4Å: Chain D: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, S.234, F.244, T.245, G.246, S.247, T.248, V.250, L.253, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.17 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:P.168, D:F.402, D:F.402 Hydrogen bonds: D:I.167, D:W.169, D:N.170, D:K.193, D:E.196, D:Q.197, D:G.246, D:S.247, D:S.247, D:E.269, D:C.303, D:Q.350, D:K.353

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

CL.5: 6 residues within 4Å: Chain A: R.143, T.155, H.157, V.489 Chain B: P.465, Y.481 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: P.465, Y.481 Chain B: R.143, T.155, H.157, V.489 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain C: R.143, T.155, H.157, V.489 Chain D: P.465, Y.481 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain C: P.465, Y.481 Chain D: R.143, T.155, H.157, V.489 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takahashi, C. et al., Development of substituted benzimidazoles as inhibitors of human aldehyde dehydrogenase 1A isoenzymes. Chem.Biol.Interact. (2024)

Release Date

2024-05-01

Peptides

Aldehyde dehydrogenase 1A1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Aldehyde dehydrogenase 1A1

Related Entries With Identical Sequence