SMTL ID : 7um9.1

Human ALDH1A1 with bound compound CM38

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x NQR: (4-methylfuro[3,2-c]quinolin-2-yl)(piperidin-1-yl)methanone(Non-covalent)

NQR.1: 10 residues within 4Å: Chain A: F.171, M.175, W.178, H.293, G.294, Y.297, C.303, I.304, G.458, F.466 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.178, A:Y.297, A:F.466 pi-Stacking: A:Y.297, A:Y.297 NQR.7: 10 residues within 4Å: Chain B: F.171, M.175, W.178, H.293, G.294, Y.297, C.303, I.304, G.458, F.466 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.178, B:Y.297, B:F.466 pi-Stacking: B:Y.297, B:Y.297 NQR.13: 10 residues within 4Å: Chain C: F.171, M.175, W.178, H.293, G.294, Y.297, C.303, I.304, G.458, F.466 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.178, C:Y.297, C:F.466 pi-Stacking: C:Y.297, C:Y.297 NQR.19: 10 residues within 4Å: Chain D: F.171, M.175, W.178, H.293, G.294, Y.297, C.303, I.304, G.458, F.466 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.178, D:Y.297, D:F.466 pi-Stacking: D:Y.297, D:Y.297

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

YB.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.3: 1 residues within 4Å: Ligands: NAD.5 No protein-ligand interaction detected (PLIP) YB.4: 1 residues within 4Å: Chain A: D.283 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.283, A:D.283 YB.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.9: 1 residues within 4Å: Ligands: NAD.11 No protein-ligand interaction detected (PLIP) YB.10: 1 residues within 4Å: Chain B: D.283 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.283, B:D.283 YB.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.15: 1 residues within 4Å: Ligands: NAD.17 No protein-ligand interaction detected (PLIP) YB.16: 1 residues within 4Å: Chain C: D.283 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.283, C:D.283 YB.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.21: 1 residues within 4Å: Ligands: NAD.23 No protein-ligand interaction detected (PLIP) YB.22: 1 residues within 4Å: Chain D: D.283 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.283, D:D.283

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

NAD.5: 29 residues within 4Å: Chain A: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.168, A:F.402, A:F.402 Hydrogen bonds: A:I.167, A:N.170, A:K.193, 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:Q.197, A:T.248, A:T.248, A:E.349 NAD.11: 29 residues within 4Å: Chain B: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.9 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.168, B:F.402, B:F.402 Hydrogen bonds: B:I.167, B:N.170, B:K.193, 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:Q.197, B:T.248, B:T.248, B:E.349 NAD.17: 29 residues within 4Å: Chain C: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.15 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:P.168, C:F.402, C:F.402 Hydrogen bonds: C:I.167, C:N.170, C:K.193, 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:Q.197, C:T.248, C:T.248, C:E.349 NAD.23: 29 residues within 4Å: Chain D: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.21 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:P.168, D:F.402, D:F.402 Hydrogen bonds: D:I.167, D:N.170, D:K.193, 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:Q.197, D:T.248, D:T.248, D:E.349

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

CL.6: 3 residues within 4Å: Chain A: R.143, T.155, H.157 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.143, T.155, H.157 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: R.143, T.155, H.157 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: R.143, T.155, H.157 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muralikrishnan, V. et al., A Novel ALDH1A1 Inhibitor Blocks Platinum-Induced Senescence and Stemness in Ovarian Cancer. Cancers (Basel) (2022)

Release Date

2023-04-26

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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