SMTL ID : 6dum.1

ALDH1A1 N121S in complex with 6-{[(3-fluorophenyl)methyl]sulfanyl}-2-(oxetan-3-yl)-5-phenyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one (compound 13g)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 4 residues within 4Å: Ligands: NAI.4, CL.5, CL.10, CL.11 No protein-ligand interaction detected (PLIP) YB.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.13: 4 residues within 4Å: Ligands: NAI.15, CL.16, CL.21, CL.22 No protein-ligand interaction detected (PLIP) YB.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.24: 4 residues within 4Å: Ligands: NAI.26, CL.27, CL.32, CL.33 No protein-ligand interaction detected (PLIP) YB.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.35: 4 residues within 4Å: Ligands: NAI.37, CL.38, CL.43, CL.44 No protein-ligand interaction detected (PLIP)

4 x A5Y: 6-{[(3-fluorophenyl)methyl]sulfanyl}-2-(oxetan-3-yl)-5-phenyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

A5Y.3: 15 residues within 4Å: Chain A: G.125, T.129, F.171, M.175, W.178, H.293, G.294, Y.297, C.302, C.303, I.304, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.178, A:I.304, A:F.466 pi-Stacking: A:F.171, A:Y.297 A5Y.14: 15 residues within 4Å: Chain B: G.125, T.129, F.171, M.175, W.178, H.293, G.294, Y.297, C.302, C.303, I.304, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.178, B:I.304, B:F.466 pi-Stacking: B:F.171, B:Y.297 A5Y.25: 15 residues within 4Å: Chain C: G.125, T.129, F.171, M.175, W.178, H.293, G.294, Y.297, C.302, C.303, I.304, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.178, C:I.304, C:F.466 pi-Stacking: C:F.171, C:Y.297 A5Y.36: 15 residues within 4Å: Chain D: G.125, T.129, F.171, M.175, W.178, H.293, G.294, Y.297, C.302, C.303, I.304, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.178, D:I.304, D:F.466 pi-Stacking: D:F.171, D:Y.297

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.4: 30 residues within 4Å: Chain A: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, I.254, E.269, L.270, C.303, Q.350, K.353, E.400, F.402 Ligands: YB.2, CL.5, CL.10 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.168, 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:Q.350, A:Q.350, A:K.353, A:K.353, A:E.400 Water bridges: A:T.248, A:T.248, A:C.303 NAI.15: 30 residues within 4Å: Chain B: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, I.254, E.269, L.270, C.303, Q.350, K.353, E.400, F.402 Ligands: YB.13, CL.16, CL.21 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:P.168, 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:Q.350, B:Q.350, B:K.353, B:K.353, B:E.400 Water bridges: B:T.248, B:T.248, B:C.303 NAI.26: 30 residues within 4Å: Chain C: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, I.254, E.269, L.270, C.303, Q.350, K.353, E.400, F.402 Ligands: YB.24, CL.27, CL.32 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:P.168, 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:Q.350, C:Q.350, C:K.353, C:K.353 Water bridges: C:T.248, C:T.248, C:C.303 NAI.37: 30 residues within 4Å: Chain D: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, L.253, I.254, E.269, L.270, C.303, Q.350, K.353, E.400, F.402 Ligands: YB.35, CL.38, CL.43 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.168, 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:Q.350, D:Q.350, D:K.353, D:K.353 Water bridges: D:T.248, D:T.248, D:C.303

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

CL.5: 5 residues within 4Å: Chain A: E.349 Ligands: YB.2, NAI.4, CL.10, CL.11 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: D.283 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: E.46, K.378 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: H.484 Chain B: H.484 Ligands: CL.19 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.143, T.155, H.157 Chain B: Y.481 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: E.349 Ligands: YB.2, NAI.4, CL.5, CL.11 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: E.349 Ligands: YB.2, CL.5, CL.10 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: E.349 Ligands: YB.13, NAI.15, CL.21, CL.22 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: D.283 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: E.46, K.378 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: H.484 Chain B: H.484 Ligands: CL.8 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: Y.481 Chain B: R.143, T.155, H.157 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain B: E.349 Ligands: YB.13, NAI.15, CL.16, CL.22 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: E.349 Ligands: YB.13, CL.16, CL.21 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain C: E.349 Ligands: YB.24, NAI.26, CL.32, CL.33 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain C: D.283 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain C: E.46, K.378 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: H.484 Chain D: H.484 Ligands: CL.41 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: R.143, T.155, H.157 Chain D: Y.481 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain C: E.349 Ligands: YB.24, NAI.26, CL.27, CL.33 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain C: E.349 Ligands: YB.24, CL.27, CL.32 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain D: E.349 Ligands: YB.35, NAI.37, CL.43, CL.44 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain D: D.283 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain D: E.46, K.378 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain C: H.484 Chain D: H.484 Ligands: CL.30 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain C: Y.481 Chain D: R.143, T.155, H.157 Ligand excluded by PLIP CL.43: 5 residues within 4Å: Chain D: E.349 Ligands: YB.35, NAI.37, CL.38, CL.44 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain D: E.349 Ligands: YB.35, CL.38, CL.43 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huddle, B.C. et al., Structure-Based Optimization of a Novel Class of Aldehyde Dehydrogenase 1A (ALDH1A) Subfamily-Selective Inhibitors as Potential Adjuncts to Ovarian Cancer Chemotherapy. J.Med.Chem. (2018)

Release Date

2019-05-01

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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