SMTL ID : 4x4l.1

Structure of human ALDH1A1 with inhibitor CM037

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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: CL.5, CL.6, CL.7, NAI.8 No protein-ligand interaction detected (PLIP) YB.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.11: 4 residues within 4Å: Ligands: CL.14, CL.15, CL.16, NAI.17 No protein-ligand interaction detected (PLIP) YB.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.20: 4 residues within 4Å: Ligands: CL.23, CL.24, CL.25, NAI.26 No protein-ligand interaction detected (PLIP) YB.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.29: 4 residues within 4Å: Ligands: CL.32, CL.33, CL.34, NAI.35 No protein-ligand interaction detected (PLIP)

4 x 3XG: ethyl ({4-oxo-3-[3-(pyrrolidin-1-yl)propyl]-3,4-dihydro[1]benzothieno[3,2-d]pyrimidin-2-yl}sulfanyl)acetate(Non-covalent)

3XG.3: 15 residues within 4Å: Chain A: S.121, G.125, T.129, F.171, V.174, M.175, W.178, 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:V.174, A:V.460 pi-Stacking: A:F.171, A:W.178, A:F.466 3XG.12: 15 residues within 4Å: Chain B: S.121, G.125, T.129, F.171, V.174, M.175, W.178, 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:V.174, B:V.460 pi-Stacking: B:F.171, B:W.178, B:F.466 3XG.21: 15 residues within 4Å: Chain C: S.121, G.125, T.129, F.171, V.174, M.175, W.178, 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:V.174, C:V.460 pi-Stacking: C:F.171, C:W.178, C:F.466 3XG.30: 15 residues within 4Å: Chain D: S.121, G.125, T.129, F.171, V.174, M.175, W.178, 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:V.174, D:V.460 pi-Stacking: D:F.171, D:W.178, D:F.466

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

CL.4: 3 residues within 4Å: Chain A: R.143, T.155, H.157 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: E.349 Ligands: YB.2, CL.6, CL.7, NAI.8 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Ligands: YB.2, CL.5, CL.7 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: E.349 Ligands: YB.2, CL.5, CL.6, NAI.8 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: R.143, T.155, H.157 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: E.349 Ligands: YB.11, CL.15, CL.16, NAI.17 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Ligands: YB.11, CL.14, CL.16 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: E.349 Ligands: YB.11, CL.14, CL.15, NAI.17 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: R.143, T.155, H.157 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain C: E.349 Ligands: YB.20, CL.24, CL.25, NAI.26 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Ligands: YB.20, CL.23, CL.25 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain C: E.349 Ligands: YB.20, CL.23, CL.24, NAI.26 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain D: R.143, T.155, H.157 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain D: E.349 Ligands: YB.29, CL.33, CL.34, NAI.35 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Ligands: YB.29, CL.32, CL.34 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain D: E.349 Ligands: YB.29, CL.32, CL.33, NAI.35 Ligand excluded by PLIP

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

NAI.8: 31 residues within 4Å: Chain A: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.2, CL.5, CL.7 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.168 Hydrogen bonds: A:I.167, 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:K.353 Water bridges: A:T.248 pi-Stacking: A:F.402 NAI.17: 31 residues within 4Å: Chain B: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.11, CL.14, CL.16 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.168 Hydrogen bonds: B:I.167, 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:K.353 Water bridges: B:T.248 pi-Stacking: B:F.402 NAI.26: 31 residues within 4Å: Chain C: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.20, CL.23, CL.25 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:P.168 Hydrogen bonds: C:I.167, 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, C:K.353, C:E.400 Water bridges: C:T.248 pi-Stacking: C:F.402 NAI.35: 31 residues within 4Å: Chain D: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, Q.197, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.29, CL.32, CL.34 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.168 Hydrogen bonds: D:I.167, 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, D:K.353, D:E.400 Water bridges: D:T.248 pi-Stacking: D:F.402

4 x NA: SODIUM ION(Non-functional Binders)

NA.9: 5 residues within 4Å: Chain A: H.484, E.485 Chain B: H.484, E.485 Ligands: NA.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.485 NA.18: 5 residues within 4Å: Chain A: H.484, E.485 Chain B: H.484, E.485 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.485 NA.27: 5 residues within 4Å: Chain C: H.484, E.485 Chain D: H.484, E.485 Ligands: NA.36 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.485 NA.36: 5 residues within 4Å: Chain C: H.484, E.485 Chain D: H.484, E.485 Ligands: NA.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.485

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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