SMTL ID : 5tei.1

Structure of human ALDH1A1 with inhibitor CM039

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 29 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, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.3 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:G.246, A:S.247, A:C.303, A:Q.350, A:K.353, A:K.353 Water bridges: A:Q.197, A:G.226, A:S.247, A:S.247, A:T.248 NAI.6: 29 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, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.8 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:G.246, B:S.247, B:C.303, B:Q.350, B:K.353, B:K.353 Water bridges: B:Q.197, B:G.226, B:S.247, B:S.247, B:T.248 NAI.11: 29 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, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.13 19 PLIP interactions: 19 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:G.246, C:S.247, C:C.303, C:Q.350, C:K.353, C:K.353, C:E.400 Water bridges: C:Q.197, C:G.226, C:S.247, C:S.247, C:T.248 NAI.16: 29 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, I.254, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.18 19 PLIP interactions: 19 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:G.246, D:S.247, D:C.303, D:Q.350, D:K.353, D:K.353, D:E.400 Water bridges: D:Q.197, D:G.226, D:S.247, D:S.247, D:T.248

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

YB.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.3: 1 residues within 4Å: Ligands: NAI.1 No protein-ligand interaction detected (PLIP) YB.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.8: 1 residues within 4Å: Ligands: NAI.6 No protein-ligand interaction detected (PLIP) YB.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.13: 1 residues within 4Å: Ligands: NAI.11 No protein-ligand interaction detected (PLIP) YB.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.18: 1 residues within 4Å: Ligands: NAI.16 No protein-ligand interaction detected (PLIP)

4 x M39: 6-{[(3-fluorophenyl)methyl]sulfanyl}-5-(2-methylphenyl)-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

M39.4: 11 residues within 4Å: Chain A: S.121, F.171, M.175, H.293, G.294, Y.297, C.303, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.171, A:F.171, A:V.460 Hydrogen bonds: A:H.293 pi-Stacking: A:Y.297 M39.9: 11 residues within 4Å: Chain B: S.121, F.171, M.175, H.293, G.294, Y.297, C.303, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.171, B:F.171, B:V.460 Hydrogen bonds: B:H.293 pi-Stacking: B:Y.297 M39.14: 11 residues within 4Å: Chain C: S.121, F.171, M.175, H.293, G.294, Y.297, C.303, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.171, C:F.171, C:V.460 Hydrogen bonds: C:H.293 pi-Stacking: C:Y.297 M39.19: 11 residues within 4Å: Chain D: S.121, F.171, M.175, H.293, G.294, Y.297, C.303, Y.457, G.458, V.460, F.466 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.171, D:F.171, D:V.460 Hydrogen bonds: D:H.293 pi-Stacking: D:Y.297

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

CL.5: 3 residues within 4Å: Chain A: R.143, T.155, H.157 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: R.143, T.155, H.157 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: R.143, T.155, H.157 Ligand excluded by PLIP CL.20: 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

Hurley, T.D. et al., Structure of human ALDH1A1 with inhibitor CM039. To Be Published

Release Date

2017-09-27

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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