SMTL ID : 8fh8.1

Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003 Soaked In Hydrogen Peroxide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 31 residues within 4Å: Chain A: G.19, T.20, W.21, D.44, Y.49, K.78, H.111, W.112, S.160, N.161, Q.184, Y.210, S.211, P.212, L.213, G.214, S.215, P.216, D.217, L.229, A.246, I.261, P.262, K.263, S.264, V.265, T.266, R.269, N.273, C.299 Ligands: XY0.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.210, A:Y.210, A:Y.210 Hydrogen bonds: A:T.20, A:W.21, A:W.21, A:D.44, A:H.111, A:N.161, A:Q.184, A:S.211, A:L.213, A:S.215, A:S.215, A:S.215, A:D.217, A:K.263, A:S.264, A:V.265, A:T.266, A:N.273, A:N.273 Water bridges: A:R.269, A:R.269 Salt bridges: A:K.263, A:R.269 pi-Cation interactions: A:R.269

1 x XY0: {7-[(5-chloro-1,3-benzothiazol-2-yl)methyl]-8-oxo-7,8-dihydropyrazino[2,3-d]pyridazin-5-yl}acetic acid(Non-covalent)

XY0.2: 15 residues within 4Å: Chain A: W.21, Y.49, H.111, W.112, F.123, S.211, S.215, R.218, P.219, V.298, C.299, L.301, L.302, S.303 Ligands: NAP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.21, A:Y.49 Hydrogen bonds: A:Y.49, A:Y.49 Water bridges: A:W.21 Salt bridges: A:H.111 pi-Stacking: A:W.21, A:W.21, A:W.21, A:F.123

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 10 residues within 4Å: Chain A: S.3, P.14, I.15, L.16, G.39, Y.40, R.41, H.42, F.274, F.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.15, A:L.16, A:G.39, A:R.41 EDO.4: 8 residues within 4Å: Chain A: H.47, W.80, T.82, Y.83, G.119, K.120, E.121, F.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.47, A:Y.83 Water bridges: A:G.119 EDO.5: 11 residues within 4Å: Chain A: R.4, A.11, K.12, M.13, P.14, E.71, E.72, L.73, F.74, D.106, K.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.4, A:K.12, A:K.12 Water bridges: A:K.12 EDO.6: 3 residues within 4Å: Chain A: E.151, G.152, L.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.151

13 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.7: 3 residues within 4Å: Chain A: Q.27, V.265 Ligands: PEO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.27 PEO.8: 1 residues within 4Å: Ligands: PEO.7 No protein-ligand interaction detected (PLIP) PEO.9: 3 residues within 4Å: Chain A: E.121, F.122, F.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.122, A:F.123 PEO.10: 3 residues within 4Å: Chain A: K.177, Y.178, K.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.177, A:K.179 PEO.11: 7 residues within 4Å: Chain A: H.47, Y.83, A.92, K.95, T.96, Y.108 Ligands: PEO.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.92, A:A.92, A:T.96 PEO.12: 7 residues within 4Å: Chain A: A.46, H.47, V.48, K.78, L.79, W.80, H.111 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.47, A:V.48, A:K.78, A:K.78, A:H.111 PEO.13: 7 residues within 4Å: Chain A: T.20, C.45, A.46, Y.49, N.51, E.52, V.55 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.46, A:N.51, A:N.51, A:N.51 PEO.14: 11 residues within 4Å: Chain A: C.81, T.82, Y.83, H.84, E.85, L.88, G.115, F.116, P.118, S.134, T.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.81, A:T.82, A:H.84, A:E.85, A:F.116 PEO.15: 7 residues within 4Å: Chain A: C.187, H.188, T.192, F.252, P.253, R.256, L.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.256 PEO.16: 7 residues within 4Å: Chain A: L.213, G.214, P.216, S.227, L.228, L.229, W.296 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.213, A:L.213, A:S.227, A:L.228, A:L.229 PEO.17: 8 residues within 4Å: Chain A: L.18, G.19, Y.40, P.262, K.263, S.264, I.270, N.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.40, A:P.262, A:N.273 PEO.18: 10 residues within 4Å: Chain A: M.13, H.42, D.44, V.76, K.78, L.107, L.109, Q.184, T.208, I.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.42, A:D.44, A:D.44, A:D.44, A:Q.184 PEO.19: 8 residues within 4Å: Chain A: H.47, K.78, L.79, W.80, Y.83, A.92, Y.108 Ligands: PEO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.80, A:Y.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arenas, R. et al., Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003 Soaked In Hydrogen Peroxide. To Be Published

Release Date

2023-12-20

Peptides

Aldo-keto reductase family 1 member B1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aldo-keto reductase family 1 member B1

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