SMTL ID : 5urc.1

Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-HMF for the Treatment of Sickle Cell Disease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-mer

Ligands

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.1: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 CMO.4: 6 residues within 4Å: Chain B: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.63 CMO.6: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 CMO.9: 6 residues within 4Å: Chain D: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.63

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 19 residues within 4Å: Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.1 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:F.43, A:F.46, A:V.62, A:A.65, A:L.66, A:L.83, A:L.91, A:V.93, A:F.98, A:F.98, A:F.98, A:L.101, A:L.136 Water bridges: A:H.58, A:K.61, A:K.61 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.87, A:H.87 Metal complexes: A:H.87 HEM.5: 16 residues within 4Å: Chain B: T.38, F.41, F.42, H.63, K.66, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106 Ligands: CMO.4 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.71, B:L.88, B:L.91, B:L.96, B:V.98, B:N.102, B:F.103, B:F.103, B:L.106 Water bridges: B:H.63 pi-Cation interactions: B:H.92 Metal complexes: B:H.92 HEM.7: 18 residues within 4Å: Chain C: Y.42, F.43, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.6 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.43, C:F.46, C:V.62, C:A.65, C:L.66, C:L.83, C:L.91, C:V.93, C:F.98, C:F.98, C:L.101, C:L.136 Water bridges: C:K.61, C:K.61 Salt bridges: C:K.61 pi-Stacking: C:H.58, C:H.87 Metal complexes: C:H.87 HEM.10: 17 residues within 4Å: Chain D: T.38, F.41, F.42, F.45, H.63, K.66, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106 Ligands: CMO.9 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:F.71, D:F.71, D:L.88, D:L.91, D:L.96, D:V.98, D:F.103, D:L.106 Metal complexes: D:H.92

1 x 8MV: (5-formylfuran-2-yl)methyl acetate(Covalent)

8MV.3: 7 residues within 4Å: Chain A: V.1, L.2, K.127, A.130, S.131 Chain C: T.134, S.138 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.1, A:K.127, A:A.130 Water bridges: C:T.134

1 x FUX: 5-HYDROXYMETHYL-FURFURAL(Covalent)

FUX.8: 7 residues within 4Å: Chain A: T.134, S.138 Chain C: V.1, L.2, K.127, A.130, S.131 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:T.134, C:V.1 Water bridges: C:D.126, C:D.126, C:D.126, C:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, G.G. et al., Design, Synthesis, and Biological Evaluation of Ester and Ether Derivatives of Antisickling Agent 5-HMF for the Treatment of Sickle Cell Disease. Mol. Pharm. (2017)

Release Date

2017-03-15

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

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