SMTL ID : 1qxd.1 (1 other biounit)

Structural Basis for the Potent Antisickling Effect of a Novel Class of 5-Membered Heterocyclic Aldehydic Compounds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-2-2-mer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: H.20, Y.24, H.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.24 Salt bridges: A:H.20, A:H.112 SO4.4: 3 residues within 4Å: Chain B: K.82, H.143 Chain D: H.143 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Water bridges: B:K.82 Salt bridges: B:K.82, B:H.143, D:H.143 SO4.5: 6 residues within 4Å: Chain B: V.1, L.78, D.79, N.80, L.81, K.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.1, B:V.1, B:L.81, B:K.82 SO4.6: 4 residues within 4Å: Chain B: P.100, R.104, H.146 Chain D: R.104 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Salt bridges: D:R.104, D:H.146, B:R.104, B:H.146 Water bridges: B:R.104 SO4.8: 6 residues within 4Å: Chain C: K.16, V.17, H.20, Y.24, H.112, L.113 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.24, C:H.112 Salt bridges: C:H.20 SO4.9: 2 residues within 4Å: Chain C: H.89, K.90 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.89, C:K.90 SO4.12: 5 residues within 4Å: Chain D: V.1, L.78, N.80, L.81, K.82 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:V.1, D:L.81, D:K.82 Water bridges: D:K.82, D:K.82 Salt bridges: D:K.82

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

HEM.2: 20 residues within 4Å: Chain A: M.32, 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, V.132, L.136 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, 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.83, A:L.86, A:L.91, A:V.93, A:F.98, A:L.101, A:V.132, A:L.136 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:F.98 Metal complexes: A:H.87, H2O.1 HEM.7: 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, L.141 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:T.38, B:F.41, B:F.42, B:F.42, B:F.71, B:F.71, B:L.88, B:L.96, B:V.98, B:V.98, B:N.102, B:L.141 Metal complexes: B:H.92, H2O.4 HEM.10: 19 residues within 4Å: Chain C: M.32, 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, V.132, L.136 25 PLIP interactions: 24 interactions with chain C, 1 Ligand-Water interactions, 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.83, C:L.91, C:V.93, C:F.98, C:L.101, C:L.101, C:V.132, C:L.136 Water bridges: C:H.58, C:K.61 Salt bridges: C:H.58, C:K.61 pi-Stacking: C:H.58 Metal complexes: C:H.87, H2O.7 HEM.13: 18 residues within 4Å: Chain D: T.38, F.41, F.42, H.63, K.66, A.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141 21 PLIP interactions: 20 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:F.71, D:F.71, D:F.85, D:L.88, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:V.137, D:L.141 Salt bridges: D:K.66 pi-Stacking: D:H.92 Metal complexes: D:H.92, H2O.9

2 x FU2: FURFURAL(Covalent)

FU2.3: 8 residues within 4Å: Chain A: V.1, L.2, K.127, A.130, S.131, T.134 Chain C: T.134, S.138 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:T.134, A:V.1, A:L.2, A:K.127, A:A.130 FU2.11: 8 residues within 4Å: Chain A: T.134, S.138 Chain C: V.1, L.2, K.127, A.130, S.131, T.134 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.1, C:L.2, C:K.127, C:A.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safo, M.K. et al., Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds. J.Med.Chem. (2004)

Release Date

2003-09-16

Peptides

Hemoglobin alpha chain: AC
Hemoglobin beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin alpha chain

Hemoglobin beta chain

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