SMTL ID : 4rom.1

Deoxyhemoglobin in complex with imidazolylacryloyl derivatives

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 19 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, L.136 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:F.46, A:V.62, A:V.62, A:A.65, A:L.66, A:L.83, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:V.93, A:F.98, A:F.98, A:L.101, A:L.136 Water bridges: A:H.45 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.58 Metal complexes: A:H.87 HEM.3: 17 residues within 4Å: Chain B: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:L.31, B:F.41, B:F.42, B:F.42, B:K.66, B:K.66, B:V.67, B:F.85, B:L.88, B:L.91, B:L.96, B:L.96, B:V.98, B:V.98, B:N.102, B:F.103, B:L.141 Salt bridges: B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.5: 19 residues within 4Å: Chain C: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.105, L.136 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:Y.42, C:F.43, C:F.46, C:K.61, C:V.62, C:L.83, C:L.83, C:L.86, C:L.91, C:L.91, C:V.93, C:V.93, C:F.98, C:L.101, C:L.105, C:L.136 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58 Metal complexes: C:H.87 HEM.7: 18 residues within 4Å: Chain D: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.71, F.85, L.88, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:L.31, D:F.41, D:F.41, D:F.42, D:K.66, D:V.67, D:F.71, D:F.85, D:L.88, D:L.96, D:L.96, D:V.98, D:V.98, D:F.103, D:V.137, D:L.141 Water bridges: D:S.44 Salt bridges: D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

2 x 3U8: 4-{2-chloro-4-[3-(1H-imidazol-2-yl)propanoyl]phenoxy}butanoic acid(Covalent)

3U8.2: 10 residues within 4Å: Chain A: V.1, L.2, K.99, K.127, A.130, S.131 Chain C: P.95, K.99, T.137, R.141 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:V.1, A:K.127, A:A.130, C:P.95 Hydrogen bonds: A:V.1, A:K.127, C:R.141 Water bridges: A:K.99, C:P.95, C:K.99, C:K.99, C:K.99 Salt bridges: A:K.99, C:K.99 3U8.6: 8 residues within 4Å: Chain A: T.137, R.141 Chain C: V.1, L.2, K.99, K.127, A.130, S.131 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.1, C:K.127, C:A.130 Hydrogen bonds: C:V.1, C:L.2, C:K.127, A:R.141 Water bridges: C:K.99, C:K.99, C:S.131, C:S.131 Salt bridges: C:K.99

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

SO4.4: 5 residues within 4Å: Chain B: V.1, L.78, D.79, N.80, L.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.81 Water bridges: B:K.82 SO4.8: 5 residues within 4Å: Chain D: D.79, N.80, L.81, K.82, G.83 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.79, D:N.80, D:K.82, D:G.83 Water bridges: D:L.81, D:L.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Omar, A.M. et al., Identification of a novel class of covalent modifiers of hemoglobin as potential antisickling agents. Org.Biomol.Chem. (2015)

Release Date

2015-05-20

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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