SMTL ID : 6xd9.1

Carbonmonoxy hemoglobin in complex with the antisickling agent 2-hydroxy-6-((6-(hydroxymethyl)pyridin-2-yl)methoxy)benzaldehyde (VZHE039)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

CMO.1: 5 residues within 4Å: Chain A: L.29, F.43, H.58, V.62 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 No protein-ligand interaction detected (PLIP) CMO.6: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) 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)(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: 24 interactions with chain A, 1 Ligand-Ligand interactions 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.91, A:V.93, A:N.97, A:F.98, A:F.98, A:F.98, A:L.136 Water bridges: A:H.58, A:K.61, A:K.61, A:K.61 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:F.98 Metal complexes: A:H.87, CMO.1 HEM.5: 18 residues within 4Å: Chain B: 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, L.141 Ligands: CMO.4 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Ligand interactions 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:L.106, B:L.141 Water bridges: B:S.44 Metal complexes: B:H.92, CMO.4 HEM.7: 19 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, V.132, L.136 Ligands: CMO.6 23 PLIP interactions: 22 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.43, C:F.46, C:K.61, C:V.62, C:A.65, C:L.83, C:L.86, C:L.91, C:V.93, C:N.97, C:F.98, C:F.98, C:L.101, C:V.132, C:L.136 Water bridges: C:Q.54, C:K.61 Salt bridges: C:K.61 Metal complexes: C:H.87, CMO.6 HEM.10: 19 residues within 4Å: Chain D: T.38, F.41, F.42, F.45, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.9 18 PLIP interactions: 17 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:V.67, D:A.70, D:F.71, D:F.71, D:L.88, D:L.96, D:V.98, D:L.106, D:L.141 Salt bridges: D:H.63 Metal complexes: D:H.92, CMO.9

2 x V39: 3-{[6-(hydroxymethyl)pyridin-2-yl]methoxy}-2-methylphenol(Covalent)

V39.3: 12 residues within 4Å: Chain A: V.1, V.73, M.76, P.77, K.127, A.130, S.131, T.134 Chain C: V.1, T.134, S.138 Ligands: V39.8 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:V.1, C:T.134, A:V.1, A:P.77 Hydrogen bonds: C:S.138, A:V.1, A:V.73, A:M.76 Water bridges: A:S.131 V39.8: 14 residues within 4Å: Chain A: V.1, T.134, S.138 Chain C: V.1, V.73, D.74, D.75, M.76, P.77, K.127, A.130, S.131, T.134 Ligands: V39.3 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.1, C:P.77, A:V.1, A:T.134 Hydrogen bonds: C:V.1, C:V.1, C:V.73, C:M.76, A:S.138 Water bridges: C:S.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abdulmalik, O. et al., VZHE-039, a novel antisickling agent that prevents erythrocyte sickling under both hypoxic and anoxic conditions. Sci Rep (2020)

Release Date

2020-12-23

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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