SMTL ID : 8egi.1

X-ray structure of carbonmonoxy hemoglobin in complex with VZHE039-NO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

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

CMO.1: 5 residues within 4Å: Chain A: F.44, H.59, V.63, H.88 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) CMO.4: 6 residues within 4Å: Chain B: L.29, F.43, H.64, V.68, H.93 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.64 CMO.6: 4 residues within 4Å: Chain C: F.44, H.59, H.88 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CMO.9: 6 residues within 4Å: Chain D: L.29, F.43, H.64, V.68, H.93 Ligands: HEM.10 No protein-ligand interaction detected (PLIP)

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

HEM.2: 19 residues within 4Å: Chain A: Y.43, F.44, H.46, F.47, H.59, K.62, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, S.134, L.137 Ligands: CMO.1 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.43, A:Y.43, A:F.44, A:F.44, A:F.47, A:A.66, A:L.67, A:L.84, A:L.92, A:V.94, A:F.99, A:F.99, A:F.99, A:L.137 Salt bridges: A:H.46, A:H.59, A:K.62 Metal complexes: A:H.88 HEM.5: 18 residues within 4Å: Chain B: T.39, F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: CMO.4 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:T.39, B:F.42, B:F.42, B:F.43, B:F.43, B:V.68, B:A.71, B:F.72, B:L.89, B:L.97, B:V.99, B:N.103, B:F.104, B:L.142 Water bridges: B:H.64, B:K.67 Salt bridges: B:K.67 Metal complexes: B:H.93 HEM.7: 19 residues within 4Å: Chain C: M.33, Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 Ligands: CMO.6 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:Y.43, C:Y.43, C:F.44, C:F.44, C:F.47, C:V.63, C:A.66, C:L.67, C:L.84, C:L.92, C:V.94, C:N.98, C:F.99, C:F.99, C:L.102, C:L.102, C:L.137 Water bridges: C:Y.43 Salt bridges: C:K.62 Metal complexes: C:H.88 HEM.10: 18 residues within 4Å: Chain D: T.39, F.42, F.43, F.46, H.64, K.67, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: CMO.9 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:T.39, D:F.42, D:F.42, D:F.43, D:F.43, D:A.71, D:L.89, D:L.92, D:L.97, D:V.99, D:V.99, D:N.103, D:F.104, D:L.107, D:L.142 Water bridges: D:H.64, D:K.67 Salt bridges: D:H.64 Metal complexes: D:H.93

2 x VZN: {6-[(3-hydroxy-2-methylphenoxy)methyl]pyridin-2-yl}methyl nitrate(Covalent)

VZN.3: 14 residues within 4Å: Chain A: V.2, V.74, D.75, D.76, M.77, P.78, K.128, A.131, S.132, T.135 Chain C: V.2, T.135, S.139 Ligands: VZN.8 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.2, A:P.78, C:V.2, C:T.135, C:T.135 Hydrogen bonds: A:V.2, C:S.139 Water bridges: A:K.8 VZN.8: 14 residues within 4Å: Chain A: V.2, T.135, S.139 Chain C: V.2, V.74, D.75, D.76, M.77, P.78, K.128, A.131, S.132, T.135 Ligands: VZN.3 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.2, C:P.78, A:V.2, A:T.135 Hydrogen bonds: C:V.2, C:V.2, C:M.77, A:S.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, B. et al., Design, Synthesis, and Investigation of Novel Nitric Oxide (NO)-Releasing Aromatic Aldehydes as Drug Candidates for the Treatment of Sickle Cell Disease. Molecules (2022)

Release Date

2022-11-16

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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