SMTL ID : 7uvb.1

CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE CELL HEMOGLOBIN) COMPLEXED WITH GBT021601

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 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: 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, N.97, F.98, L.101, V.132, L.136 Ligands: FOR.2 23 PLIP interactions: 22 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:L.66, A:L.83, A:L.83, A:L.86, A:L.91, A:N.97, A:F.98, A:F.98, A:L.101, A:V.132, A:L.136 Salt bridges: A:H.45, A:H.58, A:K.61 pi-Stacking: A:H.58, A:H.87, A:H.87 Metal complexes: FOR.2 HEM.4: 18 residues within 4Å: Chain B: T.38, F.41, F.42, 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: FOR.5 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.38, B:F.42, B:F.42, B:K.66, B:V.67, B:F.71, B:L.88, B:L.91, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Salt bridges: B:H.63 Metal complexes: B:H.92, FOR.5 HEM.6: 20 residues within 4Å: Chain C: 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 Ligands: FOR.7 18 PLIP interactions: 17 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.42, C:F.43, C:F.43, C:V.62, C:V.62, C:L.83, C:L.91, C:V.93, C:N.97, C:V.132, C:L.136 Salt bridges: C:H.45, C:H.58, C:K.61 pi-Stacking: C:H.58, C:H.87 Metal complexes: C:H.87, FOR.7 HEM.9: 18 residues within 4Å: Chain D: T.38, F.41, F.42, F.45, H.63, K.66, V.67, A.70, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: FOR.10 19 PLIP interactions: 18 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:L.88, D:L.91, D:L.96, D:V.98, D:V.98, D:N.102, D:L.106, D:L.141 Salt bridges: D:H.63 pi-Cation interactions: D:H.63 Metal complexes: FOR.10

4 x FOR: FORMYL GROUP(Non-covalent)

FOR.2: 4 residues within 4Å: Chain A: H.58, V.62, H.87 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) FOR.5: 4 residues within 4Å: Chain B: H.63, V.67, H.92 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) FOR.7: 4 residues within 4Å: Chain C: H.58, V.62, H.87 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) FOR.10: 4 residues within 4Å: Chain D: H.63, V.67, H.92 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

2 x OHF: 2-hydroxy-6-({(3S)-4-[2-(2-hydroxyethyl)pyridine-3-carbonyl]morpholin-3-yl}methoxy)benzaldehyde(Covalent)

OHF.3: 15 residues within 4Å: Chain A: V.1, A.123, D.126, K.127, A.130, S.131, T.134 Chain B: Y.35, W.37, L.105 Chain C: P.95, T.134, T.137, S.138 Ligands: OHF.8 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:T.134, C:T.134, A:V.1, B:W.37 Hydrogen bonds: C:T.137, A:D.126, A:D.126 OHF.8: 16 residues within 4Å: Chain A: V.1, M.76, S.131, T.134, V.135, S.138 Chain C: V.1, L.2, M.76, P.77, K.127, A.130, S.131, T.134, V.135 Ligands: OHF.3 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:V.1, C:V.1, C:A.130, A:T.134, A:T.134, A:V.135 Hydrogen bonds: A:V.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dufu, K. et al., GBT021601 improves red blood cell health and the pathophysiology of sickle cell disease in a murine model. Br.J.Haematol. (2023)

Release Date

2023-04-05

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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