SMTL ID : 7jy3.1

Structure of HbA with compound 23 (PF-07059013)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: OXY.2 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:F.43, A:F.46, A:L.66, A:L.83, A:L.91, A:V.93, A:F.98, A:F.98, A:L.136 Salt bridges: A:H.45 pi-Stacking: A:H.87 Metal complexes: A:H.87 HEM.5: 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: OXY.6 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:V.67, B:F.71, B:F.71, B:L.88, B:L.88, B:L.96, B:V.98, B:N.102, B:F.103, B:F.103, B:L.106, B:L.141, B:L.141 Water bridges: B:F.41, B:S.44 Salt bridges: B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.9: 18 residues within 4Å: Chain C: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: OXY.10 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.43, C:F.46, C:L.66, C:L.83, C:L.91, C:V.93, C:F.98, C:F.98, C:L.136 Salt bridges: C:H.45 pi-Stacking: C:H.87 Metal complexes: C:H.87 HEM.13: 18 residues within 4Å: Chain D: 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: OXY.14 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:F.71, D:F.71, D:L.88, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Salt bridges: D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 5 residues within 4Å: Chain A: L.29, F.43, H.58, V.62 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 OXY.6: 4 residues within 4Å: Chain B: F.42, H.63, V.67 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) OXY.10: 4 residues within 4Å: Chain C: F.43, H.58, V.62 Ligands: HEM.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 OXY.14: 4 residues within 4Å: Chain D: F.42, H.63, V.67 Ligands: HEM.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.63

5 x O4B: 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE(Non-covalent)

O4B.3: 5 residues within 4Å: Chain A: F.33, L.34, P.37, K.40, L.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.40 O4B.7: 3 residues within 4Å: Chain B: P.58, K.59, A.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.59 O4B.11: 4 residues within 4Å: Chain C: L.34, P.37, K.40, L.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.40 O4B.12: 6 residues within 4Å: Chain C: K.7, K.11, V.70, A.71, V.73, D.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.11 O4B.15: 3 residues within 4Å: Chain D: P.58, K.59, A.62 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.59

2 x VUD: 6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)pyridin-2(1H)-one(Non-covalent)

VUD.4: 10 residues within 4Å: Chain A: V.1, L.2, V.73, D.74, S.131 Chain C: D.74, P.77, T.134, V.135 Ligands: VUD.8 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:P.77, C:V.135, A:V.1, A:V.1, A:L.2 Hydrogen bonds: C:D.74, A:L.2 Water bridges: C:M.76, C:N.78 VUD.8: 9 residues within 4Å: Chain A: D.74, P.77, T.134, V.135 Chain C: V.1, L.2, V.73, D.74 Ligands: VUD.4 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:V.1, C:V.1, C:L.2, A:P.77, A:V.135 Hydrogen bonds: C:L.2, A:D.74 Water bridges: C:K.7, A:M.76, A:N.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gopalsamy, A. et al., PF-07059013: A Noncovalent Modulator of Hemoglobin for Treatment of Sickle Cell Disease. J.Med.Chem. (2021)

Release Date

2021-01-13

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

Related Entries With Identical Sequence