SMTL ID : 5ufj.1

Crystal Structure of Carbonmonoxy Hemoglobin S (Liganded Sickle Cell Hemoglobin) Complexed with GBT Compound 6

Coordinates

PDB Format Compare

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

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

CMO.2: 3 residues within 4Å: Chain A: H.58, V.62 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.5: 4 residues within 4Å: Chain B: F.42, H.63, V.67 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CMO.7: 4 residues within 4Å: Chain C: H.58, V.62, H.87 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) CMO.10: 3 residues within 4Å: Chain D: H.63, V.67 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

2 x 86M: 5-[(imidazo[1,2-a]pyridin-8-yl)methoxy]-2-methoxypyridine-4-carbaldehyde(Covalent)

86M.3: 12 residues within 4Å: Chain A: V.1, L.2, P.77, K.127, A.130, S.131, T.134, V.135 Chain C: V.1, T.134, S.138 Ligands: 86M.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.1, A:V.135, C:V.1, C:T.134 86M.8: 12 residues within 4Å: Chain A: V.1, T.134, S.138 Chain C: V.1, L.2, P.77, K.127, A.130, S.131, T.134, V.135 Ligands: 86M.3 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.1, A:T.134, C:V.1, C:V.135 Hydrogen bonds: C:T.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metcalf, B. et al., Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med Chem Lett (2017)

Release Date

2017-02-22

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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