SMTL ID : 5e83.1

CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE CELL HEMOGLOBIN) COMPLEXED WITH GBT440, CO-CRYSTALLIZATION EXPERIMENT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:F.43, A:F.43, A:F.46, A:V.62, A:V.62, A:L.66, A:L.83, A:L.91, A:V.93, A:F.98, A:F.98, A:L.136 Water bridges: A:K.61, A:K.61 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.87, A:H.87, A:H.87 Metal complexes: A:H.87 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.6 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:A.70, 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 Hydrogen bonds: B:S.44 pi-Cation interactions: B:H.92 Metal complexes: B:H.92 HEM.7: 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.8 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.43, C:F.43, C:A.65, 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, C:K.61 pi-Stacking: C:H.58, C:H.87, C:H.87 Metal complexes: C:H.87 HEM.10: 18 residues within 4Å: Chain D: 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.11 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:A.70, 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:H.63, D:K.66 pi-Cation interactions: D:H.92 Metal complexes: D:H.92

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

CMO.2: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 CMO.6: 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.8: 5 residues within 4Å: Chain C: L.29, F.43, H.58, V.62 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CMO.11: 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

1 x 5L7: 2-methyl-3-({2-[1-(propan-2-yl)-1H-pyrazol-5-yl]pyridin-3-yl}methoxy)phenol(Covalent)

5L7.3: 10 residues within 4Å: Chain A: V.1, P.77, A.130, S.131, T.134, V.135 Chain C: V.1, S.131, T.134, S.138 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.1, A:A.130, A:T.134, A:V.135, C:V.1, C:T.134 Hydrogen bonds: C:S.138 Water bridges: C:S.138

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: K.139 Chain D: P.36, Q.39, L.48, S.49, T.50, P.51, V.54 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.39, D:Q.39, D:T.50, A:K.139 GOL.12: 7 residues within 4Å: Chain D: P.100, E.101, F.103, R.104, A.138, N.139, A.142 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.101, D:E.101, D:R.104 Water bridges: D:N.139 GOL.13: 7 residues within 4Å: Chain D: V.1, H.2, L.3, K.8, L.78, L.81, G.136 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.2, D:L.3, D:L.3, D:K.132 Water bridges: D:K.8, D:G.136

1 x UNL: UNKNOWN LIGAND

UNL.9: 6 residues within 4Å: Chain B: Q.39, L.48, S.49, T.50, P.51 Chain C: K.139 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.51, C:K.139 Hydrogen bonds: B:Q.39, B:Q.39, C:K.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oksenberg, D. et al., GBT440 increases haemoglobin oxygen affinity, reduces sickling and prolongs RBC half-life in a murine model of sickle cell disease. Br.J.Haematol. (2016)

Release Date

2016-07-20

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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