SMTL ID : 5jlj.1

Crystal Structure of KPT8602 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 26 residues within 4Å: Chain A: D.39, G.40, G.41, T.42, G.43, K.44, T.45, T.46, F.56, E.57, K.58, K.59, Y.60, A.62, T.63, A.88, G.89, Q.90, N.143, K.144, D.146, I.147, S.171, A.172, K.173 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.41, A:T.42, A:T.42, A:G.43, A:K.44, A:K.44, A:K.44, A:T.45, A:T.45, A:T.46, A:T.46, A:E.57, A:T.63, A:T.63, A:G.89, A:N.143, A:K.144, A:K.144, A:A.172, A:K.173 Water bridges: A:T.45, A:Q.90, A:Q.90 Salt bridges: A:D.146 pi-Stacking: A:F.56, A:F.56

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.45, T.63 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.45, A:T.63, H2O.1, H2O.1

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.39, N.121, N.124, W.125, D.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.121 GOL.6: 6 residues within 4Å: Chain A: Y.167, Y.168, D.169 Chain C: E.360, K.363, D.426 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.426, A:D.169, A:D.169 GOL.7: 7 residues within 4Å: Chain C: G.207, S.208, S.210, F.245, S.248, D.250, T.251 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.207, C:S.210, C:S.248, C:S.248 GOL.8: 6 residues within 4Å: Chain C: N.935, S.938, V.939, P.940, S.952, N.953 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.935, C:N.953, C:N.953 GOL.9: 4 residues within 4Å: Chain C: L.808, N.812, D.853, W.857 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.812, C:W.857

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: K.173, D.232, D.235 Ligand excluded by PLIP

1 x 6L8: (2R)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-2-(pyrimidin-5-yl)propanamide(Non-covalent)

6L8.5: 12 residues within 4Å: Chain C: L.502, C.505, V.506, K.514, I.521, M.522, F.538, T.541, V.542, K.545, L.546, F.549 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.502, C:I.521, C:K.545, C:F.549

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hing, Z.A. et al., Next-generation XPO1 inhibitor shows improved efficacy and in vivo tolerability in hematological malignancies. Leukemia (2016)

Release Date

2016-06-29

Peptides

GTP-binding nuclear protein Ran: A
Ran-specific GTPase-activating protein 1: B
Exportin-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTP-binding nuclear protein Ran

Ran-specific GTPase-activating protein 1

Exportin-1

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