SMTL ID : 4wvf.1

Crystal structure of KPT276 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, F.35, E.36, K.37, K.38, Y.39, A.41, T.42, A.67, G.68, Q.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:T.21, A:G.22, A:K.23, A:K.23, A:K.23, A:T.24, A:T.24, A:T.25, A:T.25, A:E.36, A:Y.39, A:T.42, A:T.42, A:T.66, A:G.68, A:Q.69, A:N.122, A:K.123, A:K.123, A:A.151, A:K.152 Water bridges: A:V.40 Salt bridges: A:D.125 pi-Stacking: A:F.35, A:F.35

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.24, T.42 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.9, H2O.9

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: N.100, N.103, W.104, R.106, D.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.100, A:N.103, A:R.106, A:D.107 Water bridges: A:R.106 EDO.8: 4 residues within 4Å: Chain C: Y.933, Q.954, S.958, T.985 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.958

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: H.139, R.140, L.144, Q.145, Y.146 Chain C: Q.316, E.358, E.360 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:R.140, A:Q.145, A:Q.145, A:Y.146, C:E.358 Water bridges: C:Y.304, C:Q.316, C:E.360 GOL.6: 4 residues within 4Å: Chain C: W.466, S.467, W.468, N.513 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.468, C:N.513, C:N.513 Water bridges: C:S.467 GOL.7: 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 Water bridges: C:N.812 GOL.12: 5 residues within 4Å: Chain C: E.194, R.230, Y.231, E.234, T.235 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.230, C:R.230, C:E.234

1 x K76: (2E)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-1-(3,3-difluoroazetidin-1-yl)prop-2-en-1-one(Covalent)

K76.5: 13 residues within 4Å: Chain C: L.502, C.505, V.506, K.514, I.521, M.522, V.525, F.538, T.541, V.542, K.545, L.546, F.549 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.502, C:I.521, C:K.545, C:F.549 Water bridges: C:K.545 pi-Cation interactions: C:K.545 Halogen bonds: C:V.542

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

CL.9: 3 residues within 4Å: Chain C: T.973, S.974, E.975 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: K.571, C.572, K.573, Y.574 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: P.64, Q.65, N.116 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haines, J.D. et al., Nuclear export inhibitors avert progression in preclinical models of inflammatory demyelination. Nat.Neurosci. (2015)

Release Date

2015-07-15

Peptides

GTP-binding nuclear protein Ran: A
Ran-specific GTPase-activating protein 1: B
Crm1p: 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

Crm1p

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