SMTL ID : 4gmx.1

Crystal structure of KPT185 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 29 PLIP interactions: 29 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:N.122, A:K.123, A:K.123, A:A.151, A:K.152 Water bridges: A:T.24, A:V.40, A:Q.69, A:Q.69 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.7, H2O.8

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

EDO.3: 4 residues within 4Å: Chain A: N.100, N.103, W.104, D.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.100, A:N.103 EDO.10: 5 residues within 4Å: Chain C: Y.720, G.724, Y.728, V.788 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.720 Water bridges: C:G.724, C:Y.727

1 x K85: propan-2-yl 3-{3-[3-methoxy-5-(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}propanoate(Covalent)

K85.4: 14 residues within 4Å: Chain C: L.538, C.541, K.550, A.554, I.557, M.558, V.561, F.574, T.577, V.578, K.581, L.582, F.585, E.588 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.538, C:A.554, C:I.557, C:K.581, C:E.588 Water bridges: C:K.581 Halogen bonds: C:V.578

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain C: E.193, R.229, Y.230, E.233, T.234 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.193, C:R.229, C:R.229, C:E.233 GOL.6: 4 residues within 4Å: Chain C: W.502, S.503, W.504, N.549 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.504, C:N.549, C:N.549 Water bridges: C:S.503 GOL.7: 4 residues within 4Å: Chain C: L.844, N.848, D.889, W.893 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.848 Water bridges: C:N.848 GOL.8: 4 residues within 4Å: Chain C: G.724, H.725, Y.728 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.725 Water bridges: C:H.725, C:Y.728 GOL.9: 6 residues within 4Å: Chain A: R.166, K.167, D.171, P.172 Chain C: A.306, Q.311 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.167, C:Q.311 Water bridges: A:W.163, C:E.357 GOL.14: 5 residues within 4Å: Chain C: A.570, H.571, W.572, N.573, F.574 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.573, C:N.573, C:F.574 Water bridges: C:N.573

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

CL.11: 3 residues within 4Å: Chain C: T.1009, S.1010, E.1011 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: K.607, C.608, K.609, Y.610 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: P.63, Q.64, N.115 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lapalombella, R. et al., Selective inhibitors of nuclear export show that CRM1/XPO1 is a target in chronic lymphocytic leukemia. Blood (2012)

Release Date

2012-10-17

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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