SMTL ID : 7ypz.1

Zafirlukast in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.24, T.42 Ligands: GTP.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.1

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 3 residues within 4Å: Chain A: Y.98, K.99, P.102 No protein-ligand interaction detected (PLIP) DMS.3: 4 residues within 4Å: Chain A: N.114, I.115, P.116, K.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.167 Water bridges: A:I.117 DMS.16: 2 residues within 4Å: Chain C: N.791, D.832 No protein-ligand interaction detected (PLIP) DMS.17: 2 residues within 4Å: Chain C: S.446, W.447 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.447 Water bridges: C:H.448 pi-Cation interactions: C:W.447 DMS.19: 4 residues within 4Å: Chain C: R.414, E.415, V.418, Y.419 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.414 Water bridges: C:E.415 Salt bridges: C:E.415 DMS.20: 4 residues within 4Å: Chain C: D.55, I.93, F.96 Ligands: NA.13 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:D.55 pi-Cation interactions: C:F.96

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

EDO.4: 5 residues within 4Å: Chain A: R.166, K.167, P.172 Chain C: A.307, Q.312 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.312 Water bridges: A:Q.145 EDO.5: 4 residues within 4Å: Chain A: D.125, S.153, Y.155 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.153 EDO.6: 2 residues within 4Å: Chain A: D.148 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.129 EDO.9: 6 residues within 4Å: Chain A: L.144, Q.145 Chain C: Q.316, E.358, E.360, L.361 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:E.360, C:E.360 Hydrogen bonds: A:Q.145 EDO.14: 6 residues within 4Å: Chain C: R.80, K.81, H.950, I.984, K.985, E.986 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.80, C:R.80, C:I.984 EDO.22: 3 residues within 4Å: Chain C: Q.348, E.388, Q.392 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.348 EDO.23: 4 residues within 4Å: Chain C: E.194, R.230, Y.231, T.235 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.194, C:R.230, C:R.230 EDO.24: 4 residues within 4Å: Chain C: P.617, N.646, I.647, T.650 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.646

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.7: 27 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, V.40, A.41, T.42, A.67, G.68, L.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.1 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:G.22, A:K.23, A:T.24, A:T.25, A:T.25, A:E.36, A:Y.39, A:T.42, A:T.66, A:G.68, A:N.122, A:K.123, A:K.123, A:S.150, A:A.151, A:K.152 Water bridges: A:T.24, A:V.40, A:T.42, A:D.65, A:L.69, A:L.69, A:K.152 Salt bridges: A:K.23, A:K.23, A:D.125 pi-Stacking: A:F.35, A:F.35

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

CL.8: 3 residues within 4Å: Chain A: K.152, D.211 Chain B: E.44 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: A.327, R.328, R.330, A.331 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 6 residues within 4Å: Chain C: W.51, E.52, K.53, V.54, D.55 Ligands: DMS.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.51, C:V.54, C:D.55

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 6 residues within 4Å: Chain C: I.356, E.357, E.358, R.359, F.362, N.400 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.356, C:E.358, C:N.400 GOL.18: 5 residues within 4Å: Chain C: R.403, E.405, W.455, R.498, Y.502 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.403, C:E.405, C:W.455 Water bridges: C:K.546

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.21: 10 residues within 4Å: Chain A: V.137, R.140, K.141 Chain C: M.320, T.323, T.324, A.327, T.364, D.367, Y.368 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.323 Salt bridges: A:R.140, A:K.141

1 x ZLK: zafirlukast(Non-covalent)

ZLK.25: 9 residues within 4Å: Chain C: K.478, L.481, I.500, N.516, F.517, T.520, V.521, K.524, F.528 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:K.478, C:L.481, C:L.481, C:I.500, C:I.500, C:F.517, C:F.517, C:T.520, C:K.524, C:F.528

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, W. et al., Searching for Novel Noncovalent Nuclear Export Inhibitors through a Drug Repurposing Approach. J.Med.Chem. (2023)

Release Date

2023-08-16

Peptides

GTP-binding nuclear protein Ran: A
YRB1 isoform 1: B
CRM1 isoform 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTP-binding nuclear protein Ran

YRB1 isoform 1

CRM1 isoform 1

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