SMTL ID : 8hug.1

F1 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.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.1

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: D.125, S.153, Y.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.153 GOL.7: 7 residues within 4Å: Chain C: I.356, E.357, E.358, R.359, F.362, N.400, V.402 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.356, C:E.358, C:R.359, C:N.400 GOL.8: 5 residues within 4Å: Chain C: M.320, T.323, A.327, T.364, Y.368 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.364 GOL.9: 5 residues within 4Å: Chain C: L.286, Q.287, E.341, L.342, N.345 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.286, C:N.345 Water bridges: C:L.342

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

GTP.3: 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 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:G.22, 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:S.150, A:A.151, A:K.152 Water bridges: A:V.40, A:V.40, A:L.69, A:L.69 Salt bridges: A:K.23, A:K.23, A:D.125 pi-Stacking: A:F.35, A:F.35

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

CL.4: 4 residues within 4Å: Chain C: A.327, R.328, R.330, A.331 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain C: R.80, K.985 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP

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

DMS.6: 5 residues within 4Å: Chain C: W.51, L.77, K.81, L.84, L.85 No protein-ligand interaction detected (PLIP) DMS.10: 1 residues within 4Å: Chain C: Y.671 No protein-ligand interaction detected (PLIP) DMS.12: 6 residues within 4Å: Chain C: S.882, F.885, F.886, T.889, M.943, A.947 No protein-ligand interaction detected (PLIP)

1 x N59: 4-[4-(3-chlorophenyl)piperazin-1-yl]-3-[(3-fluorophenyl)sulfonylamino]benzoic acid(Non-covalent)

N59.13: 11 residues within 4Å: Chain C: I.477, K.478, L.481, I.500, M.501, N.516, F.517, T.520, V.521, K.524, F.528 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.481, C:I.500, C:F.517, C:T.520, C:K.524, C:F.528 Hydrogen bonds: C:N.516 Water bridges: C:F.517

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C. et al., Discovery of a Hidden Pocket beneath the NES Groove by Novel Noncovalent CRM1 Inhibitors. J.Med.Chem. (2023)

Release Date

2023-12-27

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

Related Entries With Identical Sequence