SMTL ID : 8huf.1

B28 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.24, T.42, D.65 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.2

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: V.124, S.153, Y.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.153, A:S.153 GOL.7: 6 residues within 4Å: Chain C: I.356, E.357, E.358, R.359, F.362, N.400 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.356, C:E.358, C:R.359, C:N.400 GOL.8: 7 residues within 4Å: Chain C: M.320, T.323, T.324, T.364, D.367, Y.368 Ligands: BR.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.323

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

GTP.3: 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, L.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.1 25 PLIP interactions: 25 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:G.68, A:N.122, A:K.123, A:K.123, A:A.151, A:K.152 Water bridges: A:T.42, A:T.42, 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

1 x BR: BROMIDE ION(Non-functional Binders)

BR.4: 1 residues within 4Å: Ligands: GOL.8 Ligand excluded by PLIP

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

CL.5: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP

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

NA.6: 1 residues within 4Å: Chain C: W.447 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.447

1 x N5X: 3-[(4-chlorophenyl)carbonylamino]-4-[4-(2,5-dimethylphenyl)piperazin-1-yl]benzoic acid(Non-covalent)

N5X.9: 12 residues within 4Å: Chain C: V.473, I.477, L.481, I.500, V.504, F.510, L.511, F.517, T.520, V.521, K.524, F.528 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.473, C:I.477, C:L.481, C:I.500, C:I.500, C:V.504, C:F.510, C:L.511, C:F.517, C:V.521, C:K.524, C:F.528, C:F.528

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

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