SMTL ID : 6lq9.1

S109 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1: 25 residues within 4Å: Chain A: D.37, G.38, G.39, T.40, G.41, K.42, T.43, T.44, F.54, E.55, K.56, K.57, Y.58, A.60, T.61, A.86, G.87, N.141, K.142, D.144, I.145, S.169, A.170, K.171 Ligands: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:G.39, A:T.40, A:T.40, A:G.41, A:K.42, A:T.43, A:T.43, A:T.44, A:T.44, A:E.55, A:V.59, A:T.61, A:T.61, A:T.85, A:G.87, A:N.141, A:K.142, A:K.142, A:S.169, A:A.170, A:K.171 Water bridges: A:V.59, A:Q.88, A:Q.88 Salt bridges: A:K.42, A:K.42, A:D.144 pi-Stacking: A:F.54, A:F.54

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.43, T.61 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.43, A:T.61, H2O.1, H2O.1

5 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 3 residues within 4Å: Chain A: N.122, W.123, D.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.122 NO3.4: 5 residues within 4Å: Chain A: T.112, S.113, R.114, K.149 Chain C: R.864 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.114 Water bridges: A:T.112, A:V.115 NO3.5: 6 residues within 4Å: Chain A: H.158, R.159, L.163, Q.164 Chain C: Q.316, L.361 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:L.163 Water bridges: C:Q.316, C:Q.316 NO3.8: 2 residues within 4Å: Chain C: P.940, T.951 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.942 NO3.9: 4 residues within 4Å: Chain C: L.808, N.812, D.853, W.857 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.812

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

CL.6: 3 residues within 4Å: Chain A: R.148, K.151, A.152 Ligand excluded by PLIP

1 x EQF: (3~{R},4~{S})-1-[[6-chloranyl-5-(trifluoromethyl)pyridin-2-yl]amino]-3,4-dimethyl-pyrrolidine-2,5-dione(Covalent)

EQF.7: 10 residues within 4Å: Chain C: L.502, C.505, K.514, V.517, A.518, I.521, T.541, V.542, K.545, F.549 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.502, C:V.517, C:A.518, C:I.521, C:K.545, C:K.545, C:F.549 Hydrogen bonds: C:K.545

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain C: V.495, K.499, F.531, H.535, F.538 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, Y. et al., Structure-Guided Design of the First Noncovalent Small-Molecule Inhibitor of CRM1. J.Med.Chem. (2021)

Release Date

2021-06-23

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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