SMTL ID : 7cnd.1

NCI-1 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.2

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

GTP.2: 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.25, A:T.25, A:E.36, A:Y.39, A:V.40, A:T.42, A:T.66, A:G.68, A:N.122, A:K.123, A:A.151, A:K.152 Water bridges: A:V.40, A:T.42, A:T.42, A:L.69, A:L.69, A:K.123, A:K.123 Salt bridges: A:K.23, A:K.23, A:D.125 pi-Stacking: A:F.35, A:F.35

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

DMS.3: 3 residues within 4Å: Chain A: D.125, S.153, Y.155 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: R.76, N.103, W.104, R.106, D.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.76, A:R.106 Water bridges: A:R.106 Salt bridges: A:D.107 pi-Cation interactions: A:W.104 DMS.8: 5 residues within 4Å: Chain C: L.286, Q.287, A.290, L.342, N.345 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.345 DMS.9: 6 residues within 4Å: Chain C: S.882, F.885, F.886, T.889, M.943, A.947 No protein-ligand interaction detected (PLIP) DMS.11: 4 residues within 4Å: Chain C: R.414, E.415, V.418, Y.419 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.414 Water bridges: C:R.414 Salt bridges: C:E.415 pi-Cation interactions: C:Y.419 DMS.18: 3 residues within 4Å: Chain C: N.791, D.832, W.836 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.832

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

CL.5: 3 residues within 4Å: Chain A: P.49, L.50, V.51 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: M.189 Chain B: A.98 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: A.327, R.328, R.330, A.331 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain C: W.447 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain C: E.605 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: Q.316, E.360 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: F.897, L.981 Ligand excluded by PLIP

1 x G6U: ~{N}-[(~{E})-3-[3,5-bis(trifluoromethyl)phenyl]sulfinylprop-2-enyl]-3-methyl-butan-1-amine(Non-covalent)

G6U.7: 12 residues within 4Å: Chain C: L.481, T.484, K.490, K.493, A.494, A.497, I.500, F.517, T.520, V.521, K.524, F.528 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.481, C:K.493, C:A.494, C:F.528, C:F.528 Water bridges: C:T.484 Halogen bonds: C:T.520

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain C: S.148, S.151, V.152, C.155, V.203, L.212 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.151

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

MPO.15: 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 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.323 Water bridges: A:R.140 Salt bridges: A:R.140, A:K.141

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

2021-06-09

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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