Fluorine in PDB 7cnd: Nci-1 in Complex with CRM1-Ran-RANBP1

Protein crystallography data

The structure of Nci-1 in Complex with CRM1-Ran-RANBP1, PDB code: 7cnd was solved by Q.Sun, Y.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.56 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.333, 105.333, 304.205, 90, 90, 90
R / Rfree (%) 20.2 / 23.2

Other elements in 7cnd:

The structure of Nci-1 in Complex with CRM1-Ran-RANBP1 also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms
Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Nci-1 in Complex with CRM1-Ran-RANBP1 (pdb code 7cnd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Nci-1 in Complex with CRM1-Ran-RANBP1, PDB code: 7cnd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7cnd

Go back to Fluorine Binding Sites List in 7cnd
Fluorine binding site 1 out of 6 in the Nci-1 in Complex with CRM1-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Nci-1 in Complex with CRM1-Ran-RANBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:84.5
occ:0.83
F19 C:G6U1101 0.0 84.5 0.8
C18 C:G6U1101 1.3 81.9 0.8
F20 C:G6U1101 2.1 82.3 0.8
F21 C:G6U1101 2.1 80.3 0.8
C16 C:G6U1101 2.3 80.8 0.8
C15 C:G6U1101 2.9 82.0 0.8
C17 C:G6U1101 3.4 79.3 0.8
CA C:VAL576 3.7 38.5 1.0
CB C:LYS579 3.7 44.3 1.0
CG2 C:VAL576 3.9 38.7 1.0
O C:THR575 4.0 40.6 1.0
CG C:LYS579 4.0 46.1 1.0
CG2 C:THR575 4.0 42.8 1.0
N C:VAL576 4.1 39.1 1.0
CE C:MET556 4.1 36.1 0.6
C C:THR575 4.2 40.0 1.0
C14 C:G6U1101 4.2 83.2 0.8
CB C:VAL576 4.4 37.8 1.0
C12 C:G6U1101 4.6 79.7 0.8
O C:VAL576 4.7 37.5 1.0
C C:VAL576 4.7 37.6 1.0
C13 C:G6U1101 4.9 81.6 0.8
CB C:THR575 4.9 42.6 1.0
O C:HOH1362 5.0 47.5 1.0

Fluorine binding site 2 out of 6 in 7cnd

Go back to Fluorine Binding Sites List in 7cnd
Fluorine binding site 2 out of 6 in the Nci-1 in Complex with CRM1-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Nci-1 in Complex with CRM1-Ran-RANBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:82.3
occ:0.83
F20 C:G6U1101 0.0 82.3 0.8
C18 C:G6U1101 1.3 81.9 0.8
F19 C:G6U1101 2.1 84.5 0.8
F21 C:G6U1101 2.2 80.3 0.8
C16 C:G6U1101 2.3 80.8 0.8
C15 C:G6U1101 2.8 82.0 0.8
C17 C:G6U1101 3.4 79.3 0.8
CE1 C:PHE572 3.7 45.5 1.0
CZ C:PHE572 3.9 44.6 1.0
C14 C:G6U1101 4.1 83.2 0.8
CG2 C:VAL576 4.4 38.7 1.0
C12 C:G6U1101 4.6 79.7 0.8
CG2 C:THR575 4.6 42.8 1.0
CD1 C:PHE572 4.7 45.0 1.0
CD1 C:LEU536 4.8 47.7 1.0
F24 C:G6U1101 4.8 84.3 0.8
CG2 C:ILE532 4.8 41.4 1.0
CD2 C:LEU536 4.8 47.0 1.0
C13 C:G6U1101 4.8 81.6 0.8

Fluorine binding site 3 out of 6 in 7cnd

Go back to Fluorine Binding Sites List in 7cnd
Fluorine binding site 3 out of 6 in the Nci-1 in Complex with CRM1-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Nci-1 in Complex with CRM1-Ran-RANBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:80.3
occ:0.83
F21 C:G6U1101 0.0 80.3 0.8
C18 C:G6U1101 1.3 81.9 0.8
F19 C:G6U1101 2.1 84.5 0.8
F20 C:G6U1101 2.2 82.3 0.8
C16 C:G6U1101 2.3 80.8 0.8
C17 C:G6U1101 2.7 79.3 0.8
CE C:MET556 3.5 36.1 0.6
C15 C:G6U1101 3.6 82.0 0.8
CG2 C:ILE555 3.6 37.7 1.0
SD C:MET556 3.9 35.7 0.6
C12 C:G6U1101 4.1 79.7 0.8
CG2 C:VAL576 4.1 38.7 1.0
C14 C:G6U1101 4.7 83.2 0.8
CZ C:PHE572 4.8 44.6 1.0
CA C:VAL576 4.8 38.5 1.0
O11 C:G6U1101 4.9 77.0 0.8
CG2 C:VAL559 4.9 37.6 1.0
CG C:LYS579 4.9 46.1 1.0
CB C:VAL576 4.9 37.8 1.0
C13 C:G6U1101 4.9 81.6 0.8
CB C:ILE555 5.0 37.0 1.0

Fluorine binding site 4 out of 6 in 7cnd

Go back to Fluorine Binding Sites List in 7cnd
Fluorine binding site 4 out of 6 in the Nci-1 in Complex with CRM1-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Nci-1 in Complex with CRM1-Ran-RANBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:84.3
occ:0.83
F24 C:G6U1101 0.0 84.3 0.8
C22 C:G6U1101 1.3 84.6 0.8
F23 C:G6U1101 2.2 85.5 0.8
F25 C:G6U1101 2.2 84.9 0.8
C14 C:G6U1101 2.3 83.2 0.8
C15 C:G6U1101 2.8 82.0 0.8
C13 C:G6U1101 3.5 81.6 0.8
C16 C:G6U1101 4.1 80.8 0.8
C12 C:G6U1101 4.6 79.7 0.8
CD2 C:LEU536 4.7 47.0 1.0
F20 C:G6U1101 4.8 82.3 0.8
C17 C:G6U1101 4.9 79.3 0.8
CD1 C:LEU536 4.9 47.7 1.0

Fluorine binding site 5 out of 6 in 7cnd

Go back to Fluorine Binding Sites List in 7cnd
Fluorine binding site 5 out of 6 in the Nci-1 in Complex with CRM1-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Nci-1 in Complex with CRM1-Ran-RANBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:85.5
occ:0.83
F23 C:G6U1101 0.0 85.5 0.8
C22 C:G6U1101 1.3 84.6 0.8
F24 C:G6U1101 2.2 84.3 0.8
F25 C:G6U1101 2.2 84.9 0.8
C14 C:G6U1101 2.3 83.2 0.8
C13 C:G6U1101 2.7 81.6 0.8
C15 C:G6U1101 3.6 82.0 0.8
C12 C:G6U1101 4.1 79.7 0.8
C09 C:G6U1101 4.7 78.0 0.8
OE2 C:GLU540 4.7 79.1 1.0
O C:HOH1202 4.7 93.2 1.0
C16 C:G6U1101 4.7 80.8 0.8
CD2 C:LEU536 4.8 47.0 1.0
NZ C:LYS579 4.8 53.5 1.0
CE C:LYS579 4.8 51.0 1.0
C17 C:G6U1101 4.9 79.3 0.8

Fluorine binding site 6 out of 6 in 7cnd

Go back to Fluorine Binding Sites List in 7cnd
Fluorine binding site 6 out of 6 in the Nci-1 in Complex with CRM1-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Nci-1 in Complex with CRM1-Ran-RANBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:84.9
occ:0.83
F25 C:G6U1101 0.0 84.9 0.8
C22 C:G6U1101 1.3 84.6 0.8
F24 C:G6U1101 2.2 84.3 0.8
F23 C:G6U1101 2.2 85.5 0.8
C14 C:G6U1101 2.3 83.2 0.8
C15 C:G6U1101 3.0 82.0 0.8
C13 C:G6U1101 3.3 81.6 0.8
CE C:LYS579 3.4 51.0 1.0
NZ C:LYS579 3.6 53.5 1.0
C16 C:G6U1101 4.3 80.8 0.8
C12 C:G6U1101 4.5 79.7 0.8
CD C:LYS579 4.8 48.5 1.0
C17 C:G6U1101 4.9 79.3 0.8

Reference:

Y.Lei, Q.An, X.F.Shen, M.Sui, C.Li, D.Jia, Y.Luo, Q.Sun. Structure-Guided Design of the First Noncovalent Small-Molecule Inhibitor of CRM1. J.Med.Chem. V. 64 6596 2021.
ISSN: ISSN 0022-2623
PubMed: 33974430
DOI: 10.1021/ACS.JMEDCHEM.0C01675
Page generated: Sat Jul 10 14:04:57 2021

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