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Chlorine in PDB 7ee8: The Crystal Structure of Mif Bound to Compound D5

Enzymatic activity of The Crystal Structure of Mif Bound to Compound D5

All present enzymatic activity of The Crystal Structure of Mif Bound to Compound D5:
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of The Crystal Structure of Mif Bound to Compound D5, PDB code: 7ee8 was solved by C.P.Fan, D.Y.Guo, L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.41 / 1.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.775, 68.144, 86.162, 90, 90, 90
R / Rfree (%) 21.4 / 24.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of Mif Bound to Compound D5 (pdb code 7ee8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the The Crystal Structure of Mif Bound to Compound D5, PDB code: 7ee8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 7ee8

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Chlorine binding site 1 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:26.2
occ:1.00
 N A:SER53 3.1 18.9 1.0
CA A:SER52 3.7 19.5 1.0
CB A:SER52 3.9 20.2 1.0
C A:SER52 3.9 18.4 1.0
CA A:SER53 4.0 19.4 1.0
CB A:SER53 4.0 20.7 1.0
OG A:SER53 4.5 22.4 1.0
C A:SER53 4.6 18.9 1.0
O A:GLY51 4.8 25.6 1.0
N A:GLU54 4.8 18.9 1.0
OE2 A:GLU54 4.8 29.4 1.0

Chlorine binding site 2 out of 9 in 7ee8

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Chlorine binding site 2 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:24.8
occ:1.00
 NE2 A:GLN71 3.2 17.9 1.0
N A:GLN71 3.4 16.4 1.0
N A:ALA70 3.5 17.6 1.0
C A:GLY68 3.5 16.2 1.0
CA A:GLY68 3.6 15.9 1.0
O A:HOH389 3.6 36.9 1.0
CG A:GLN71 3.6 15.9 1.0
N A:GLY69 3.6 16.2 1.0
CD A:GLN71 3.9 17.5 1.0
CB A:GLN71 4.0 15.2 1.0
CB A:ALA70 4.0 18.0 1.0
CA A:ALA70 4.1 17.4 1.0
O A:GLY68 4.1 16.4 1.0
C A:ALA70 4.2 17.1 1.0
N A:GLY68 4.3 15.1 1.0
CA A:GLN71 4.3 15.0 1.0
C A:GLY69 4.3 16.6 1.0
CA A:GLY69 4.4 16.8 1.0
O A:HOH396 4.6 30.8 1.0
C A:ILE67 4.9 15.3 1.0
O A:ILE67 4.9 16.7 1.0
O A:HOH307 4.9 38.1 1.0

Chlorine binding site 3 out of 9 in 7ee8

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Chlorine binding site 3 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:16.1
occ:1.00
 O C:HOH327 3.0 15.4 1.0
N A:ASN102 3.1 12.3 1.0
ND2 A:ASN105 3.2 14.3 1.0
CA A:MET101 3.8 11.8 1.0
CG A:ASN102 3.8 18.9 1.0
CB A:ASN102 3.8 14.7 1.0
CB A:ASN105 3.9 13.3 1.0
C A:MET101 4.0 12.5 1.0
O A:HOH397 4.0 20.4 1.0
CE A:MET101 4.0 16.5 1.0
ND2 A:ASN102 4.0 20.1 1.0
CG A:ASN105 4.0 13.5 1.0
O C:HOH438 4.1 19.6 1.0
CA A:ASN102 4.1 12.8 1.0
O A:ASP100 4.2 13.9 1.0
OD1 A:ASN102 4.2 21.4 1.0
SD A:MET101 4.3 15.6 1.0
O A:HOH303 4.5 20.5 1.0
CB A:MET101 4.5 12.4 1.0
O C:HOH366 4.6 17.9 1.0
O A:ASN102 4.7 12.7 1.0
O A:HOH336 4.7 32.3 1.0
O C:HOH437 4.8 31.4 1.0
N A:MET101 4.9 11.8 1.0
C A:ASN102 4.9 13.1 1.0
O C:TYR98 4.9 12.8 1.0
C A:ASP100 5.0 13.0 1.0

Chlorine binding site 4 out of 9 in 7ee8

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Chlorine binding site 4 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:29.5
occ:1.00
 NE2 B:GLN71 3.3 20.0 1.0
N B:GLN71 3.4 18.9 1.0
N B:ALA70 3.5 20.1 1.0
O B:HOH435 3.5 33.8 1.0
CG B:GLN71 3.6 19.1 1.0
C B:GLY68 3.6 17.2 1.0
CA B:GLY68 3.6 16.2 1.0
N B:GLY69 3.6 17.9 1.0
CD B:GLN71 3.9 19.6 1.0
CB B:GLN71 3.9 18.7 1.0
CB B:ALA70 4.0 20.9 1.0
CA B:ALA70 4.1 20.0 1.0
O B:GLY68 4.1 17.0 1.0
C B:ALA70 4.2 19.9 1.0
C B:GLY69 4.3 19.4 1.0
CA B:GLN71 4.3 18.9 1.0
O B:HOH387 4.3 31.1 1.0
N B:GLY68 4.3 16.2 1.0
CA B:GLY69 4.4 18.9 1.0
C B:ILE67 4.9 16.8 1.0
O B:ILE67 5.0 17.7 1.0

Chlorine binding site 5 out of 9 in 7ee8

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Chlorine binding site 5 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:34.2
occ:1.00
 O B:HOH371 3.1 30.2 1.0
N B:LEU19 3.3 20.0 1.0
N B:PHE18 3.3 21.5 1.0
O A:HOH433 3.5 38.2 1.0
N B:GLY17 3.5 27.9 1.0
CG B:LEU19 3.6 21.1 1.0
CB B:LEU19 3.8 20.7 1.0
C B:GLY17 3.9 23.4 1.0
CA B:GLY17 4.0 25.6 1.0
O B:PRO15 4.1 26.6 1.0
CA B:PHE18 4.1 20.8 1.0
CD1 B:LEU19 4.1 21.9 1.0
CA B:LEU19 4.2 19.7 1.0
C B:PHE18 4.2 19.9 1.0
CB B:PHE18 4.3 21.1 1.0
C B:ASP16 4.4 29.7 1.0
CA B:ASP16 4.7 30.4 1.0
CD1 A:LEU46 4.8 17.0 1.0
CD2 B:LEU19 4.8 21.7 1.0
O B:GLY17 4.8 22.8 1.0
N B:SER20 4.9 19.7 1.0

Chlorine binding site 6 out of 9 in 7ee8

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Chlorine binding site 6 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:16.1
occ:1.00
 O B:HOH393 3.0 35.5 1.0
O A:HOH341 3.0 15.9 1.0
N B:ASN102 3.2 13.4 1.0
ND2 B:ASN105 3.2 14.5 1.0
CB B:ASN102 3.8 15.9 1.0
CG B:ASN102 3.8 19.8 1.0
CA B:MET101 3.8 13.5 1.0
O B:HOH388 3.9 22.9 1.0
CB B:ASN105 3.9 13.0 1.0
CE B:MET101 3.9 16.6 1.0
ND2 B:ASN102 3.9 21.0 1.0
C B:MET101 4.0 13.3 1.0
CG B:ASN105 4.0 14.2 1.0
O A:HOH448 4.1 18.3 1.0
CA B:ASN102 4.1 13.6 1.0
O B:ASP100 4.2 15.3 1.0
SD B:MET101 4.3 16.3 1.0
OD1 B:ASN102 4.3 22.9 1.0
CB B:MET101 4.5 14.2 1.0
O B:HOH306 4.5 17.9 1.0
O A:HOH450 4.6 40.1 1.0
O B:ASN102 4.7 13.3 1.0
O A:HOH365 4.8 16.4 1.0
N B:MET101 4.9 14.4 1.0
C B:ASN102 4.9 13.1 1.0
O A:TYR98 5.0 12.4 1.0
C B:ASP100 5.0 14.6 1.0

Chlorine binding site 7 out of 9 in 7ee8

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Chlorine binding site 7 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:18.4
occ:1.00
 O B:HOH342 3.0 15.6 1.0
N C:ASN102 3.1 14.6 1.0
ND2 C:ASN105 3.2 16.0 1.0
CB C:ASN102 3.7 17.7 1.0
CG C:ASN102 3.7 21.7 1.0
CA C:MET101 3.8 13.6 1.0
C C:MET101 3.9 13.8 1.0
CB C:ASN105 4.0 14.1 1.0
CA C:ASN102 4.0 15.9 1.0
CE C:MET101 4.0 17.2 1.0
O C:HOH392 4.1 23.0 1.0
O B:HOH439 4.1 19.2 1.0
CG C:ASN105 4.1 14.9 1.0
ND2 C:ASN102 4.1 23.0 1.0
OD1 C:ASN102 4.1 23.7 1.0
O C:ASP100 4.2 14.2 1.0
SD C:MET101 4.3 16.7 1.0
O C:HOH313 4.5 21.2 1.0
CB C:MET101 4.6 15.0 1.0
O C:ASN102 4.6 16.4 1.0
O B:HOH355 4.6 17.2 1.0
O B:HOH440 4.6 34.8 1.0
C C:ASN102 4.8 16.0 1.0
N C:MET101 4.9 12.5 1.0
O B:TYR98 4.9 12.1 1.0

Chlorine binding site 8 out of 9 in 7ee8

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Chlorine binding site 8 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:28.0
occ:1.00
 O C:HOH399 2.6 48.3 1.0
N C:ILE64 3.2 14.1 1.0
N C:PRO1 3.2 18.9 1.0
CD C:PRO1 3.4 19.4 1.0
CA C:PRO1 3.6 18.0 1.0
CG C:PRO1 3.7 20.3 1.0
CG1 C:ILE64 3.8 15.0 1.0
CB C:ILE64 3.9 14.4 1.0
CA C:SER63 3.9 13.3 1.0
C C:SER63 4.0 13.4 1.0
OG C:SER63 4.0 14.0 1.0
CA C:ILE64 4.1 14.7 1.0
NZ C:LYS32 4.1 20.1 1.0
CD1 C:ILE64 4.1 15.1 1.0
CE C:LYS32 4.2 19.6 1.0
CB C:PRO1 4.3 19.2 1.0
CB C:SER63 4.5 13.7 1.0
CD C:LYS32 4.6 19.6 1.0
O C:ILE64 4.7 17.5 1.0
C C:ILE64 4.8 16.0 1.0
O C:HIS62 4.8 14.4 1.0
C C:PRO1 5.0 16.7 1.0

Chlorine binding site 9 out of 9 in 7ee8

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Chlorine binding site 9 out of 9 in the The Crystal Structure of Mif Bound to Compound D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of The Crystal Structure of Mif Bound to Compound D5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:29.9
occ:1.00
 NE C:ARG73 3.1 20.9 1.0
O C:HOH354 3.1 23.2 1.0
NH2 C:ARG73 3.7 22.6 1.0
CZ C:ARG73 3.8 22.2 1.0
CD C:ARG73 4.0 19.6 1.0
CB C:ALA70 4.1 17.5 1.0
CA C:ALA70 4.2 16.5 1.0
CB C:ARG73 4.6 15.5 1.0
O C:ALA70 4.7 15.7 1.0
CG C:ARG73 4.9 17.9 1.0
O C:HOH412 4.9 19.0 1.0
C C:ALA70 5.0 15.4 1.0

Reference:

L.Yang, C.Yang, L.Wang, Z.Yang, D.Guo, C.Fan. Repurposing Old Drugs As Novel Inhibitors of Human Mif From Structural and Functional Analysis. Bioorg.Med.Chem.Lett. V. 55 28445 2022.
ISSN: ESSN 1464-3405
PubMed: 34758374
DOI: 10.1016/J.BMCL.2021.128445
Page generated: Sun Jul 13 00:22:14 2025

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