Chlorine in PDB 7knw: Crystal Structure of SND1 in Complex with C-26-A2

All present enzymatic activity of Crystal Structure of SND1 in Complex with C-26-A2:
3.1.31.1;

The structure of Crystal Structure of SND1 in Complex with C-26-A2, PDB code: 7knw was solved by Y.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.24, 86.154, 82.426, 82.71, 72, 65.42
R / Rfree (%)	26.4 / 33.8

The binding sites of Chlorine atom in the Crystal Structure of SND1 in Complex with C-26-A2 (pdb code 7knw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of SND1 in Complex with C-26-A2, PDB code: 7knw:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of SND1 in Complex with C-26-A2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of SND1 in Complex with C-26-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1002 b:33.9 occ:1.00 CL A:QOY1002 0.0 33.9 1.0 C3 A:QOY1002 1.7 37.1 1.0 C5 A:QOY1002 2.7 39.9 1.0 C1 A:QOY1002 2.7 31.4 1.0 N A:ILE284 3.1 33.9 1.0 O A:GLY282 3.2 33.2 1.0 CA A:ILE284 3.4 33.4 1.0 CD1 A:LEU287 3.5 41.2 1.0 C A:GLY282 3.5 34.4 1.0 O A:HOH1147 3.5 19.4 1.0 CB A:ILE284 3.6 38.0 1.0 C A:ASN283 3.6 32.1 1.0 CD1 A:ILE284 3.7 42.9 1.0 N A:ASN283 3.9 37.2 1.0 C4 A:QOY1002 4.0 39.7 1.0 C A:QOY1002 4.0 28.4 1.0 CA A:GLY282 4.1 33.3 1.0 CA A:ASN283 4.2 35.3 1.0 O A:ASN283 4.2 24.6 1.0 CG1 A:ILE284 4.2 45.0 1.0 N A:GLY282 4.3 32.2 1.0 C2 A:QOY1002 4.5 28.9 1.0 CG A:LEU287 4.5 40.1 1.0 C A:ILE284 4.8 33.7 1.0 CG2 A:ILE284 4.9 37.8 1.0 C A:ASN281 4.9 29.3 1.0 CB A:LEU287 5.0 31.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of SND1 in Complex with C-26-A2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of SND1 in Complex with C-26-A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1002 b:39.5 occ:1.00 CL B:QOY1002 0.0 39.5 1.0 C3 B:QOY1002 1.7 44.4 1.0 C1 B:QOY1002 2.7 45.8 1.0 C5 B:QOY1002 2.7 44.9 1.0 CD1 B:LEU287 3.3 39.8 1.0 O B:GLY282 3.4 31.6 1.0 N B:ILE284 3.4 37.6 1.0 C B:GLY282 3.4 37.7 1.0 CA B:ILE284 3.6 38.4 1.0 C B:ASN283 3.7 38.1 1.0 CA B:GLY282 3.8 36.3 1.0 N B:ASN283 3.8 42.2 1.0 CD1 B:ILE284 3.9 37.7 1.0 CB B:ILE284 4.0 40.2 1.0 C B:QOY1002 4.0 43.9 1.0 C4 B:QOY1002 4.0 45.9 1.0 N B:GLY282 4.1 40.2 1.0 CG B:LEU287 4.1 43.1 1.0 O B:ASN283 4.2 34.2 1.0 O B:HOH1142 4.2 9.9 1.0 CA B:ASN283 4.3 40.3 1.0 C2 B:QOY1002 4.5 40.0 1.0 C B:ASN281 4.5 38.5 1.0 CG1 B:ILE284 4.5 42.7 1.0 O B:ASN281 4.6 34.9 1.0 CB B:LEU287 4.7 32.0 1.0 O B:HOH1190 5.0 27.4 1.0 C B:ILE284 5.0 39.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of SND1 in Complex with C-26-A2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of SND1 in Complex with C-26-A2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2001 b:49.4 occ:1.00 CL C:QOY2001 0.0 49.4 1.0 C3 C:QOY2001 1.7 38.0 1.0 C1 C:QOY2001 2.7 38.9 1.0 C5 C:QOY2001 2.7 35.6 1.0 N C:ILE284 3.1 45.4 1.0 O C:GLY282 3.3 34.8 1.0 CA C:ILE284 3.4 44.0 1.0 C C:GLY282 3.4 43.7 1.0 CD1 C:LEU287 3.4 39.7 1.0 C C:ASN283 3.5 47.8 1.0 CB C:ILE284 3.7 39.9 1.0 CD1 C:ILE284 3.7 42.2 1.0 N C:ASN283 3.8 51.5 1.0 O C:HOH2131 3.9 21.0 1.0 C C:QOY2001 4.0 35.1 1.0 CA C:GLY282 4.0 37.1 1.0 C4 C:QOY2001 4.0 31.0 1.0 O C:ASN283 4.1 41.9 1.0 CA C:ASN283 4.1 49.3 1.0 N C:GLY282 4.3 31.8 1.0 CG C:LEU287 4.3 39.0 1.0 CG1 C:ILE284 4.3 38.7 1.0 C2 C:QOY2001 4.5 28.3 1.0 CB C:LEU287 4.7 35.4 1.0 C C:ILE284 4.8 45.1 1.0 C C:ASN281 4.8 30.7 1.0 O C:ASN281 5.0 29.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of SND1 in Complex with C-26-A2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of SND1 in Complex with C-26-A2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1002 b:46.5 occ:1.00 CL D:QOY1002 0.0 46.5 1.0 C3 D:QOY1002 1.7 49.1 1.0 C1 D:QOY1002 2.7 39.6 1.0 C5 D:QOY1002 2.7 45.1 1.0 CG2 D:ILE284 2.9 56.4 1.0 O D:GLY282 3.1 42.4 1.0 O D:HOH1128 3.2 21.6 1.0 C D:GLY282 3.4 48.8 1.0 N D:ILE284 3.4 54.5 1.0 CA D:ILE284 3.8 48.9 1.0 CA D:GLY282 3.8 45.0 1.0 CB D:ILE284 3.8 54.9 1.0 CD1 D:LEU287 3.9 57.6 1.0 N D:GLY282 3.9 42.8 1.0 C D:ASN283 4.0 65.2 1.0 C D:QOY1002 4.0 36.0 1.0 N D:ASN283 4.0 62.4 1.0 C4 D:QOY1002 4.0 40.8 1.0 CA D:ASN283 4.4 65.1 1.0 C2 D:QOY1002 4.5 37.0 1.0 C D:ASN281 4.5 42.5 1.0 O D:ASN283 4.6 75.2 1.0 CG1 D:ILE284 4.7 63.5 1.0 O D:ASN281 4.8 46.7 1.0 CB D:HIS279 5.0 41.5 1.0

M.Shen, Y.Wei, H.Kim, L.Wan, Y.Z.Jiang, X.Hang, M.Raba, S.Remiszewski, M.Rowicki, C.G.Wu, S.Wu, L.Zhang, X.Lu, M.Yuan, H.A.Smith, A.Zheng, J.Bertino, J.F.Jin, Y.Xing, Z.M.Shao, Y.Kang. Small-Molecule Inhibitors That Disrupt the Mtdh-SND1 Complex Suppress Breast Cancer Progression and Metastasis Nat Cancer 2021.
ISSN: ESSN 2662-1347
DOI: 10.1038/S43018-021-00279-5