Chlorine in PDB 7knx: Crystal Structure of SND1 in Complex with C-26-A6

All present enzymatic activity of Crystal Structure of SND1 in Complex with C-26-A6:
3.1.31.1;

The structure of Crystal Structure of SND1 in Complex with C-26-A6, PDB code: 7knx 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 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.127, 81.88, 81.882, 83.77, 70.89, 70.91
R / Rfree (%)	26 / 32.9

The binding sites of Chlorine atom in the Crystal Structure of SND1 in Complex with C-26-A6 (pdb code 7knx). 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-A6, PDB code: 7knx:
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-A6


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-A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:37.6 occ:1.00 CL A:QOV402 0.0 37.6 1.0 C3 A:QOV402 1.7 38.0 1.0 C5 A:QOV402 2.7 37.1 1.0 C1 A:QOV402 2.8 38.7 1.0 N A:ILE284 3.1 32.9 1.0 O A:GLY282 3.2 38.4 1.0 CA A:ILE284 3.4 31.6 1.0 C A:GLY282 3.4 39.4 1.0 CD1 A:ILE284 3.5 29.4 1.0 C A:ASN283 3.5 35.6 1.0 CB A:ILE284 3.7 29.4 1.0 CD1 A:LEU287 3.8 43.2 1.0 N A:ASN283 3.9 40.2 1.0 O A:ASN283 3.9 35.2 1.0 CA A:GLY282 3.9 39.6 1.0 C4 A:QOV402 4.0 37.3 1.0 O A:HOH514 4.0 45.2 1.0 C A:QOV402 4.1 38.3 1.0 CA A:ASN283 4.1 38.4 1.0 CG1 A:ILE284 4.2 28.9 1.0 N A:GLY282 4.2 39.4 1.0 CG A:LEU287 4.5 43.3 1.0 C2 A:QOV402 4.5 37.6 1.0 C A:ILE284 4.8 31.9 1.0 CB A:LEU287 4.8 41.3 1.0 C A:ASN281 4.9 40.9 1.0 CD A:ARG255 4.9 34.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of SND1 in Complex with C-26-A6


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-A6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2001 b:49.8 occ:1.00 CL B:QOV2001 0.0 49.8 1.0 C3 B:QOV2001 1.7 50.6 1.0 C1 B:QOV2001 2.7 50.8 1.0 C5 B:QOV2001 2.7 50.6 1.0 N B:ILE284 3.1 34.1 1.0 O B:GLY282 3.2 35.0 1.0 CA B:ILE284 3.3 32.9 1.0 C B:GLY282 3.4 36.3 1.0 CD1 B:ILE284 3.5 31.0 1.0 C B:ASN283 3.5 35.1 1.0 CD1 B:LEU287 3.6 39.5 1.0 CB B:ILE284 3.7 31.1 1.0 N B:ASN283 3.9 37.0 1.0 O B:ASN283 3.9 34.3 1.0 CA B:GLY282 3.9 37.3 1.0 C B:QOV2001 4.0 47.5 1.0 O B:HOH2135 4.0 15.8 1.0 C4 B:QOV2001 4.0 49.9 1.0 CA B:ASN283 4.1 36.3 1.0 CG1 B:ILE284 4.2 30.6 1.0 N B:GLY282 4.3 37.4 1.0 CG B:LEU287 4.3 40.0 1.0 C2 B:QOV2001 4.6 47.7 1.0 CB B:LEU287 4.7 39.2 1.0 C B:ILE284 4.7 33.3 1.0 CD B:ARG255 4.8 37.6 1.0 C B:ASN281 4.9 39.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of SND1 in Complex with C-26-A6


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-A6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2001 b:46.5 occ:1.00 CL C:QOV2001 0.0 46.5 1.0 C3 C:QOV2001 1.7 45.5 1.0 C1 C:QOV2001 2.7 46.0 1.0 C5 C:QOV2001 2.7 44.1 1.0 O C:GLY282 3.2 39.3 1.0 N C:ILE284 3.3 38.1 1.0 CD1 C:ILE284 3.4 37.7 1.0 CA C:ILE284 3.4 38.4 1.0 C C:GLY282 3.5 41.3 1.0 C C:ASN283 3.6 39.7 1.0 CB C:ILE284 3.7 36.5 1.0 CD1 C:LEU287 3.8 53.6 1.0 O C:HOH2141 3.9 43.5 1.0 N C:ASN283 4.0 43.0 1.0 C4 C:QOV2001 4.0 43.9 1.0 C C:QOV2001 4.0 44.1 1.0 CA C:GLY282 4.0 42.7 1.0 O C:ASN283 4.1 38.4 1.0 CG1 C:ILE284 4.1 36.6 1.0 CA C:ASN283 4.3 41.8 1.0 N C:GLY282 4.3 42.4 1.0 C2 C:QOV2001 4.6 43.0 1.0 CG C:LEU287 4.6 52.8 1.0 CD C:ARG255 4.8 48.4 1.0 C C:ILE284 4.9 39.4 1.0 CB C:LEU287 4.9 50.2 1.0 C C:ASN281 4.9 43.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of SND1 in Complex with C-26-A6


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-A6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1002 b:52.8 occ:1.00 CL D:QOV1002 0.0 52.8 1.0 C3 D:QOV1002 1.7 51.5 1.0 C1 D:QOV1002 2.6 52.0 1.0 C5 D:QOV1002 2.7 50.4 1.0 N D:ILE284 3.3 38.9 1.0 O D:GLY282 3.3 43.5 1.0 CD1 D:ILE284 3.4 36.1 1.0 CA D:ILE284 3.5 37.0 1.0 C D:GLY282 3.5 45.7 1.0 C D:ASN283 3.6 41.5 1.0 CD1 D:LEU287 3.6 49.0 1.0 CB D:ILE284 3.8 35.5 1.0 C D:QOV1002 3.9 52.8 1.0 N D:ASN283 3.9 44.9 1.0 CA D:GLY282 3.9 48.4 1.0 C4 D:QOV1002 4.0 50.2 1.0 O D:ASN283 4.0 42.1 1.0 O D:HOH1117 4.1 26.1 1.0 CG1 D:ILE284 4.2 34.9 1.0 N D:GLY282 4.2 50.8 1.0 CA D:ASN283 4.2 43.5 1.0 CG D:LEU287 4.4 49.8 1.0 C2 D:QOV1002 4.5 50.0 1.0 CB D:LEU287 4.7 47.9 1.0 CD D:ARG255 4.7 40.6 1.0 C D:ASN281 4.8 55.0 1.0 C D:ILE284 4.9 36.8 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