Fluorine in PDB 7y4u: Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y

All present enzymatic activity of Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y:
2.7.10.1;

The structure of Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y, PDB code: 7y4u was solved by L.Z.Qu, Y.H.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.61 / 2.26
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.625, 65.625, 187.911, 90, 90, 90
R / Rfree (%)	23.8 / 27.8

The binding sites of Fluorine atom in the Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y (pdb code 7y4u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y, PDB code: 7y4u:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y within 5.0Å range: probe atom residue distance (Å) B Occ A:F1401 b:53.0 occ:1.00 FBK A:I941401 0.0 53.0 1.0 CBJ A:I941401 1.3 56.8 1.0 FBM A:I941401 2.2 60.5 1.0 FBL A:I941401 2.2 75.3 1.0 CBC A:I941401 2.2 53.1 1.0 CBD A:I941401 2.5 49.6 1.0 O A:ARG1208 3.1 45.2 1.0 CB A:ARG1208 3.3 42.4 1.0 CBB A:I941401 3.5 52.4 1.0 O A:HOH1541 3.6 46.2 1.0 CG A:ASP1164 3.8 50.9 1.0 CA A:ARG1208 3.8 43.3 1.0 C A:ARG1208 3.8 45.0 1.0 CAY A:I941401 3.9 49.9 1.0 OD2 A:ASP1164 4.0 51.6 1.0 CB A:ASP1164 4.0 47.4 1.0 OD1 A:ASP1164 4.1 54.0 1.0 O A:HOH1511 4.2 45.6 1.0 CBF A:I941401 4.2 56.2 1.0 CB A:TYR1230 4.3 49.0 1.0 CG A:ARG1208 4.3 45.2 1.0 OBG A:I941401 4.5 56.0 1.0 CD A:ARG1208 4.5 46.0 1.0 CBA A:I941401 4.6 50.4 1.0 CAV A:I941401 4.7 47.5 1.0 CB A:ASP1231 4.7 53.9 1.0 CAU A:I941401 4.7 46.1 1.0 CAZ A:I941401 4.7 51.0 1.0 O A:TYR1230 4.8 52.9 1.0 C A:TYR1230 4.9 52.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y within 5.0Å range: probe atom residue distance (Å) B Occ A:F1401 b:75.3 occ:1.00 FBL A:I941401 0.0 75.3 1.0 CBJ A:I941401 1.4 56.8 1.0 FBK A:I941401 2.2 53.0 1.0 FBM A:I941401 2.2 60.5 1.0 CBC A:I941401 2.3 53.1 1.0 CBF A:I941401 2.8 56.2 1.0 CBB A:I941401 2.8 52.4 1.0 OBG A:I941401 3.0 56.0 1.0 OD1 A:ASP1164 3.0 54.0 1.0 O A:HOH1541 3.1 46.2 1.0 ND2 A:ASN1167 3.3 64.3 1.0 NBH A:I941401 3.4 56.7 1.0 CG A:ASP1164 3.4 50.9 1.0 CBD A:I941401 3.4 49.6 1.0 OD2 A:ASP1164 3.7 51.6 1.0 CBI A:I941401 4.1 54.8 1.0 CBA A:I941401 4.2 50.4 1.0 CB A:ASP1164 4.3 47.4 1.0 O A:HOH1506 4.3 49.0 1.0 O A:HOH1511 4.4 45.6 1.0 CG A:ASN1167 4.5 54.9 1.0 CAY A:I941401 4.6 49.9 1.0 CB A:ARG1208 4.9 42.4 1.0 CAZ A:I941401 4.9 51.0 1.0 O A:ARG1208 4.9 45.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Cmet Kinase Domain Bound By Compound 9Y within 5.0Å range: probe atom residue distance (Å) B Occ A:F1401 b:60.5 occ:1.00 FBM A:I941401 0.0 60.5 1.0 CBJ A:I941401 1.3 56.8 1.0 FBK A:I941401 2.2 53.0 1.0 FBL A:I941401 2.2 75.3 1.0 CBC A:I941401 2.2 53.1 1.0 O A:TYR1230 2.9 52.9 1.0 OBG A:I941401 3.0 56.0 1.0 CBB A:I941401 3.0 52.4 1.0 CBD A:I941401 3.1 49.6 1.0 CBF A:I941401 3.3 56.2 1.0 C A:TYR1230 3.4 52.3 1.0 CB A:TYR1230 3.6 49.0 1.0 CB A:ASP1231 3.8 53.9 1.0 N A:ASP1231 4.0 55.0 1.0 CA A:TYR1230 4.2 49.5 1.0 CA A:ASP1231 4.3 54.1 1.0 CBA A:I941401 4.3 50.4 1.0 CAY A:I941401 4.3 49.9 1.0 CG A:ASP1231 4.4 55.9 1.0 NBH A:I941401 4.5 56.7 1.0 O A:HOH1541 4.5 46.2 1.0 OD2 A:ASP1231 4.5 57.7 1.0 O A:HOH1511 4.6 45.6 1.0 CAZ A:I941401 4.8 51.0 1.0 CG A:TYR1230 5.0 47.6 1.0

C.Wang, J.Li, L.Qu, X.Tang, X.Song, F.Yang, X.Chen, Q.Lin, W.Lin, Y.Zhou, Z.Tu, Y.Chen, Z.Zhang, X.Lu. Discovery of D6808, A Highly Selective and Potent Macrocyclic C-Met Inhibitor For Gastric Cancer Harboring Met Gene Alteration Treatment. J.Med.Chem. V. 65 15140 2022.
ISSN: ISSN 0022-2623
PubMed: 36355693
DOI: 10.1021/ACS.JMEDCHEM.2C00981