Fluorine in PDB 8r9u: A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp

The structure of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp, PDB code: 8r9u was solved by M.Mukherjee, A.Cleasby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.34 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.303, 127.711, 142.684, 90, 90, 90
R / Rfree (%)	27.5 / 34

The binding sites of Fluorine atom in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp (pdb code 8r9u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp, PDB code: 8r9u:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:31.0 occ:0.93 F32 A:YNK401 0.0 31.0 0.9 C31 A:YNK401 1.3 29.7 0.9 F34 A:YNK401 2.1 29.1 0.9 F33 A:YNK401 2.1 29.4 0.9 C13 A:YNK401 2.4 29.5 0.9 H53 A:YNK401 2.8 28.1 0.9 C14 A:YNK401 3.0 29.6 0.9 C17 A:YNK401 3.0 28.1 0.9 C16 A:YNK401 3.1 28.7 0.9 C12 A:YNK401 3.5 30.0 0.9 CD A:LYS41 3.5 51.5 1.0 CD1 A:PHE91 3.6 32.4 1.0 H52 A:YNK401 3.6 30.0 0.9 N18 A:YNK401 4.0 28.3 0.9 O A:HOH510 4.1 20.0 1.0 CG1 A:VAL26 4.1 44.7 1.0 CE1 A:PHE91 4.1 33.2 1.0 C26 A:YNK401 4.2 28.6 0.9 NZ A:LYS41 4.2 55.8 1.0 CB A:ALA39 4.2 39.2 1.0 CE A:LYS41 4.2 54.1 1.0 N15 A:YNK401 4.3 29.3 0.9 CG A:PHE91 4.3 32.6 1.0 H38 A:YNK401 4.5 28.3 0.9 CB A:PHE91 4.5 33.1 1.0 C19 A:YNK401 4.6 28.9 0.9 N11 A:YNK401 4.6 29.8 0.9 CG A:LYS41 4.8 47.3 1.0 C10 A:YNK401 4.9 29.1 0.9 O A:ALA39 4.9 39.0 1.0 CB A:LYS41 5.0 42.5 1.0

Fluorine binding site 2 out of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:29.4 occ:0.93 F33 A:YNK401 0.0 29.4 0.9 C31 A:YNK401 1.3 29.7 0.9 F34 A:YNK401 2.1 29.1 0.9 F32 A:YNK401 2.1 31.0 0.9 H52 A:YNK401 2.3 30.0 0.9 C13 A:YNK401 2.4 29.5 0.9 C12 A:YNK401 2.7 30.0 0.9 CB A:PHE91 3.0 33.1 1.0 CG A:PHE91 3.3 32.6 1.0 CD1 A:PHE91 3.4 32.4 1.0 O A:ASP92 3.6 31.4 1.0 CD1 A:ILE75 3.7 20.4 0.5 C14 A:YNK401 3.7 29.6 0.9 CG1 A:ILE75 3.9 20.5 0.5 H53 A:YNK401 3.9 28.1 0.9 CB A:ALA39 4.0 39.2 1.0 N11 A:YNK401 4.0 29.8 0.9 CD2 A:PHE91 4.3 32.9 1.0 CE1 A:PHE91 4.4 33.2 1.0 CA A:PHE91 4.4 34.0 1.0 CD1 A:ILE75 4.4 26.1 0.5 O A:HOH510 4.4 20.0 1.0 C16 A:YNK401 4.4 28.7 0.9 C17 A:YNK401 4.4 28.1 0.9 CG2 A:ILE75 4.5 23.3 0.5 C A:PHE91 4.6 34.4 1.0 N15 A:YNK401 4.7 29.3 0.9 CD1 A:LEU144 4.8 26.9 1.0 C10 A:YNK401 4.8 29.1 0.9 C A:ASP92 4.8 31.3 1.0 O A:ALA39 4.8 39.0 1.0 N A:PHE91 4.9 35.6 1.0 O A:PHE91 5.0 35.3 1.0

Fluorine binding site 3 out of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:29.1 occ:0.93 F34 A:YNK401 0.0 29.1 0.9 C31 A:YNK401 1.3 29.7 0.9 H53 A:YNK401 2.0 28.1 0.9 F33 A:YNK401 2.1 29.4 0.9 F32 A:YNK401 2.1 31.0 0.9 C13 A:YNK401 2.4 29.5 0.9 C17 A:YNK401 2.8 28.1 0.9 C14 A:YNK401 3.1 29.6 0.9 O A:HOH510 3.3 20.0 1.0 C16 A:YNK401 3.3 28.7 0.9 C12 A:YNK401 3.3 30.0 0.9 H52 A:YNK401 3.5 30.0 0.9 CD1 A:LEU144 3.8 26.9 1.0 CB A:ALA154 3.8 21.3 1.0 CD1 A:ILE75 4.0 26.1 0.5 N18 A:YNK401 4.0 28.3 0.9 NZ A:LYS41 4.2 55.8 1.0 N15 A:YNK401 4.3 29.3 0.9 H38 A:YNK401 4.3 28.3 0.9 OD1 A:ASP155 4.4 36.2 1.0 CD1 A:ILE75 4.4 20.4 0.5 CD1 A:PHE91 4.5 32.4 1.0 N11 A:YNK401 4.5 29.8 0.9 CG1 A:ILE75 4.5 20.5 0.5 C26 A:YNK401 4.6 28.6 0.9 CG A:PHE91 4.6 32.6 1.0 CG2 A:ILE75 4.7 23.3 0.5 CD A:LYS41 4.8 51.5 1.0 CB A:PHE91 4.8 33.1 1.0 C10 A:YNK401 4.8 29.1 0.9 CE1 A:PHE91 4.9 33.2 1.0 CE A:LYS41 4.9 54.1 1.0 C19 A:YNK401 4.9 28.9 0.9 N A:ASP155 5.0 26.2 1.0

Fluorine binding site 4 out of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:26.8 occ:0.84 F32 B:YNK401 0.0 26.8 0.8 C31 B:YNK401 1.3 27.9 0.8 F34 B:YNK401 2.1 28.8 0.8 F33 B:YNK401 2.1 26.6 0.8 H52 B:YNK401 2.3 30.1 0.8 C13 B:YNK401 2.4 29.2 0.8 C12 B:YNK401 2.7 30.1 0.8 O B:ASP92 2.8 42.7 1.0 CB B:PHE91 2.9 40.9 1.0 CD1 B:ILE75 3.4 23.4 0.5 CG B:PHE91 3.5 40.7 1.0 CG1 B:ILE75 3.7 22.8 0.5 C14 B:YNK401 3.7 29.3 0.8 CB B:ALA39 3.8 52.0 1.0 CD1 B:PHE91 3.9 40.6 1.0 N11 B:YNK401 4.0 30.3 0.8 C B:ASP92 4.0 41.1 1.0 H53 B:YNK401 4.1 29.6 0.8 C B:PHE91 4.1 40.8 1.0 CA B:PHE91 4.1 41.5 1.0 CD2 B:PHE91 4.3 41.1 1.0 N B:ASP92 4.3 41.6 1.0 O B:PHE91 4.5 39.4 1.0 C16 B:YNK401 4.5 29.4 0.8 O B:ALA39 4.5 51.8 1.0 C17 B:YNK401 4.6 29.6 0.8 CG2 B:ILE75 4.6 25.7 0.5 N15 B:YNK401 4.8 29.7 0.8 CA B:ASP92 4.8 42.4 1.0 CD1 B:LEU144 4.8 19.0 1.0 C10 B:YNK401 4.8 30.2 0.8 CG B:MET94 4.9 33.0 1.0 CE1 B:PHE91 5.0 40.9 1.0 N B:PHE91 5.0 42.5 1.0

Fluorine binding site 5 out of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:26.6 occ:0.84 F33 B:YNK401 0.0 26.6 0.8 C31 B:YNK401 1.3 27.9 0.8 H53 B:YNK401 2.1 29.6 0.8 F32 B:YNK401 2.1 26.8 0.8 F34 B:YNK401 2.1 28.8 0.8 C13 B:YNK401 2.4 29.2 0.8 C17 B:YNK401 2.7 29.6 0.8 C14 B:YNK401 3.1 29.3 0.8 C16 B:YNK401 3.2 29.4 0.8 C12 B:YNK401 3.5 30.1 0.8 H52 B:YNK401 3.7 30.1 0.8 N18 B:YNK401 3.9 30.2 0.8 CD1 B:PHE91 4.1 40.6 1.0 CG B:PHE91 4.1 40.7 1.0 CG1 B:ILE75 4.2 22.8 0.5 CB B:PHE91 4.2 40.9 1.0 CD1 B:LEU144 4.3 19.0 1.0 H38 B:YNK401 4.3 30.2 0.8 N15 B:YNK401 4.3 29.7 0.8 CB B:ALA154 4.4 31.6 1.0 CD1 B:ILE75 4.4 29.0 0.5 CD1 B:ILE75 4.4 23.4 0.5 C26 B:YNK401 4.5 29.9 0.8 CE1 B:PHE91 4.6 40.9 1.0 CD2 B:PHE91 4.6 41.1 1.0 OD1 B:ASP155 4.7 44.9 1.0 N11 B:YNK401 4.7 30.3 0.8 CG2 B:ILE75 4.8 25.7 0.5 C19 B:YNK401 4.8 30.3 0.8 O B:ASP92 4.9 42.7 1.0 CB B:ALA39 4.9 52.0 1.0 C10 B:YNK401 5.0 30.2 0.8

Fluorine binding site 6 out of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:28.8 occ:0.84 F34 B:YNK401 0.0 28.8 0.8 C31 B:YNK401 1.3 27.9 0.8 F32 B:YNK401 2.1 26.8 0.8 F33 B:YNK401 2.1 26.6 0.8 C13 B:YNK401 2.4 29.2 0.8 CB B:ALA39 3.0 52.0 1.0 C14 B:YNK401 3.2 29.3 0.8 C12 B:YNK401 3.3 30.1 0.8 H52 B:YNK401 3.4 30.1 0.8 CD1 B:PHE91 3.5 40.6 1.0 H53 B:YNK401 3.5 29.6 0.8 C16 B:YNK401 3.5 29.4 0.8 O B:ALA39 3.6 51.8 1.0 C17 B:YNK401 3.7 29.6 0.8 CB B:PHE91 3.7 40.9 1.0 CG B:PHE91 3.8 40.7 1.0 C B:ALA39 4.2 51.4 1.0 CA B:ALA39 4.2 52.0 1.0 CE1 B:PHE91 4.3 40.9 1.0 N15 B:YNK401 4.4 29.7 0.8 O B:ASP92 4.4 42.7 1.0 N11 B:YNK401 4.5 30.3 0.8 C26 B:YNK401 4.5 29.9 0.8 CG1 B:VAL26 4.6 58.8 1.0 N18 B:YNK401 4.7 30.2 0.8 CD B:LYS41 4.9 53.4 1.0 CD2 B:PHE91 4.9 41.1 1.0 C10 B:YNK401 4.9 30.2 0.8 CA B:PHE91 4.9 41.5 1.0 CB B:LYS41 4.9 50.4 1.0

M.Mukherjee, P.Day, D.Laverty, J.A.Bueren-Calabuig, A.Woodhead, C.Griffiths-Jones, S.Hiscock, C.East, S.Boyd, M.O'reilly. Protein Engineering Enables A Soakable Crystal Form of Human CDK7 Primed For High-Throughput Crystallography and Structure-Based Drug Design To Be Published.