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Bromine in PDB 6q4d: CDK2 in Complex with FRAGLITE31

Enzymatic activity of CDK2 in Complex with FRAGLITE31

All present enzymatic activity of CDK2 in Complex with FRAGLITE31:
2.7.11.22;

Protein crystallography data

The structure of CDK2 in Complex with FRAGLITE31, PDB code: 6q4d was solved by D.J.Wood, M.P.Martin, M.E.M.Noble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.40 / 1.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.368, 71.008, 72.061, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 17.7

Bromine Binding Sites:

The binding sites of Bromine atom in the CDK2 in Complex with FRAGLITE31 (pdb code 6q4d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the CDK2 in Complex with FRAGLITE31, PDB code: 6q4d:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 6q4d

Go back to Bromine Binding Sites List in 6q4d
Bromine binding site 1 out of 6 in the CDK2 in Complex with FRAGLITE31


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of CDK2 in Complex with FRAGLITE31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:16.6
occ:1.00
 BR1 A:HHT301 0.0 16.6 1.0
C4 A:HHT301 1.9 14.2 1.0
C5 A:HHT301 2.8 13.1 1.0
C3 A:HHT301 2.8 13.5 1.0
O A:HOH544 3.2 20.5 1.0
O A:HOH521 3.5 13.6 1.0
O A:HOH460 3.6 16.7 1.0
CG1 A:VAL18 4.0 13.5 1.0
NZ A:LYS33 4.0 12.9 1.0
CB A:ALA31 4.0 12.1 1.0
CE A:LYS33 4.0 13.3 1.0
C6 A:HHT301 4.1 13.4 1.0
C2 A:HHT301 4.1 13.8 1.0
CD1 A:ILE10 4.3 18.5 1.0
CG2 A:ILE10 4.4 20.3 1.0
CD1 A:LEU134 4.5 12.8 1.0
C7 A:HHT301 4.7 12.9 1.0
CB A:VAL18 5.0 12.7 1.0

Bromine binding site 2 out of 6 in 6q4d

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Bromine binding site 2 out of 6 in the CDK2 in Complex with FRAGLITE31


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of CDK2 in Complex with FRAGLITE31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:17.9
occ:1.00
 BR1 A:HHT302 0.0 17.9 1.0
C4 A:HHT302 1.9 17.1 1.0
C3 A:HHT302 2.8 19.0 1.0
C5 A:HHT302 2.9 17.9 1.0
O A:LEU32 3.2 12.4 1.0
CG A:LEU32 3.7 15.1 1.0
C A:LEU32 3.8 10.9 1.0
CD1 A:TYR19 3.8 16.9 1.0
N A:LYS34 3.9 11.6 1.0
CD2 A:LEU32 4.0 17.6 1.0
CB A:LEU32 4.1 12.8 1.0
CB A:LYS34 4.1 13.1 1.0
CB A:TYR19 4.1 13.5 1.0
C2 A:HHT302 4.1 19.0 1.0
C6 A:HHT302 4.2 20.4 1.0
N A:LYS33 4.3 10.6 1.0
CG A:TYR19 4.3 15.2 1.0
C A:LYS33 4.3 11.0 1.0
N A:TYR19 4.4 12.6 1.0
C5 A:HHT304 4.5 22.8 1.0
CD2 A:TYR77 4.5 13.5 1.0
C6 A:HHT304 4.5 24.9 1.0
O A:VAL17 4.5 12.9 1.0
CA A:LYS33 4.5 10.9 1.0
CA A:LEU32 4.6 11.4 1.0
CA A:LYS34 4.6 12.4 1.0
CE1 A:TYR19 4.6 19.2 1.0
CG1 A:VAL17 4.6 16.7 1.0
C7 A:HHT302 4.7 19.6 1.0
CE2 A:TYR77 4.7 14.8 1.0
CA A:TYR19 4.9 12.2 1.0
CD1 A:LEU32 5.0 15.7 1.0

Bromine binding site 3 out of 6 in 6q4d

Go back to Bromine Binding Sites List in 6q4d
Bromine binding site 3 out of 6 in the CDK2 in Complex with FRAGLITE31


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of CDK2 in Complex with FRAGLITE31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:26.1
occ:1.00
 BR1 A:HHT303 0.0 26.1 1.0
C4 A:HHT303 1.9 18.1 1.0
C5 A:HHT303 2.8 21.1 1.0
C3 A:HHT303 2.9 16.5 1.0
OE2 A:GLU73 3.3 44.4 1.0
OH A:TYR77 3.4 17.7 1.0
CD A:GLU73 3.6 43.7 1.0
NZ A:LYS75 3.6 44.6 1.0
OE1 A:GLU73 3.9 47.1 1.0
C6 A:HHT303 4.1 19.6 1.0
C2 A:HHT303 4.1 16.2 1.0
CG A:GLU73 4.2 26.4 1.0
CE A:LYS75 4.2 33.8 1.0
C9 A:HHT302 4.3 24.7 1.0
CZ A:TYR77 4.3 15.0 1.0
CB A:GLU73 4.4 21.4 1.0
CD A:LYS75 4.4 27.2 1.0
O2 A:HHT302 4.4 22.2 1.0
C8 A:HHT302 4.5 20.3 1.0
CE1 A:TYR77 4.6 14.9 1.0
CG2 A:THR72 4.6 15.8 1.0
C7 A:HHT303 4.7 15.4 1.0
O3 A:HHT302 4.7 33.7 1.0
O A:THR72 5.0 14.5 1.0

Bromine binding site 4 out of 6 in 6q4d

Go back to Bromine Binding Sites List in 6q4d
Bromine binding site 4 out of 6 in the CDK2 in Complex with FRAGLITE31


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of CDK2 in Complex with FRAGLITE31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:26.0
occ:1.00
 BR1 A:HHT304 0.0 26.0 1.0
C4 A:HHT304 1.8 21.1 1.0
C5 A:HHT304 2.7 22.8 1.0
C3 A:HHT304 2.8 25.4 1.0
CB A:PHE4 3.6 16.6 1.0
CD2 A:LEU32 3.8 17.6 1.0
N A:LYS6 3.9 16.6 1.0
CA A:LYS6 4.0 17.2 1.0
C6 A:HHT304 4.1 24.9 1.0
C2 A:HHT304 4.1 23.9 1.0
C A:GLN5 4.2 15.3 1.0
CB A:LYS6 4.2 22.9 1.0
CB A:ALA21 4.2 13.7 1.0
O A:PHE4 4.4 23.2 1.0
C8 A:HHT303 4.4 16.2 1.0
C A:PHE4 4.4 18.7 1.0
O A:GLN5 4.5 16.7 1.0
CG A:PHE4 4.6 15.7 1.0
C7 A:HHT304 4.6 24.8 1.0
CA A:PHE4 4.6 15.6 1.0
N A:GLN5 4.7 16.2 1.0
C5 A:HHT302 4.7 17.9 1.0
CA A:GLN5 4.9 17.8 1.0
CD2 A:PHE4 5.0 19.1 1.0

Bromine binding site 5 out of 6 in 6q4d

Go back to Bromine Binding Sites List in 6q4d
Bromine binding site 5 out of 6 in the CDK2 in Complex with FRAGLITE31


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of CDK2 in Complex with FRAGLITE31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br305

b:24.8
occ:1.00
 BR1 A:HHT305 0.0 24.8 1.0
C4 A:HHT305 1.8 18.6 1.0
C5 A:HHT305 2.8 24.3 1.0
C3 A:HHT305 2.8 23.1 1.0
CA A:LEU255 3.7 12.3 1.0
N A:LEU255 3.8 12.7 1.0
CG1 A:VAL197 3.9 13.4 1.0
CG A:PRO254 3.9 17.1 1.0
C A:PRO254 3.9 13.7 1.0
CD1 A:LEU255 4.0 13.1 1.0
CD1 A:LEU101 4.0 18.4 1.0
O A:HOH579 4.0 16.2 1.0
CD A:PRO254 4.1 15.5 1.0
C6 A:HHT305 4.1 25.8 1.0
C2 A:HHT305 4.1 28.4 1.0
O A:PRO254 4.1 16.0 1.0
CB A:LEU255 4.3 11.1 1.0
CG2 A:VAL197 4.5 10.9 1.0
CD2 A:LEU101 4.5 21.7 1.0
N A:PRO254 4.6 13.9 1.0
CG A:LEU101 4.6 17.1 1.0
C7 A:HHT305 4.6 26.9 1.0
CB A:VAL197 4.7 10.5 1.0
CB A:LEU101 4.7 15.6 1.0
CA A:PRO254 4.7 14.9 1.0
CG A:LEU255 4.8 11.2 1.0
CB A:PRO254 4.9 17.4 1.0
C A:LEU255 5.0 11.4 1.0

Bromine binding site 6 out of 6 in 6q4d

Go back to Bromine Binding Sites List in 6q4d
Bromine binding site 6 out of 6 in the CDK2 in Complex with FRAGLITE31


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of CDK2 in Complex with FRAGLITE31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:67.0
occ:1.00
 BR1 A:HHT306 0.0 67.0 1.0
C4 A:HHT306 1.9 32.1 1.0
C5 A:HHT306 2.9 34.9 1.0
C3 A:HHT306 2.9 35.0 1.0
ND1 A:HIS161 4.1 35.0 1.0
O A:HIS161 4.1 45.7 1.0
C6 A:HHT306 4.2 42.6 1.0
C2 A:HHT306 4.2 53.1 1.0
CG A:HIS161 4.4 26.5 1.0
CB A:HIS161 4.5 27.9 1.0
CA A:HIS161 4.5 27.2 1.0
CE1 A:HIS161 4.7 29.9 1.0
C7 A:HHT306 4.7 47.9 1.0
C A:HIS161 4.8 30.2 1.0

Reference:

D.J.Wood, J.D.Lopez-Fernandez, L.E.Knight, I.Al-Khawaldeh, C.Gai, S.Lin, M.P.Martin, D.C.Miller, C.Cano, J.A.Endicott, I.R.Hardcastle, M.E.M.Noble, M.J.Waring. Fraglites-Minimal, Halogenated Fragments Displaying Pharmacophore Doublets. An Efficient Approach to Druggability Assessment and Hit Generation. J.Med.Chem. V. 62 3741 2019.
ISSN: ISSN 0022-2623
PubMed: 30860382
DOI: 10.1021/ACS.JMEDCHEM.9B00304
Page generated: Mon Jul 7 10:16:16 2025

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