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Chlorine in PDB 4yhf: Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor

Enzymatic activity of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor

All present enzymatic activity of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor:
2.7.10.2;

Protein crystallography data

The structure of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor, PDB code: 4yhf was solved by V.O.Paavilainen, J.M.Mcfarland, J.Taunton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.55 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.770, 77.090, 88.030, 90.00, 96.43, 90.00
R / Rfree (%) 17.4 / 20.8

Other elements in 4yhf:

The structure of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor also contains other interesting chemical elements:

Sodium (Na) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor (pdb code 4yhf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor, PDB code: 4yhf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 4yhf

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Chlorine binding site 1 out of 7 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl714

b:58.6
occ:1.00
 H A:LYS625 2.5 19.8 1.0
H A:GLU624 2.7 21.7 1.0
HB2 A:SER623 2.7 23.5 1.0
HG3 A:LYS625 2.7 41.4 1.0
NA A:NA702 2.8 30.1 1.0
N A:GLU624 3.2 18.1 1.0
N A:LYS625 3.3 16.5 1.0
HB2 A:LYS625 3.5 31.9 1.0
CB A:SER623 3.5 19.6 1.0
HG A:SER623 3.6 24.3 1.0
CG A:LYS625 3.6 34.5 1.0
CB A:GLU624 3.6 17.9 1.0
OG A:SER623 3.6 20.2 1.0
CA A:GLU624 3.8 23.7 1.0
CB A:LYS625 3.9 26.6 1.0
C A:GLU624 4.0 19.3 1.0
C A:SER623 4.1 20.6 1.0
CA A:LYS625 4.2 25.5 1.0
HD3 A:LYS625 4.2 42.9 1.0
HD2 A:LYS625 4.2 42.9 1.0
HB3 A:SER623 4.2 23.5 1.0
HG2 A:LYS625 4.3 41.4 1.0
CD A:LYS625 4.3 35.8 1.0
CA A:SER623 4.3 21.1 1.0
HA A:SER623 4.4 25.3 1.0
HA A:LYS625 4.7 30.6 1.0
O A:HOH944 4.7 31.8 1.0
HA A:GLU624 4.7 28.4 1.0
H A:VAL626 4.8 15.6 1.0
HB3 A:LYS625 4.8 31.9 1.0

Chlorine binding site 2 out of 7 in 4yhf

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Chlorine binding site 2 out of 7 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl715

b:54.0
occ:1.00
 HE22 A:GLN497 2.6 39.9 1.0
NA A:NA705 2.9 62.5 1.0
O A:HIS491 3.0 31.9 1.0
NE2 A:GLN497 3.3 33.3 1.0
HB3 A:HIS491 3.6 17.0 1.0
O A:HOH814 3.6 41.7 1.0
HA A:PHE493 3.8 19.5 1.0
HE21 A:GLN497 3.9 39.9 1.0
C A:HIS491 3.9 23.1 1.0
OE1 A:GLN497 3.9 26.2 1.0
HA A:HIS491 4.0 27.9 1.0
CD A:GLN497 4.1 28.8 1.0
HD1 A:PHE493 4.1 16.2 1.0
CD1 A:PHE493 4.3 13.5 1.0
CB A:HIS491 4.3 14.2 1.0
CA A:HIS491 4.3 23.3 1.0
HE1 A:PHE493 4.4 13.7 1.0
CE1 A:PHE493 4.4 11.4 1.0
O A:HOH809 4.4 36.5 1.0
HD2 A:HIS491 4.5 19.9 1.0
O A:ARG492 4.6 18.7 1.0
CA A:PHE493 4.7 16.2 1.0
C A:ARG492 4.7 19.8 1.0
N A:PHE493 4.8 18.6 1.0
CG A:PHE493 4.9 13.6 1.0
CG A:HIS491 4.9 19.6 1.0
CD2 A:HIS491 5.0 16.6 1.0
N A:ARG492 5.0 20.0 1.0

Chlorine binding site 3 out of 7 in 4yhf

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Chlorine binding site 3 out of 7 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl716

b:61.4
occ:1.00
 HH21 A:ARG520 2.0 29.7 0.4
NA A:NA709 2.6 35.0 1.0
NH2 A:ARG520 2.7 24.8 0.4
HE A:ARG520 2.8 32.3 0.4
HB3 A:SER543 2.8 27.6 1.0
HH22 A:ARG520 3.2 29.7 0.4
HZ A:PHE574 3.3 35.7 1.0
NE A:ARG520 3.3 26.9 0.4
HB3 A:ARG520 3.3 20.9 0.4
HB3 A:ARG520 3.3 20.9 0.6
CZ A:ARG520 3.3 22.9 0.4
CZ A:PHE574 3.4 29.8 1.0
HE2 A:PHE574 3.6 36.3 1.0
CE2 A:PHE574 3.6 30.2 1.0
CB A:SER543 3.7 23.0 1.0
HB2 A:SER543 3.8 27.6 1.0
HD3 A:ARG520 3.8 32.1 0.6
HE1 A:PHE559 3.9 35.2 1.0
CE1 A:PHE574 4.2 26.0 1.0
CB A:ARG520 4.3 17.5 0.4
OG A:SER543 4.3 43.0 1.0
O A:ARG520 4.3 14.0 1.0
CB A:ARG520 4.3 17.4 0.6
CD2 A:PHE574 4.4 29.4 1.0
HE1 A:PHE574 4.5 31.2 1.0
HB2 A:ARG520 4.5 20.9 0.4
NH1 A:ARG520 4.6 23.5 0.4
CE1 A:PHE559 4.6 29.3 1.0
HB2 A:ARG520 4.6 20.9 0.6
HA A:THR552 4.6 45.1 1.0
CD A:ARG520 4.6 26.6 0.4
O A:SER543 4.6 30.3 1.0
CD A:ARG520 4.7 26.8 0.6
C A:SER543 4.7 25.4 1.0
CA A:SER543 4.8 34.0 1.0
HE A:ARG520 4.9 32.4 0.6
HH12 A:ARG520 4.9 28.2 0.4
CD1 A:PHE574 4.9 23.1 1.0
HD2 A:PHE574 4.9 35.3 1.0
CG A:ARG520 4.9 19.4 0.4
O A:THR552 4.9 38.6 1.0
CG A:ARG520 4.9 19.3 0.6
HD3 A:ARG520 4.9 31.9 0.4
HG2 A:ARG520 4.9 23.2 0.6
HG2 A:ARG520 4.9 23.3 0.4
HZ A:PHE559 5.0 40.7 1.0

Chlorine binding site 4 out of 7 in 4yhf

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Chlorine binding site 4 out of 7 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl724

b:49.7
occ:1.00
 HO2 B:EDO721 2.5 29.9 1.0
O2 B:EDO721 2.7 24.9 1.0
HA B:TYR598 2.7 16.8 1.0
H21 B:EDO721 2.8 38.6 1.0
NA A:NA717 2.9 28.6 1.0
O B:HOH820 3.0 16.6 1.0
HD1 B:TYR598 3.3 13.6 1.0
C2 B:EDO721 3.3 32.2 1.0
H B:TYR598 3.6 18.4 1.0
HD23 B:LEU616 3.6 10.0 1.0
CA B:TYR598 3.6 14.0 1.0
HD21 B:LEU614 3.9 20.2 1.0
CD1 B:TYR598 3.9 11.3 1.0
HE2 B:PHE601 4.0 29.0 1.0
H11 B:EDO721 4.0 44.4 1.0
N B:TYR598 4.1 15.3 1.0
H22 B:EDO721 4.1 38.6 1.0
HD12 B:LEU614 4.2 28.6 1.0
HD2 B:TYR617 4.2 20.3 1.0
HB3 B:TYR598 4.2 12.8 1.0
C1 B:EDO721 4.2 37.0 1.0
HA B:LEU616 4.3 13.8 1.0
CB B:TYR598 4.3 10.7 1.0
HD2 B:PHE601 4.4 26.0 1.0
CG B:TYR598 4.5 8.0 1.0
CD2 B:LEU616 4.5 8.3 1.0
HE2 B:TYR617 4.6 24.8 1.0
H B:GLU599 4.6 15.7 1.0
C B:TYR598 4.6 14.3 1.0
HD21 B:LEU616 4.7 10.0 1.0
CE2 B:PHE601 4.7 24.2 1.0
O1 B:EDO721 4.7 30.3 1.0
CE1 B:TYR598 4.8 9.1 1.0
HE1 B:TYR598 4.8 10.9 1.0
H B:TYR617 4.8 12.2 1.0
CD2 B:LEU614 4.8 16.9 1.0
HD22 B:LEU616 4.9 10.0 1.0
CD2 B:TYR617 4.9 16.9 1.0
H B:ARG600 4.9 15.6 1.0
N B:GLU599 4.9 13.1 1.0
CD2 B:PHE601 5.0 21.7 1.0
HG B:LEU614 5.0 23.4 1.0

Chlorine binding site 5 out of 7 in 4yhf

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Chlorine binding site 5 out of 7 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl725

b:65.8
occ:1.00
 HE1 B:TYR571 4.2 22.9 1.0
OH B:TYR571 4.9 27.6 1.0

Chlorine binding site 6 out of 7 in 4yhf

Go back to Chlorine Binding Sites List in 4yhf
Chlorine binding site 6 out of 7 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl726

b:63.0
occ:1.00
 HH12 B:ARG487 2.8 27.7 1.0
NA B:NA704 3.0 31.0 1.0
H5 B:4C9703 3.4 26.2 1.0
NH1 B:ARG487 3.5 23.1 1.0
O B:HOH921 3.6 21.1 1.0
HD21 B:LEU483 3.7 27.4 1.0
HD23 B:LEU483 3.7 27.4 1.0
HH11 B:ARG487 3.8 27.7 1.0
H18 B:4C9703 3.8 21.3 1.0
H15 B:4C9703 4.1 20.8 1.0
CD2 B:LEU483 4.2 22.9 1.0
C3 B:4C9703 4.3 21.9 1.0
HH22 B:ARG487 4.3 27.4 1.0
H4 B:4C9703 4.4 26.2 1.0
H16 B:4C9703 4.5 20.8 1.0
C16 B:4C9703 4.6 17.4 1.0
CZ B:ARG487 4.6 30.6 1.0
C17 B:4C9703 4.7 17.8 1.0
HD22 B:LEU483 4.8 27.4 1.0
C2 B:4C9703 4.8 20.8 1.0
NH2 B:ARG487 4.9 22.9 1.0
H19 B:4C9703 5.0 21.3 1.0

Chlorine binding site 7 out of 7 in 4yhf

Go back to Chlorine Binding Sites List in 4yhf
Chlorine binding site 7 out of 7 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl727

b:38.9
occ:1.00
 HD3 B:ARG525 2.6 16.6 1.0
O B:HOH872 2.7 17.0 1.0
NA B:NA704 2.9 31.0 1.0
HH2 B:TRP563 3.0 15.6 1.0
HH11 B:ARG525 3.0 34.1 1.0
HD22 B:LEU483 3.0 27.4 1.0
HB3 B:ARG525 3.1 18.6 1.0
O B:HOH861 3.2 10.4 1.0
O B:HOH949 3.6 35.4 1.0
CD B:ARG525 3.6 13.9 1.0
HD21 B:LEU483 3.6 27.4 1.0
CH2 B:TRP563 3.6 13.0 1.0
NH1 B:ARG525 3.7 28.4 1.0
CD2 B:LEU483 3.7 22.9 1.0
HZ2 B:TRP563 3.7 14.7 1.0
CB B:ARG525 3.9 15.5 1.0
HD23 B:LEU483 4.0 27.4 1.0
CZ2 B:TRP563 4.0 12.2 1.0
HD2 B:ARG525 4.0 16.6 1.0
HH12 B:ARG525 4.1 34.1 1.0
HG2 B:ARG525 4.1 22.5 1.0
CG B:ARG525 4.1 18.7 1.0
O B:HOH921 4.2 21.1 1.0
HB2 B:ARG525 4.3 18.6 1.0
NE B:ARG525 4.4 21.4 1.0
HE3 B:MET596 4.5 23.3 0.3
CZ B:ARG525 4.5 14.3 1.0
H B:ARG525 4.6 16.5 1.0
CZ3 B:TRP563 4.6 14.6 1.0
O B:HOH851 4.6 13.8 1.0
OE1 B:GLU589 4.7 14.5 1.0
HZ3 B:TRP563 4.8 17.5 1.0
HD13 B:LEU483 4.9 18.8 1.0
SD B:MET596 4.9 16.2 0.3
H18 B:4C9703 4.9 21.3 1.0

Reference:

J.M.Bradshaw, J.M.Mcfarland, V.O.Paavilainen, A.Bisconte, D.Tam, V.T.Phan, S.Romanov, D.Finkle, J.Shu, V.Patel, T.Ton, X.Li, D.G.Loughhead, P.A.Nunn, D.E.Karr, M.E.Gerritsen, J.O.Funk, T.O.Owens, E.Verner, K.A.Brameld, R.J.Hill, D.M.Goldstein, J.Taunton. Prolonged and Tunable Residence Time Using Reversible Covalent Kinase Inhibitors Nat.Struct.Mol.Biol. 2015.
ISSN: ESSN 1545-9985
DOI: 10.1038/NCHEMBIO.1817
Page generated: Fri Jul 26 04:05:44 2024

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