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Chlorine in PDB 3ms9: Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket

Enzymatic activity of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket

All present enzymatic activity of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket:
2.7.10.2;

Protein crystallography data

The structure of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket, PDB code: 3ms9 was solved by S.W.Cowan-Jacob, G.Rummel, G.Fendrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.92 / 1.80
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.783, 147.346, 152.833, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket (pdb code 3ms9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket, PDB code: 3ms9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3ms9

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Chlorine binding site 1 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl516

b:23.8
occ:1.00
 CL1 A:MS9516 0.0 23.8 1.0
C2 A:MS9516 1.8 25.8 1.0
C3 A:MS9516 2.7 23.1 1.0
C9 A:MS9516 2.7 21.0 1.0
O A:LEU429 3.2 18.8 1.0
N A:ALA433 3.7 17.8 1.0
CG2 A:ILE432 3.7 16.0 1.0
CB A:ILE432 3.9 17.0 1.0
CB A:ALA433 3.9 19.0 1.0
CA A:ALA433 4.0 19.1 1.0
CG1 A:VAL468 4.0 23.1 1.0
C A:LEU429 4.0 16.7 1.0
C7 A:MS9516 4.0 22.8 1.0
C5 A:MS9516 4.1 26.4 1.0
CD2 A:LEU429 4.1 22.2 1.0
CA A:LEU429 4.2 16.5 1.0
C A:ILE432 4.3 16.9 1.0
CB A:LEU429 4.3 17.2 1.0
C6 A:MS9516 4.6 25.9 1.0
CA A:ILE432 4.7 16.5 1.0
CB A:ALA344 4.7 21.9 1.0
O A:LEU340 4.8 18.9 1.0
CB A:LEU340 4.9 19.4 1.0
CG A:LEU429 4.9 19.4 1.0

Chlorine binding site 2 out of 8 in 3ms9

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Chlorine binding site 2 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl517

b:41.0
occ:1.00
 O A:HOH60 3.3 37.1 1.0
CE2 A:TYR232 3.9 31.9 1.0
CD A:LYS234 3.9 34.3 1.0
CB A:LYS234 4.1 32.5 1.0
CD2 A:TYR232 4.3 33.4 1.0
CG A:LYS234 4.3 34.8 1.0
CE A:LYS234 4.7 35.5 1.0

Chlorine binding site 3 out of 8 in 3ms9

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Chlorine binding site 3 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2

b:39.4
occ:1.00
 O A:HOH535 2.9 31.3 1.0
O A:HOH131 3.0 45.4 1.0
O A:HOH594 3.0 47.0 1.0
N A:ILE360 3.2 23.4 1.0
C50 A:STI1 3.7 24.5 1.0
CA A:PHE359 3.8 25.7 1.0
O A:ILE360 3.8 24.2 1.0
CD2 A:PHE359 4.0 37.1 1.0
C A:PHE359 4.0 25.8 1.0
CB A:ILE360 4.1 23.7 1.0
CA A:ILE360 4.1 23.4 1.0
CB A:PHE359 4.3 27.4 1.0
C A:ILE360 4.4 21.8 1.0
O A:ASN358 4.5 29.1 1.0
CG1 A:ILE360 4.5 25.4 1.0
N51 A:STI1 4.5 26.8 1.0
C54 A:STI1 4.5 27.3 1.0
C49 A:STI1 4.6 28.0 1.0
CG A:PHE359 4.6 31.3 1.0
CD1 A:ILE360 4.6 35.8 1.0
O A:HOH135 4.9 50.3 1.0
N A:PHE359 5.0 26.8 1.0
CE2 A:PHE359 5.0 38.6 1.0

Chlorine binding site 4 out of 8 in 3ms9

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Chlorine binding site 4 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl4

b:67.4
occ:1.00
 OG1 A:THR319 3.1 37.4 1.0
N A:THR319 3.3 27.4 1.0
CA A:GLY372 3.6 26.1 1.0
CA A:MET318 3.8 28.4 1.0
O A:PHE317 3.8 29.8 1.0
O A:HOH99 3.9 43.8 1.0
N A:GLU373 3.9 26.9 1.0
C A:MET318 4.1 27.0 1.0
CB A:THR319 4.1 29.9 1.0
SD A:MET318 4.2 37.7 1.0
CA A:THR319 4.3 28.6 1.0
C A:GLY372 4.3 27.9 1.0
CG A:GLU373 4.5 36.3 1.0
CB A:MET318 4.6 29.1 1.0
C A:PHE317 4.8 30.0 1.0
N A:MET318 4.8 28.7 1.0
N A:GLY372 4.9 23.7 1.0
CE A:MET318 4.9 39.9 1.0

Chlorine binding site 5 out of 8 in 3ms9

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Chlorine binding site 5 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5

b:44.8
occ:1.00
 OH A:TYR253 3.1 33.9 1.0
N A:ASN322 3.4 19.9 1.0
ND2 A:ASN322 3.5 23.0 1.0
CA A:GLY321 3.6 20.7 1.0
CE1 A:TYR253 3.8 32.0 1.0
C1 A:STI1 3.9 23.8 1.0
CZ A:TYR253 3.9 31.6 1.0
O A:HOH587 4.0 47.7 1.0
C A:GLY321 4.0 18.3 1.0
NE2 A:GLN252 4.0 51.4 1.0
CB A:ASN322 4.3 21.5 1.0
C6 A:STI1 4.3 26.4 1.0
CG A:ASN322 4.3 22.2 1.0
O A:HOH550 4.4 53.7 1.0
CA A:ASN322 4.5 20.5 1.0
CD A:GLN252 4.6 47.7 1.0
OE1 A:GLN252 4.8 46.6 1.0
O A:HOH104 4.8 25.8 1.0
CA A:GLY249 4.9 51.3 1.0
C2 A:STI1 4.9 25.6 1.0
N A:GLY321 5.0 20.2 1.0

Chlorine binding site 6 out of 8 in 3ms9

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Chlorine binding site 6 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl516

b:24.9
occ:1.00
 CL1 B:MS9516 0.0 24.9 1.0
C2 B:MS9516 1.8 25.2 1.0
C9 B:MS9516 2.7 25.9 1.0
C3 B:MS9516 2.8 23.1 1.0
O B:LEU429 3.2 19.0 1.0
CG2 B:ILE432 3.6 19.1 1.0
N B:ALA433 3.7 18.6 1.0
CB B:ALA433 3.7 19.0 1.0
CB B:ILE432 3.8 17.0 1.0
CA B:ALA433 3.9 19.7 1.0
C B:LEU429 4.0 18.2 1.0
C7 B:MS9516 4.0 24.4 1.0
CG1 B:VAL468 4.1 19.5 1.0
C5 B:MS9516 4.1 25.1 1.0
CD2 B:LEU429 4.2 22.6 1.0
CA B:LEU429 4.3 16.9 1.0
C B:ILE432 4.3 17.1 1.0
CB B:LEU429 4.4 16.4 1.0
C6 B:MS9516 4.6 24.5 1.0
CA B:ILE432 4.6 16.5 1.0
CB B:ALA344 4.6 19.6 1.0
CB B:LEU340 4.8 21.0 1.0
O B:LEU340 4.9 18.5 1.0
CE B:MET472 4.9 22.8 1.0

Chlorine binding site 7 out of 8 in 3ms9

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Chlorine binding site 7 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl3

b:39.0
occ:1.00
 N B:ILE360 3.1 24.1 1.0
O B:HOH214 3.1 51.3 1.0
O B:HOH151 3.1 40.2 1.0
CA B:PHE359 3.6 24.7 1.0
C50 B:STI1 3.7 25.0 1.0
O B:ILE360 3.7 26.4 1.0
CD2 B:PHE359 3.8 37.8 1.0
C B:PHE359 3.8 25.1 1.0
CA B:ILE360 4.1 25.2 1.0
CB B:PHE359 4.1 24.6 1.0
CB B:ILE360 4.1 25.0 1.0
C B:ILE360 4.4 23.8 1.0
CG B:PHE359 4.4 30.6 1.0
CG1 B:ILE360 4.4 26.5 1.0
O B:ASN358 4.5 28.6 1.0
N51 B:STI1 4.5 26.8 1.0
C49 B:STI1 4.5 24.0 1.0
C54 B:STI1 4.6 26.0 1.0
O B:HOH167 4.7 52.9 1.0
CD1 B:ILE360 4.8 30.8 1.0
CE2 B:PHE359 4.8 39.2 1.0
N B:PHE359 4.9 26.2 1.0
O B:PHE359 5.0 25.5 1.0

Chlorine binding site 8 out of 8 in 3ms9

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Chlorine binding site 8 out of 8 in the Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Abl Kinase in Complex with Imatinib and A Fragment (FRAG1) in the Myristate Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl6

b:40.6
occ:1.00
 OH B:TYR253 2.4 38.9 1.0
N B:ASN322 3.3 18.4 1.0
ND2 B:ASN322 3.4 23.5 1.0
CZ B:TYR253 3.4 29.9 1.0
CE1 B:TYR253 3.5 29.6 1.0
CA B:GLY321 3.6 22.3 1.0
NE2 B:GLN252 3.7 46.9 1.0
C B:GLY321 3.9 19.2 1.0
C1 B:STI1 4.0 23.6 1.0
CB B:ASN322 4.1 18.9 1.0
CG B:ASN322 4.2 20.6 1.0
CA B:ASN322 4.3 17.1 1.0
C6 B:STI1 4.3 25.8 1.0
CD B:GLN252 4.5 45.1 1.0
O B:HOH121 4.6 24.8 1.0
CE2 B:TYR253 4.6 32.5 1.0
CD1 B:TYR253 4.8 26.0 1.0
CA B:GLY249 4.8 47.8 1.0
OE1 B:GLN252 4.8 48.7 1.0
N B:GLY321 5.0 21.4 1.0

Reference:

W.Jahnke, R.M.Grotzfeld, X.Pelle, A.Strauss, G.Fendrich, S.W.Cowan-Jacob, S.Cotesta, D.Fabbro, P.Furet, J.Mestan, A.L.Marzinzik. Binding or Bending: Distinction of Allosteric Abl Kinase Agonists From Antagonists By An uc(Nmr)-Based Conformational Assay. J.Am.Chem.Soc. V. 132 7043 2010.
ISSN: ISSN 0002-7863
PubMed: 20450175
DOI: 10.1021/JA101837N
Page generated: Sat Dec 12 09:55:35 2020

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