Bromine in PDB 6bky: Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2

Enzymatic activity of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2

All present enzymatic activity of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2:
1.1.1.42;

Protein crystallography data

The structure of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2, PDB code: 6bky was solved by C.G.Jakob, W.Qiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 137.44 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.665, 274.889, 116.798, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.1

Other elements in 6bky:

The structure of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Bromine atom in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 (pdb code 6bky). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 12 binding sites of Bromine where determined in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2, PDB code: 6bky:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 1 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br503

b:57.0
occ:1.00
 BR1 D:K32503 0.0 57.0 1.0
C5 D:K32503 2.0 50.8 1.0
C7 D:K32503 2.9 43.8 1.0
C2 D:K32503 3.1 57.0 1.0
N14 D:K32503 3.2 40.9 1.0
BR2 D:K32503 3.5 64.0 1.0
CB D:SER280 3.6 35.2 1.0
OE1 D:GLN277 3.7 32.2 1.0
CG2 D:VAL281 3.9 26.3 1.0
CH2 D:TRP124 4.1 27.1 1.0
N D:VAL281 4.2 26.0 1.0
C8 D:K32503 4.2 44.4 1.0
C D:SER280 4.2 31.6 1.0
CG1 D:VAL255 4.4 29.9 1.0
CZ2 D:TRP124 4.4 26.5 1.0
C3 D:K32503 4.4 56.4 1.0
CG D:MET259 4.5 34.9 1.0
O D:SER280 4.5 28.5 1.0
C13 D:K32503 4.6 43.2 1.0
CA D:VAL281 4.6 24.9 1.0
CA D:SER280 4.6 30.7 1.0
OG D:SER280 4.7 56.5 1.0
CZ3 D:TRP267 4.7 27.1 1.0
CH2 D:TRP267 4.8 27.4 1.0
CB D:VAL281 4.9 27.4 1.0
C4 D:K32503 4.9 50.5 1.0
O D:GLN277 5.0 33.7 1.0
CD D:GLN277 5.0 42.3 1.0

Bromine binding site 2 out of 12 in 6bky

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Bromine binding site 2 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br503

b:64.0
occ:1.00
 BR2 D:K32503 0.0 64.0 1.0
C2 D:K32503 1.9 57.0 1.0
C5 D:K32503 2.8 50.8 1.0
C3 D:K32503 3.0 56.4 1.0
CE C:MET259 3.4 35.5 1.0
BR4 D:K32503 3.5 64.3 1.0
BR1 D:K32503 3.5 57.0 1.0
CG D:MET259 3.6 34.9 1.0
CG2 D:VAL121 3.7 27.7 1.0
CH2 D:TRP124 3.9 27.1 1.0
C7 D:K32503 4.1 43.8 1.0
CZ2 D:TRP124 4.1 26.5 1.0
CE D:MET259 4.2 34.5 1.0
C4 D:K32503 4.3 50.5 1.0
SD D:MET259 4.4 39.3 1.0
SD C:MET259 4.4 40.3 1.0
CB D:MET259 4.6 31.6 1.0
C8 D:K32503 4.6 44.4 1.0
O D:SER280 4.7 28.5 1.0
CZ3 D:TRP124 4.9 26.3 1.0
CA D:GLY284 5.0 24.0 1.0
CA D:MET259 5.0 28.1 1.0

Bromine binding site 3 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 3 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br503

b:55.9
occ:1.00
 BR3 D:K32503 0.0 55.9 1.0
C4 D:K32503 2.0 50.5 1.0
C8 D:K32503 2.9 44.4 1.0
C3 D:K32503 3.1 56.4 1.0
N6 D:K32503 3.2 41.5 1.0
BR4 D:K32503 3.5 64.3 1.0
CB C:SER280 3.7 34.0 1.0
OE1 C:GLN277 3.8 35.3 1.0
CG2 C:VAL281 3.9 26.6 1.0
CH2 C:TRP124 4.1 28.1 1.0
N C:VAL281 4.2 25.0 1.0
C7 D:K32503 4.2 43.8 1.0
C C:SER280 4.2 30.7 1.0
CG1 C:VAL255 4.4 31.3 1.0
C2 D:K32503 4.4 57.0 1.0
CZ2 C:TRP124 4.4 27.8 1.0
CG C:MET259 4.4 35.9 1.0
O C:SER280 4.5 27.2 1.0
CA C:VAL281 4.5 24.0 1.0
C13 D:K32503 4.6 43.2 1.0
CA C:SER280 4.6 30.3 1.0
CZ3 C:TRP267 4.7 25.7 1.0
OG C:SER280 4.7 51.9 1.0
CH2 C:TRP267 4.8 26.2 1.0
CB C:VAL281 4.9 27.7 1.0
C5 D:K32503 4.9 50.8 1.0
O C:GLN277 5.0 32.6 1.0
CD C:GLN277 5.0 44.0 1.0

Bromine binding site 4 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 4 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br503

b:64.3
occ:1.00
 BR4 D:K32503 0.0 64.3 1.0
C3 D:K32503 1.9 56.4 1.0
C4 D:K32503 2.8 50.5 1.0
C2 D:K32503 3.0 57.0 1.0
CE D:MET259 3.4 34.5 1.0
BR2 D:K32503 3.5 64.0 1.0
BR3 D:K32503 3.5 55.9 1.0
CG C:MET259 3.6 35.9 1.0
CG2 C:VAL121 3.7 27.5 1.0
CH2 C:TRP124 3.9 28.1 1.0
C8 D:K32503 4.1 44.4 1.0
CZ2 C:TRP124 4.1 27.8 1.0
CE C:MET259 4.2 35.5 1.0
C5 D:K32503 4.3 50.8 1.0
SD C:MET259 4.4 40.3 1.0
SD D:MET259 4.4 39.3 1.0
CB C:MET259 4.6 32.0 1.0
C7 D:K32503 4.7 43.8 1.0
O C:SER280 4.7 27.2 1.0
CZ3 C:TRP124 4.8 27.1 1.0
CA C:MET259 5.0 28.4 1.0
CA C:GLY284 5.0 25.2 1.0

Bromine binding site 5 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 5 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:60.4
occ:1.00
 BR1 A:K32502 0.0 60.4 1.0
C5 A:K32502 2.0 51.5 1.0
C7 A:K32502 2.9 44.5 1.0
C2 A:K32502 3.1 58.2 1.0
OG B:SER280 3.3 45.2 1.0
N14 A:K32502 3.3 41.3 1.0
BR2 A:K32502 3.7 65.6 1.0
OE1 B:GLN277 3.9 48.2 1.0
CG2 B:VAL281 3.9 37.2 1.0
CH2 B:TRP124 4.0 47.8 1.0
CB B:SER280 4.0 38.8 1.0
C8 A:K32502 4.2 43.0 1.0
CZ2 B:TRP124 4.3 47.3 1.0
N B:VAL281 4.3 33.8 1.0
C B:SER280 4.4 38.5 1.0
CG1 B:VAL255 4.4 37.1 1.0
CG B:MET259 4.4 42.4 1.0
C3 A:K32502 4.4 57.5 1.0
CZ3 B:TRP267 4.6 33.6 1.0
C13 A:K32502 4.6 42.0 1.0
CA B:VAL281 4.6 34.0 1.0
CH2 B:TRP267 4.7 34.4 1.0
O B:SER280 4.8 39.7 1.0
CA B:SER280 4.8 35.5 1.0
C4 A:K32502 4.9 48.8 1.0
CB B:VAL281 4.9 37.6 1.0

Bromine binding site 6 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 6 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:65.6
occ:1.00
 BR2 A:K32502 0.0 65.6 1.0
C2 A:K32502 1.9 58.2 1.0
C3 A:K32502 2.8 57.5 1.0
C5 A:K32502 2.9 51.5 1.0
BR4 A:K32502 3.3 62.7 1.0
CE A:MET259 3.4 44.8 1.0
CG B:MET259 3.6 42.4 1.0
CG2 B:VAL121 3.6 43.1 1.0
BR1 A:K32502 3.7 60.4 1.0
CH2 B:TRP124 4.0 47.8 1.0
C7 A:K32502 4.1 44.5 1.0
CE B:MET259 4.1 43.0 1.0
C4 A:K32502 4.2 48.8 1.0
CZ2 B:TRP124 4.2 47.3 1.0
SD B:MET259 4.2 46.6 1.0
SD A:MET259 4.3 47.8 1.0
CB B:MET259 4.6 39.5 1.0
C8 A:K32502 4.6 43.0 1.0
CZ3 B:TRP124 4.9 47.1 1.0
CA B:MET259 5.0 37.6 1.0
O B:SER280 5.0 39.7 1.0

Bromine binding site 7 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 7 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:54.7
occ:1.00
 BR3 A:K32502 0.0 54.7 1.0
C4 A:K32502 2.0 48.8 1.0
C8 A:K32502 2.9 43.0 1.0
C3 A:K32502 3.0 57.5 1.0
N6 A:K32502 3.2 37.6 1.0
BR4 A:K32502 3.4 62.7 1.0
CB A:SER280 3.6 38.8 1.0
OE1 A:GLN277 3.8 43.5 1.0
CG2 A:VAL281 4.0 37.6 1.0
CH2 A:TRP124 4.1 49.5 1.0
N A:VAL281 4.2 32.7 1.0
C A:SER280 4.2 37.9 1.0
C7 A:K32502 4.2 44.5 1.0
CG A:MET259 4.3 43.9 1.0
C2 A:K32502 4.3 58.2 1.0
CZ2 A:TRP124 4.4 49.6 1.0
O A:SER280 4.5 38.7 1.0
CA A:VAL281 4.5 33.7 1.0
CA A:SER280 4.6 35.3 1.0
C13 A:K32502 4.6 42.0 1.0
CG1 A:VAL255 4.6 40.3 1.0
OG A:SER280 4.7 51.5 1.0
CZ3 A:TRP267 4.9 34.0 1.0
C5 A:K32502 4.9 51.5 1.0
CB A:VAL281 4.9 38.0 1.0
O A:GLN277 5.0 36.2 1.0

Bromine binding site 8 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 8 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:62.7
occ:1.00
 BR4 A:K32502 0.0 62.7 1.0
C3 A:K32502 1.9 57.5 1.0
C4 A:K32502 2.8 48.8 1.0
C2 A:K32502 3.0 58.2 1.0
BR2 A:K32502 3.3 65.6 1.0
BR3 A:K32502 3.4 54.7 1.0
CE B:MET259 3.5 43.0 1.0
CG2 A:VAL121 3.7 46.5 1.0
CG A:MET259 3.7 43.9 1.0
CH2 A:TRP124 3.9 49.5 1.0
C8 A:K32502 4.1 43.0 1.0
CE A:MET259 4.1 44.8 1.0
CZ2 A:TRP124 4.2 49.6 1.0
C5 A:K32502 4.3 51.5 1.0
SD A:MET259 4.3 47.8 1.0
SD B:MET259 4.4 46.6 1.0
O A:SER280 4.7 38.7 1.0
CB A:MET259 4.7 39.9 1.0
C7 A:K32502 4.7 44.5 1.0
CZ3 A:TRP124 4.8 48.7 1.0
CA A:GLY284 4.9 36.0 1.0
CA A:MET259 5.0 37.3 1.0

Bromine binding site 9 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 9 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br501

b:57.6
occ:1.00
 BR1 E:K32501 0.0 57.6 1.0
C5 E:K32501 1.9 52.1 1.0
C7 E:K32501 2.9 47.8 1.0
C2 E:K32501 3.0 59.3 1.0
N14 E:K32501 3.2 43.9 1.0
BR2 E:K32501 3.4 63.4 1.0
CB F:SER280 3.6 36.7 1.0
OE1 F:GLN277 3.8 40.9 1.0
CG2 F:VAL281 4.0 37.1 1.0
CH2 F:TRP124 4.1 51.2 1.0
N F:VAL281 4.2 32.8 1.0
C8 E:K32501 4.2 50.1 1.0
C F:SER280 4.2 37.1 1.0
CG F:MET259 4.3 45.1 1.0
C3 E:K32501 4.3 59.5 1.0
CZ2 F:TRP124 4.4 51.7 1.0
O F:SER280 4.5 37.6 1.0
CG1 F:VAL255 4.5 38.8 1.0
CA F:VAL281 4.6 33.9 1.0
C13 E:K32501 4.6 47.9 1.0
CA F:SER280 4.6 33.3 1.0
OG F:SER280 4.7 51.3 1.0
C4 E:K32501 4.9 55.1 1.0
CZ3 F:TRP267 4.9 34.0 1.0
CB F:VAL281 5.0 37.5 1.0

Bromine binding site 10 out of 12 in 6bky

Go back to Bromine Binding Sites List in 6bky
Bromine binding site 10 out of 12 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br501

b:63.4
occ:1.00
 BR2 E:K32501 0.0 63.4 1.0
C2 E:K32501 2.0 59.3 1.0
C5 E:K32501 2.8 52.1 1.0
C3 E:K32501 3.0 59.5 1.0
BR1 E:K32501 3.4 57.6 1.0
BR4 E:K32501 3.4 65.7 1.0
CG F:MET259 3.6 45.1 1.0
CE E:MET259 3.6 42.6 1.0
CG2 F:VAL121 3.6 45.2 1.0
CH2 F:TRP124 3.9 51.2 1.0
CZ2 F:TRP124 4.1 51.7 1.0
C7 E:K32501 4.1 47.8 1.0
CE F:MET259 4.1 45.7 1.0
SD F:MET259 4.3 48.7 1.0
C4 E:K32501 4.3 55.1 1.0
SD E:MET259 4.4 46.0 1.0
CB F:MET259 4.6 41.0 1.0
C8 E:K32501 4.7 50.1 1.0
O F:SER280 4.7 37.6 1.0
CZ3 F:TRP124 4.8 50.5 1.0
CA F:GLY284 4.9 37.5 1.0
CA F:MET259 4.9 38.6 1.0

Reference:

C.G.Jakob, A.K.Upadhyay, P.L.Donner, E.Nicholl, S.N.Addo, W.Qiu, C.Ling, S.M.Gopalakrishnan, M.Torrent, S.P.Cepa, J.Shanley, A.R.Shoemaker, C.C.Sun, A.Vasudevan, K.R.Woller, J.B.Shotwell, B.Shaw, Z.Bian, J.E.Hutti. Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of HIS315. J. Med. Chem. V. 61 6647 2018.
ISSN: ISSN 1520-4804
PubMed: 30004704
DOI: 10.1021/ACS.JMEDCHEM.8B00305
Page generated: Sat Dec 12 02:32:17 2020

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