Chlorine in PDB 5x1v: PKM2 in Complex with Compound 2

Enzymatic activity of PKM2 in Complex with Compound 2

All present enzymatic activity of PKM2 in Complex with Compound 2:
2.7.1.40;

Protein crystallography data

The structure of PKM2 in Complex with Compound 2, PDB code: 5x1v was solved by Y.Matsui, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.468, 151.658, 92.079, 90.00, 102.44, 90.00
R / Rfree (%) 23.4 / 27.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the PKM2 in Complex with Compound 2 (pdb code 5x1v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the PKM2 in Complex with Compound 2, PDB code: 5x1v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 1 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:38.6
occ:1.00
CL1 A:7XX602 0.0 38.6 1.0
C8 A:7XX602 1.7 41.4 1.0
C3 A:7XX602 2.6 39.9 1.0
C9 A:7XX602 2.7 39.2 1.0
CL2 A:7XX602 3.0 41.9 1.0
OE1 A:GLU397 3.1 32.2 1.0
CD1 B:PHE26 3.7 28.6 1.0
CD1 A:LEU394 3.8 35.6 1.0
CD A:GLU397 3.8 32.9 1.0
CB B:PHE26 3.8 27.2 1.0
N B:LEU27 3.9 25.6 1.0
C1 A:7XX602 3.9 41.5 1.0
C6 A:7XX602 3.9 40.7 1.0
CA A:LEU394 4.2 36.1 1.0
CG B:PHE26 4.2 28.4 1.0
OE2 A:GLU397 4.3 32.9 1.0
CB B:LEU27 4.3 27.4 1.0
CG A:GLN393 4.4 37.9 1.0
C2 A:7XX602 4.4 39.9 1.0
CA B:LEU27 4.4 26.4 1.0
C B:PHE26 4.4 25.7 1.0
CB A:LEU394 4.5 36.2 1.0
CB A:GLU397 4.6 34.0 1.0
N A:LEU394 4.6 36.2 1.0
CA B:PHE26 4.7 26.7 1.0
CE1 B:PHE26 4.7 29.6 1.0
CG A:GLU397 4.7 33.5 1.0
CG A:LEU394 4.7 36.6 1.0
C A:GLN393 4.9 36.7 1.0

Chlorine binding site 2 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 2 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:41.9
occ:1.00
CL2 A:7XX602 0.0 41.9 1.0
C9 A:7XX602 1.7 39.2 1.0
C8 A:7XX602 2.7 41.4 1.0
C6 A:7XX602 2.7 40.7 1.0
CL1 A:7XX602 3.0 38.6 1.0
C11 A:7XX602 3.2 40.2 1.0
O16 A:7XX602 3.2 37.1 1.0
O A:TYR390 3.6 37.0 1.0
CG A:GLN393 3.7 37.9 1.0
CB A:GLN393 3.8 37.2 1.0
N A:LEU394 3.9 36.2 1.0
C3 A:7XX602 4.0 39.9 1.0
C2 A:7XX602 4.0 39.9 1.0
CE2 A:PHE26 4.0 33.7 1.0
CB A:LEU394 4.0 36.2 1.0
CA A:LEU394 4.2 36.1 1.0
CD A:GLN393 4.2 38.5 1.0
C7 A:7XX602 4.3 42.2 1.0
CB A:TYR390 4.3 37.8 1.0
CD2 A:PHE26 4.4 34.2 1.0
C A:GLN393 4.4 36.7 1.0
OE1 A:GLN393 4.5 37.6 1.0
C1 A:7XX602 4.5 41.5 1.0
C A:TYR390 4.6 37.1 1.0
CD2 A:TYR390 4.6 40.4 1.0
CD1 B:PHE26 4.6 28.6 1.0
CA A:GLN393 4.7 37.3 1.0
CD1 A:LEU394 4.9 35.6 1.0
CA A:TYR390 4.9 37.8 1.0
CG A:TYR390 4.9 39.3 1.0
NE2 A:GLN393 4.9 38.7 1.0
CG A:LEU394 5.0 36.6 1.0

Chlorine binding site 3 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 3 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:35.8
occ:1.00
CL1 B:7XX602 0.0 35.8 1.0
C8 B:7XX602 1.7 39.0 1.0
C3 B:7XX602 2.6 39.0 1.0
C9 B:7XX602 2.7 39.8 1.0
CL2 B:7XX602 3.1 38.2 1.0
OE1 B:GLU397 3.1 33.8 1.0
CD1 A:PHE26 3.7 34.2 1.0
N A:LEU27 3.8 34.1 1.0
CD1 B:LEU394 3.8 26.6 1.0
CB A:PHE26 3.8 34.2 1.0
C1 B:7XX602 3.9 39.9 1.0
CD B:GLU397 3.9 34.9 1.0
C6 B:7XX602 3.9 40.0 1.0
CB A:LEU27 4.0 35.1 1.0
CG A:PHE26 4.2 34.5 1.0
CA A:LEU27 4.2 35.7 1.0
CA B:LEU394 4.2 27.7 1.0
C A:PHE26 4.4 33.9 1.0
C2 B:7XX602 4.4 39.2 1.0
CG B:GLN393 4.5 30.1 1.0
CB B:LEU394 4.5 27.6 1.0
OE2 B:GLU397 4.5 34.9 1.0
CA A:PHE26 4.7 34.7 1.0
CE1 A:PHE26 4.7 34.2 1.0
CB B:GLU397 4.7 35.6 1.0
N B:LEU394 4.7 28.1 1.0
CG B:GLU397 4.8 35.2 1.0
CG B:LEU394 4.8 26.6 1.0
NE2 B:GLN393 5.0 32.1 1.0

Chlorine binding site 4 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 4 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:38.2
occ:1.00
CL2 B:7XX602 0.0 38.2 1.0
C9 B:7XX602 1.7 39.8 1.0
C8 B:7XX602 2.7 39.0 1.0
C6 B:7XX602 2.7 40.0 1.0
CL1 B:7XX602 3.1 35.8 1.0
C11 B:7XX602 3.1 39.4 1.0
O16 B:7XX602 3.2 37.9 1.0
O B:TYR390 3.6 26.5 1.0
CG B:GLN393 3.6 30.1 1.0
N B:LEU394 3.8 28.1 1.0
CB B:LEU394 3.9 27.6 1.0
C2 B:7XX602 4.0 39.2 1.0
C3 B:7XX602 4.0 39.0 1.0
CA B:LEU394 4.0 27.7 1.0
CB B:GLN393 4.1 28.7 1.0
CB B:TYR390 4.2 25.5 1.0
CD B:GLN393 4.2 31.4 1.0
C7 B:7XX602 4.2 40.6 1.0
C B:GLN393 4.4 27.1 1.0
CE2 B:PHE26 4.4 29.7 1.0
OE1 B:GLN393 4.5 33.9 1.0
C1 B:7XX602 4.5 39.9 1.0
C B:TYR390 4.6 26.6 1.0
CD2 B:PHE26 4.6 29.4 1.0
CD1 A:PHE26 4.6 34.2 1.0
CD2 B:TYR390 4.6 24.9 1.0
CD1 B:LEU394 4.7 26.6 1.0
CA B:GLN393 4.7 27.9 1.0
CA B:TYR390 4.8 26.1 1.0
CG B:TYR390 4.8 25.0 1.0
NE2 B:GLN393 4.8 32.1 1.0
CG B:LEU394 4.9 26.6 1.0
C5 B:7XX602 5.0 39.8 1.0

Chlorine binding site 5 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 5 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl602

b:44.5
occ:1.00
CL1 C:7XX602 0.0 44.5 1.0
C8 C:7XX602 1.7 42.6 1.0
C3 C:7XX602 2.6 41.4 1.0
C9 C:7XX602 2.7 42.5 1.0
CL2 C:7XX602 3.1 45.5 1.0
OE1 C:GLU397 3.2 37.4 1.0
CB D:PHE26 3.7 32.5 1.0
CD C:GLU397 3.7 38.1 1.0
CD1 D:PHE26 3.8 33.2 1.0
CD1 C:LEU394 3.8 30.6 1.0
N D:LEU27 3.8 31.4 1.0
C1 C:7XX602 3.9 41.0 1.0
C6 C:7XX602 4.0 40.8 1.0
OE2 C:GLU397 4.1 39.0 1.0
CG D:PHE26 4.1 32.8 1.0
CA C:LEU394 4.2 32.3 1.0
CB D:LEU27 4.2 32.2 1.0
C D:PHE26 4.3 31.6 1.0
CG C:GLN393 4.4 34.8 1.0
CA D:LEU27 4.4 32.0 1.0
C2 C:7XX602 4.4 39.1 1.0
CA D:PHE26 4.6 32.1 1.0
N C:LEU394 4.6 32.3 1.0
CB C:LEU394 4.6 30.9 1.0
CG C:GLU397 4.6 37.6 1.0
CB C:GLU397 4.7 36.0 1.0
CG C:LEU394 4.8 30.4 1.0
CE1 D:PHE26 4.8 33.9 1.0
C C:GLN393 4.9 33.1 1.0
NE2 C:GLN393 4.9 35.6 1.0
CD C:GLN393 4.9 35.9 1.0

Chlorine binding site 6 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 6 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl602

b:45.5
occ:1.00
CL2 C:7XX602 0.0 45.5 1.0
C9 C:7XX602 1.7 42.5 1.0
C8 C:7XX602 2.7 42.6 1.0
C6 C:7XX602 2.7 40.8 1.0
CL1 C:7XX602 3.1 44.5 1.0
C11 C:7XX602 3.1 40.1 1.0
O16 C:7XX602 3.2 40.9 1.0
O C:TYR390 3.6 30.6 1.0
CG C:GLN393 3.6 34.8 1.0
N C:LEU394 3.8 32.3 1.0
CB C:GLN393 3.8 33.7 1.0
C2 C:7XX602 4.0 39.1 1.0
C3 C:7XX602 4.0 41.4 1.0
CB C:LEU394 4.1 30.9 1.0
CA C:LEU394 4.1 32.3 1.0
CD C:GLN393 4.2 35.9 1.0
C7 C:7XX602 4.2 39.8 1.0
CB C:TYR390 4.2 30.2 1.0
CE2 C:PHE26 4.3 34.2 1.0
C C:GLN393 4.4 33.1 1.0
OE1 C:GLN393 4.4 36.6 1.0
C1 C:7XX602 4.5 41.0 1.0
CD2 C:PHE26 4.5 34.0 1.0
C C:TYR390 4.5 30.6 1.0
CD2 C:TYR390 4.6 30.1 1.0
CA C:GLN393 4.6 33.5 1.0
CD1 D:PHE26 4.7 33.2 1.0
CD1 C:LEU394 4.8 30.6 1.0
CA C:TYR390 4.8 30.5 1.0
CG C:TYR390 4.9 29.9 1.0
NE2 C:GLN393 4.9 35.6 1.0
CG D:PHE26 4.9 32.8 1.0
C5 C:7XX602 4.9 39.4 1.0
CG C:LEU394 4.9 30.4 1.0

Chlorine binding site 7 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 7 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl602

b:39.2
occ:1.00
CL1 D:7XX602 0.0 39.2 1.0
C8 D:7XX602 1.7 40.5 1.0
C3 D:7XX602 2.7 39.1 1.0
C9 D:7XX602 2.7 40.8 1.0
CL2 D:7XX602 3.0 43.1 1.0
OE1 D:GLU397 3.2 32.2 1.0
CD1 C:PHE26 3.7 33.7 1.0
CD D:GLU397 3.8 32.5 1.0
CD1 D:LEU394 3.8 31.0 1.0
CB C:PHE26 3.9 33.2 1.0
C1 D:7XX602 3.9 38.2 1.0
N C:LEU27 3.9 32.4 1.0
C6 D:7XX602 4.0 40.8 1.0
CA D:LEU394 4.2 31.0 1.0
CG C:PHE26 4.2 33.5 1.0
CD1 C:LEU27 4.3 34.1 1.0
CB C:LEU27 4.3 33.2 1.0
OE2 D:GLU397 4.4 32.7 1.0
CA C:LEU27 4.4 33.5 1.0
C2 D:7XX602 4.4 39.2 1.0
CB D:LEU394 4.5 31.4 1.0
C C:PHE26 4.5 32.3 1.0
CG D:GLN393 4.5 32.2 1.0
CB D:GLU397 4.6 32.2 1.0
CG D:GLU397 4.6 32.4 1.0
N D:LEU394 4.6 31.1 1.0
CE1 C:PHE26 4.7 34.8 1.0
CG D:LEU394 4.8 30.4 1.0
CA C:PHE26 4.8 32.4 1.0
C D:GLN393 4.9 31.2 1.0
O D:GLN393 4.9 31.5 1.0
CG C:LEU27 5.0 33.5 1.0

Chlorine binding site 8 out of 8 in 5x1v

Go back to Chlorine Binding Sites List in 5x1v
Chlorine binding site 8 out of 8 in the PKM2 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of PKM2 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl602

b:43.1
occ:1.00
CL2 D:7XX602 0.0 43.1 1.0
C9 D:7XX602 1.7 40.8 1.0
C8 D:7XX602 2.7 40.5 1.0
C6 D:7XX602 2.7 40.8 1.0
CL1 D:7XX602 3.0 39.2 1.0
C11 D:7XX602 3.1 39.7 1.0
O16 D:7XX602 3.2 38.2 1.0
O D:TYR390 3.6 28.3 1.0
CB D:GLN393 3.8 31.2 1.0
CG D:GLN393 3.8 32.2 1.0
N D:LEU394 3.8 31.1 1.0
CB D:LEU394 3.9 31.4 1.0
C3 D:7XX602 4.0 39.1 1.0
C2 D:7XX602 4.0 39.2 1.0
CA D:LEU394 4.1 31.0 1.0
CD D:GLN393 4.2 32.6 1.0
CE2 D:PHE26 4.2 33.7 1.0
C7 D:7XX602 4.2 40.1 1.0
CB D:TYR390 4.3 27.1 1.0
C D:GLN393 4.3 31.2 1.0
OE1 D:GLN393 4.4 33.8 1.0
C1 D:7XX602 4.5 38.2 1.0
CD2 D:PHE26 4.5 33.0 1.0
CD1 C:PHE26 4.6 33.7 1.0
C D:TYR390 4.6 28.3 1.0
CA D:GLN393 4.6 31.3 1.0
CD2 D:TYR390 4.6 26.8 1.0
CD1 D:LEU394 4.8 31.0 1.0
CA D:TYR390 4.9 28.0 1.0
CG D:TYR390 4.9 26.7 1.0
NE2 D:GLN393 4.9 31.9 1.0
CG D:LEU394 4.9 30.4 1.0

Reference:

Y.Matsui, I.Yasumatsu, T.Asahi, T.Kitamura, K.Kanai, O.Ubukata, H.Hayasaka, S.Takaishi, H.Hanzawa, S.Katakura. Discovery and Structure-Guided Fragment-Linking of 4-(2,3-Dichlorobenzoyl)-1-Methyl-Pyrrole-2-Carboxamide As A Pyruvate Kinase M2 Activator Bioorg. Med. Chem. V. 25 3540 2017.
ISSN: ESSN 1464-3391
PubMed: 28511909
DOI: 10.1016/J.BMC.2017.05.004
Page generated: Sat Dec 12 12:38:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy