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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

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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

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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

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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

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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

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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

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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

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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

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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 Jul 12 10:28:53 2025

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