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Chlorine in PDB 5dtq: Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone], PDB code: 5dtq was solved by C.Scheufler, C.Be, H.Moebitz, F.Stauffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.80 / 2.61
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.651, 158.651, 74.179, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone] (pdb code 5dtq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone], PDB code: 5dtq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5dtq

Go back to Chlorine Binding Sites List in 5dtq
Chlorine binding site 1 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:61.2
occ:1.00
 CL7 A:5F6401 0.0 61.2 1.0
C1 A:5F6401 1.8 53.3 1.0
C6 A:5F6401 2.7 50.8 1.0
C2 A:5F6401 2.8 47.6 1.0
C9 A:5F6401 3.1 43.9 1.0
OG A:SER140 3.4 45.2 1.0
CA A:SER140 3.5 36.0 1.0
CB A:SER140 3.6 38.2 1.0
CD2 A:PHE131 3.6 62.1 1.0
O10 A:5F6401 3.7 45.1 1.0
C11 A:5F6401 3.7 39.1 1.0
CE2 A:PHE131 3.8 63.3 1.0
O A:SER140 3.9 35.8 1.0
O A:HOH602 3.9 45.1 1.0
CG2 A:VAL144 4.0 28.3 1.0
C5 A:5F6401 4.0 51.9 1.0
CB A:LEU143 4.1 27.2 1.0
C3 A:5F6401 4.1 43.0 1.0
C A:SER140 4.2 36.2 1.0
CD2 A:LEU143 4.2 29.2 1.0
C12 A:5F6401 4.2 36.5 1.0
N A:SER140 4.5 39.3 1.0
CG A:LEU143 4.6 31.8 1.0
C4 A:5F6401 4.6 46.5 1.0
N A:VAL144 4.6 26.1 1.0
C16 A:5F6401 4.7 38.7 1.0
CZ A:PHE239 4.8 31.1 1.0
CG A:PHE131 4.9 62.7 1.0

Chlorine binding site 2 out of 4 in 5dtq

Go back to Chlorine Binding Sites List in 5dtq
Chlorine binding site 2 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:52.8
occ:1.00
 CL8 A:5F6401 0.0 52.8 1.0
C5 A:5F6401 1.7 51.9 1.0
C6 A:5F6401 2.7 50.8 1.0
C4 A:5F6401 2.8 46.5 1.0
C9 A:5F6401 2.9 43.9 1.0
C A:SER268 3.2 28.9 1.0
N A:SER269 3.3 27.9 1.0
O10 A:5F6401 3.3 45.1 1.0
O A:SER268 3.6 27.6 1.0
C11 A:5F6401 3.6 39.1 1.0
C12 A:5F6401 3.7 36.5 1.0
CA A:SER268 3.7 24.3 1.0
CA A:SER269 3.8 28.2 1.0
C1 A:5F6401 4.0 53.3 1.0
CB A:SER269 4.0 28.0 1.0
CB A:TYR312 4.0 30.5 1.0
C3 A:5F6401 4.0 43.0 1.0
N A:SER268 4.1 24.4 1.0
CZ A:PHE239 4.1 31.1 1.0
O A:VAL240 4.2 37.5 1.0
CE2 A:PHE239 4.3 32.7 1.0
CG1 A:VAL267 4.4 28.3 1.0
C A:VAL267 4.4 26.6 1.0
OG A:SER269 4.5 33.8 1.0
C2 A:5F6401 4.5 47.6 1.0
O A:VAL267 4.5 25.1 1.0
C16 A:5F6401 4.6 38.7 1.0
CE1 A:PHE239 4.7 31.4 1.0
C13 A:5F6401 4.8 39.7 1.0
CA A:ASN241 4.8 36.5 1.0
C A:VAL240 4.8 36.7 1.0
CG A:TYR312 5.0 31.4 1.0
CD2 A:PHE239 5.0 29.5 1.0

Chlorine binding site 3 out of 4 in 5dtq

Go back to Chlorine Binding Sites List in 5dtq
Chlorine binding site 3 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:62.6
occ:1.00
 CL7 B:5F6401 0.0 62.6 1.0
C1 B:5F6401 1.8 59.3 1.0
C6 B:5F6401 2.7 59.2 1.0
C2 B:5F6401 2.8 56.8 1.0
C9 B:5F6401 3.0 55.4 1.0
O10 B:5F6401 3.6 55.6 1.0
CA B:SER140 3.6 39.9 1.0
OG B:SER140 3.6 51.3 1.0
C11 B:5F6401 3.7 51.8 1.0
CB B:SER140 3.7 43.5 1.0
CD2 B:PHE131 3.8 72.7 1.0
O B:SER140 3.9 41.3 1.0
CG2 B:VAL144 3.9 33.2 1.0
CE2 B:PHE131 3.9 73.9 1.0
C5 B:5F6401 4.0 62.2 1.0
CB B:LEU143 4.1 31.2 1.0
C3 B:5F6401 4.1 56.8 1.0
C12 B:5F6401 4.1 50.0 1.0
CD2 B:LEU143 4.1 39.1 1.0
O B:HOH587 4.2 46.6 1.0
C B:SER140 4.2 40.3 1.0
CG B:LEU143 4.5 36.4 1.0
N B:VAL144 4.6 31.5 1.0
C4 B:5F6401 4.6 60.4 1.0
C16 B:5F6401 4.6 54.6 1.0
N B:SER140 4.6 42.2 1.0
CZ B:PHE239 4.8 34.8 1.0

Chlorine binding site 4 out of 4 in 5dtq

Go back to Chlorine Binding Sites List in 5dtq
Chlorine binding site 4 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [(2,6- Dichlorophenyl)(Quinolin-6-Yl)Methanone] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:68.0
occ:1.00
 CL8 B:5F6401 0.0 68.0 1.0
C5 B:5F6401 1.7 62.2 1.0
C6 B:5F6401 2.7 59.2 1.0
C4 B:5F6401 2.7 60.4 1.0
C9 B:5F6401 3.0 55.4 1.0
C B:SER268 3.2 45.5 1.0
N B:SER269 3.3 42.6 1.0
O10 B:5F6401 3.4 55.6 1.0
O B:SER268 3.5 44.8 1.0
C11 B:5F6401 3.6 51.8 1.0
CA B:SER268 3.6 41.0 1.0
C12 B:5F6401 3.8 50.0 1.0
CA B:SER269 3.8 41.4 1.0
C1 B:5F6401 4.0 59.3 1.0
N B:SER268 4.0 40.6 1.0
CB B:SER269 4.0 41.2 1.0
C3 B:5F6401 4.0 56.8 1.0
CB B:TYR312 4.1 44.1 1.0
O B:VAL240 4.1 54.2 1.0
CZ B:PHE239 4.1 34.8 1.0
CE2 B:PHE239 4.3 37.1 1.0
C B:VAL267 4.4 43.8 1.0
CG1 B:VAL267 4.4 43.0 1.0
O B:VAL267 4.4 40.6 1.0
OG B:SER269 4.4 45.9 1.0
C2 B:5F6401 4.5 56.8 1.0
C16 B:5F6401 4.6 54.6 1.0
CE1 B:PHE239 4.7 35.7 1.0
C B:VAL240 4.7 50.9 1.0
CA B:ASN241 4.7 46.7 1.0
C13 B:5F6401 4.8 52.4 1.0
N B:ASN241 4.9 46.9 1.0

Reference:

C.Scheufler, H.Mobitz, C.Gaul, C.Ragot, C.Be, C.Fernandez, K.S.Beyer, R.Tiedt, F.Stauffer. Optimization of A Fragment-Based Screening Hit Toward Potent DOT1L Inhibitors Interacting in An Induced Binding Pocket. Acs Med.Chem.Lett. V. 7 730 2016.
ISSN: ISSN 1948-5875
PubMed: 27563394
DOI: 10.1021/ACSMEDCHEMLETT.6B00168
Page generated: Fri Jul 26 06:56:47 2024

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