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Chlorine in PDB 5dtr: Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine], PDB code: 5dtr 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) 42.46 / 2.34
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.435, 158.435, 73.955, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 21

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine] (pdb code 5dtr). 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 CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine], PDB code: 5dtr:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5dtr

Go back to Chlorine Binding Sites List in 5dtr
Chlorine binding site 1 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine]


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 CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:51.2
occ:1.00
 CL1 A:5F7401 0.0 51.2 1.0
C17 A:5F7401 1.7 54.1 1.0
C16 A:5F7401 2.7 55.3 1.0
C12 A:5F7401 2.8 56.2 1.0
N11 A:5F7401 3.1 57.8 1.0
C22 A:5F7401 3.4 49.9 1.0
CG A:LEU143 3.6 39.4 1.0
O A:LEU143 3.7 30.5 1.0
C A:LEU143 3.8 31.6 1.0
CD2 A:LEU143 3.9 42.7 1.0
CG A:TYR312 3.9 33.0 1.0
CB A:MET147 3.9 32.9 1.0
CD1 A:TYR312 4.0 35.1 1.0
C15 A:5F7401 4.0 54.3 1.0
C8 A:5F7401 4.0 62.4 1.0
CB A:LEU143 4.0 33.4 1.0
C13 A:5F7401 4.1 58.3 1.0
N A:VAL144 4.1 27.9 1.0
CG A:MET147 4.2 38.9 1.0
CB A:TYR312 4.2 32.3 1.0
CE2 A:PHE239 4.2 30.9 1.0
CD2 A:TYR312 4.3 33.9 1.0
CA A:VAL144 4.3 26.9 1.0
C9 A:5F7401 4.4 58.3 1.0
CE1 A:TYR312 4.4 34.5 1.0
CA A:LEU143 4.5 31.2 1.0
C14 A:5F7401 4.6 53.6 1.0
CG2 A:VAL144 4.7 31.5 1.0
CZ A:PHE239 4.7 30.1 1.0
CE2 A:TYR312 4.8 35.4 1.0
CG1 A:VAL267 4.8 36.9 1.0
CZ A:TYR312 4.8 42.2 1.0
CD1 A:LEU143 4.9 38.6 1.0

Chlorine binding site 2 out of 4 in 5dtr

Go back to Chlorine Binding Sites List in 5dtr
Chlorine binding site 2 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine]


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 CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:65.4
occ:1.00
 CL2 A:5F7401 0.0 65.4 1.0
C13 A:5F7401 1.7 58.3 1.0
C14 A:5F7401 2.7 53.6 1.0
C12 A:5F7401 2.7 56.2 1.0
N11 A:5F7401 2.9 57.8 1.0
C8 A:5F7401 3.0 62.4 1.0
C9 A:5F7401 3.3 58.3 1.0
CE1 A:PHE131 3.5 88.7 1.0
CG A:ASN241 3.5 51.6 1.0
CB A:ASN241 3.6 38.0 1.0
C7 A:5F7401 3.7 65.8 1.0
C22 A:5F7401 3.8 49.9 1.0
ND2 A:ASN241 3.8 47.9 1.0
CD1 A:PHE131 3.8 88.6 1.0
OD1 A:ASN241 3.8 40.7 1.0
CB A:SER269 3.9 31.8 1.0
C15 A:5F7401 4.0 54.3 1.0
C17 A:5F7401 4.0 54.1 1.0
OG A:SER269 4.1 35.0 1.0
C10 A:5F7401 4.2 60.0 1.0
O A:HOH654 4.2 51.9 1.0
CA A:ASN241 4.3 36.0 1.0
CZ A:PHE239 4.3 30.1 1.0
CZ A:PHE131 4.4 87.9 1.0
C16 A:5F7401 4.5 55.3 1.0
C4 A:5F7401 4.5 67.2 1.0
CE1 A:PHE239 4.6 31.0 1.0
C5 A:5F7401 4.7 67.0 1.0
O A:HOH623 4.8 61.4 1.0
CA A:SER269 4.9 31.5 1.0
CG A:PHE131 4.9 87.2 1.0

Chlorine binding site 3 out of 4 in 5dtr

Go back to Chlorine Binding Sites List in 5dtr
Chlorine binding site 3 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine]


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 CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:58.4
occ:1.00
 CL1 B:5F7401 0.0 58.4 1.0
C17 B:5F7401 1.7 58.6 1.0
C16 B:5F7401 2.7 57.2 1.0
C12 B:5F7401 2.7 60.2 1.0
N11 B:5F7401 3.1 60.1 1.0
C22 B:5F7401 3.4 51.6 1.0
O B:LEU143 3.5 38.3 1.0
CG B:LEU143 3.7 47.1 1.0
C B:LEU143 3.7 37.7 1.0
CB B:MET147 3.9 43.5 1.0
C8 B:5F7401 3.9 66.2 1.0
CG B:TYR312 3.9 46.2 1.0
CD1 B:TYR312 4.0 47.4 1.0
C15 B:5F7401 4.0 57.1 1.0
C13 B:5F7401 4.0 62.5 1.0
CB B:LEU143 4.0 37.4 1.0
CD2 B:LEU143 4.1 51.7 1.0
N B:VAL144 4.1 32.0 1.0
CG B:MET147 4.2 49.4 1.0
CB B:TYR312 4.2 45.5 1.0
CE2 B:PHE239 4.2 38.8 1.0
C9 B:5F7401 4.3 66.9 1.0
CA B:VAL144 4.3 31.1 1.0
CD2 B:TYR312 4.4 47.6 1.0
CA B:LEU143 4.5 35.4 1.0
CE1 B:TYR312 4.5 49.5 1.0
C14 B:5F7401 4.6 58.9 1.0
CG2 B:VAL144 4.6 34.0 1.0
CZ B:PHE239 4.7 37.3 1.0
CE2 B:TYR312 4.8 48.1 1.0
CG1 B:VAL267 4.9 46.9 1.0
CZ B:TYR312 4.9 56.3 1.0
CD1 B:LEU143 5.0 48.1 1.0

Chlorine binding site 4 out of 4 in 5dtr

Go back to Chlorine Binding Sites List in 5dtr
Chlorine binding site 4 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine]


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 CPD5 [N-(2,6- Dichlorophenyl)-4-Methoxy-N-Methylquinolin-6-Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:70.3
occ:1.00
 CL2 B:5F7401 0.0 70.3 1.0
C13 B:5F7401 1.7 62.5 1.0
C12 B:5F7401 2.7 60.2 1.0
C14 B:5F7401 2.7 58.9 1.0
N11 B:5F7401 2.9 60.1 1.0
C8 B:5F7401 3.1 66.2 1.0
C9 B:5F7401 3.4 66.9 1.0
CE1 B:PHE131 3.5 87.9 1.0
CG B:ASN241 3.5 65.0 1.0
CB B:ASN241 3.6 46.7 1.0
C7 B:5F7401 3.6 67.8 1.0
C22 B:5F7401 3.7 51.6 1.0
CD1 B:PHE131 3.7 87.3 1.0
OD1 B:ASN241 3.8 53.0 1.0
CB B:SER269 3.9 46.6 1.0
ND2 B:ASN241 4.0 60.9 1.0
C17 B:5F7401 4.0 58.6 1.0
O B:HOH643 4.0 57.9 1.0
C15 B:5F7401 4.0 57.1 1.0
OG B:SER269 4.1 54.4 1.0
CA B:ASN241 4.2 48.7 1.0
C10 B:5F7401 4.2 68.8 1.0
CZ B:PHE239 4.4 37.3 1.0
C4 B:5F7401 4.4 69.0 1.0
C16 B:5F7401 4.5 57.2 1.0
CE1 B:PHE239 4.6 38.6 1.0
CZ B:PHE131 4.6 87.8 1.0
C5 B:5F7401 4.7 71.6 1.0
CA B:SER269 4.9 44.8 1.0
N B:ASN241 5.0 48.0 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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