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Chlorine in PDB 5mvs: Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine], PDB code: 5mvs was solved by C.Be, E.Koch, C.Gaul, F.Stauffer, H.Moebitz, C.Scheufler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.98 / 2.18
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.211, 158.211, 73.826, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 18.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine] (pdb code 5mvs). 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 Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine], PDB code: 5mvs:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5mvs

Go back to Chlorine Binding Sites List in 5mvs
Chlorine binding site 1 out of 4 in the Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine]


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 Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:31.8
occ:1.00
 CL1 A:5JJ402 0.0 31.8 1.0
C17 A:5JJ402 1.7 29.1 1.0
C16 A:5JJ402 2.7 24.9 1.0
C12 A:5JJ402 2.7 31.1 1.0
N11 A:5JJ402 3.1 32.1 1.0
C20 A:5JJ402 3.3 28.6 1.0
CG A:LEU143 3.7 33.0 1.0
O A:LEU143 3.7 27.5 1.0
C A:LEU143 3.8 27.4 1.0
CD1 A:TYR312 3.8 32.5 1.0
CG A:TYR312 3.8 30.4 1.0
CD2 A:LEU143 3.9 35.4 1.0
C8 A:5JJ402 4.0 30.7 1.0
C15 A:5JJ402 4.0 25.4 1.0
CB A:LEU143 4.0 27.6 1.0
C13 A:5JJ402 4.0 31.2 1.0
CB A:MET147 4.0 30.4 1.0
N A:VAL144 4.1 23.8 1.0
CB A:TYR312 4.1 27.9 1.0
CE2 A:PHE239 4.2 28.0 1.0
CG A:MET147 4.3 36.7 1.0
CA A:VAL144 4.3 22.8 1.0
CE1 A:TYR312 4.3 32.1 1.0
CD2 A:TYR312 4.4 31.8 1.0
C9 A:5JJ402 4.4 31.0 1.0
CA A:LEU143 4.5 25.6 1.0
C14 A:5JJ402 4.5 26.5 1.0
CG2 A:VAL144 4.6 24.8 1.0
C21 A:5JJ402 4.6 28.2 1.0
CZ A:PHE239 4.6 27.1 1.0
CZ A:TYR312 4.8 42.2 1.0
CE2 A:TYR312 4.8 33.9 1.0
CD1 A:LEU143 5.0 32.0 1.0

Chlorine binding site 2 out of 4 in 5mvs

Go back to Chlorine Binding Sites List in 5mvs
Chlorine binding site 2 out of 4 in the Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine]


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 Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:35.3
occ:1.00
 CL2 A:5JJ402 0.0 35.3 1.0
C13 A:5JJ402 1.7 31.2 1.0
C12 A:5JJ402 2.7 31.1 1.0
C14 A:5JJ402 2.7 26.5 1.0
N11 A:5JJ402 3.0 32.1 1.0
C8 A:5JJ402 3.2 30.7 1.0
C9 A:5JJ402 3.5 31.0 1.0
C21 A:5JJ402 3.5 28.2 1.0
CB A:ASN241 3.6 30.5 1.0
CE1 A:PHE131 3.6 44.4 1.0
C22 A:5JJ402 3.7 31.8 1.0
CB A:SER269 3.7 27.1 1.0
C25 A:5JJ402 3.8 37.5 1.0
CD1 A:PHE131 3.8 44.6 1.0
CG A:ASN241 3.8 41.8 1.0
OD1 A:ASN241 3.8 32.4 1.0
C20 A:5JJ402 3.9 28.6 1.0
C7 A:5JJ402 3.9 28.6 1.0
C17 A:5JJ402 4.0 29.1 1.0
C15 A:5JJ402 4.0 25.4 1.0
OG A:SER269 4.1 30.9 1.0
CA A:ASN241 4.1 28.8 1.0
CZ A:PHE239 4.3 27.1 1.0
C23 A:5JJ402 4.4 34.6 1.0
CE1 A:PHE239 4.4 27.0 1.0
C10 A:5JJ402 4.4 30.2 1.0
C16 A:5JJ402 4.5 24.9 1.0
ND2 A:ASN241 4.6 32.7 1.0
CA A:SER269 4.6 25.6 1.0
N A:SER269 4.7 24.6 1.0
CZ A:PHE131 4.7 42.9 1.0
N A:ASN241 4.8 29.3 1.0
C4 A:5JJ402 4.9 29.4 1.0
O A:VAL240 4.9 28.8 1.0
CG A:PHE131 4.9 43.6 1.0

Chlorine binding site 3 out of 4 in 5mvs

Go back to Chlorine Binding Sites List in 5mvs
Chlorine binding site 3 out of 4 in the Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine]


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 Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:39.5
occ:1.00
 CL1 B:5JJ402 0.0 39.5 1.0
C17 B:5JJ402 1.7 39.3 1.0
C16 B:5JJ402 2.7 37.7 1.0
C12 B:5JJ402 2.7 39.4 1.0
N11 B:5JJ402 3.0 39.3 1.0
C20 B:5JJ402 3.3 37.8 1.0
CG B:LEU143 3.6 40.7 1.0
O B:LEU143 3.7 32.9 1.0
C B:LEU143 3.8 32.7 1.0
CD1 B:TYR312 3.9 41.6 1.0
CD2 B:LEU143 3.9 47.7 1.0
C8 B:5JJ402 3.9 39.2 1.0
CG B:TYR312 3.9 40.9 1.0
CB B:MET147 4.0 38.8 1.0
CB B:LEU143 4.0 32.7 1.0
C15 B:5JJ402 4.0 37.6 1.0
C13 B:5JJ402 4.0 40.1 1.0
N B:VAL144 4.1 28.1 1.0
CB B:TYR312 4.1 39.5 1.0
CG B:MET147 4.2 43.3 1.0
CE2 B:PHE239 4.2 33.5 1.0
C9 B:5JJ402 4.3 40.5 1.0
CA B:VAL144 4.3 28.1 1.0
CE1 B:TYR312 4.4 42.5 1.0
CD2 B:TYR312 4.5 42.7 1.0
CA B:LEU143 4.5 30.6 1.0
C14 B:5JJ402 4.5 37.8 1.0
CG2 B:VAL144 4.5 29.1 1.0
CZ B:PHE239 4.6 32.6 1.0
C21 B:5JJ402 4.6 36.5 1.0
CZ B:TYR312 4.9 47.1 1.0
CD1 B:LEU143 4.9 40.5 1.0
CE2 B:TYR312 4.9 43.1 1.0

Chlorine binding site 4 out of 4 in 5mvs

Go back to Chlorine Binding Sites List in 5mvs
Chlorine binding site 4 out of 4 in the Crystal Structure of DOT1L in Complex with Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine]


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 Adenosine and Inhibitor CPD1 [N6-(2,6-Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6- Diamine] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:44.7
occ:1.00
 CL2 B:5JJ402 0.0 44.7 1.0
C13 B:5JJ402 1.7 40.1 1.0
C14 B:5JJ402 2.7 37.8 1.0
C12 B:5JJ402 2.7 39.4 1.0
N11 B:5JJ402 3.0 39.3 1.0
C8 B:5JJ402 3.2 39.2 1.0
C21 B:5JJ402 3.5 36.5 1.0
C9 B:5JJ402 3.6 40.5 1.0
CB B:ASN241 3.6 40.4 1.0
C22 B:5JJ402 3.6 36.4 1.0
CE1 B:PHE131 3.6 48.9 1.0
C25 B:5JJ402 3.7 37.9 1.0
CB B:SER269 3.7 41.3 1.0
CG B:ASN241 3.7 57.8 1.0
OD1 B:ASN241 3.7 45.3 1.0
CD1 B:PHE131 3.8 48.3 1.0
C20 B:5JJ402 3.8 37.8 1.0
C7 B:5JJ402 3.8 37.2 1.0
OG B:SER269 4.0 44.7 1.0
CA B:ASN241 4.0 40.6 1.0
C17 B:5JJ402 4.0 39.3 1.0
C15 B:5JJ402 4.0 37.6 1.0
C23 B:5JJ402 4.3 35.7 1.0
CZ B:PHE239 4.3 32.6 1.0
CE1 B:PHE239 4.4 33.9 1.0
C10 B:5JJ402 4.5 38.1 1.0
C16 B:5JJ402 4.5 37.7 1.0
ND2 B:ASN241 4.6 45.1 1.0
CA B:SER269 4.6 39.7 1.0
CZ B:PHE131 4.7 47.8 1.0
N B:SER269 4.7 39.5 1.0
C4 B:5JJ402 4.7 36.7 1.0
N B:ASN241 4.7 40.9 1.0
O B:VAL240 4.9 39.1 1.0
C5 B:5JJ402 5.0 38.3 1.0
CG B:PHE131 5.0 47.5 1.0

Reference:

H.Mobitz, R.Machauer, P.Holzer, A.Vaupel, F.Stauffer, C.Ragot, G.Caravatti, C.Scheufler, C.Fernandez, U.Hommel, R.Tiedt, K.S.Beyer, C.Chen, H.Zhu, C.Gaul. Discovery of Potent, Selective, and Structurally Novel DOT1L Inhibitors By A Fragment Linking Approach. Acs Med Chem Lett V. 8 338 2017.
ISSN: ISSN 1948-5875
PubMed: 28337327
DOI: 10.1021/ACSMEDCHEMLETT.6B00519
Page generated: Fri Jul 26 12:57:57 2024

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