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Chlorine in PDB 5mw3: Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine], PDB code: 5mw3 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) 45.75 / 2.09
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.480, 158.480, 74.070, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 19.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine] (pdb code 5mw3). 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 CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine], PDB code: 5mw3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5mw3

Go back to Chlorine Binding Sites List in 5mw3
Chlorine binding site 1 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- 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 CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:25.4
occ:1.00
 CL1 A:5JJ401 0.0 25.4 1.0
C17 A:5JJ401 1.7 23.7 1.0
C16 A:5JJ401 2.7 22.5 1.0
C12 A:5JJ401 2.8 22.7 1.0
N11 A:5JJ401 3.1 23.2 1.0
C20 A:5JJ401 3.3 21.8 1.0
CG A:LEU143 3.6 26.1 1.0
O A:LEU143 3.7 23.8 1.0
CD1 A:TYR312 3.8 30.7 1.0
C A:LEU143 3.8 24.0 1.0
CG A:TYR312 3.9 27.3 1.0
CD2 A:LEU143 3.9 27.6 1.0
C8 A:5JJ401 4.0 24.7 1.0
CB A:LEU143 4.0 21.6 1.0
C15 A:5JJ401 4.0 22.7 1.0
CB A:MET147 4.0 25.4 1.0
C13 A:5JJ401 4.0 23.2 1.0
N A:VAL144 4.1 20.4 1.0
CB A:TYR312 4.1 24.2 1.0
CE2 A:PHE239 4.2 20.9 1.0
CA A:VAL144 4.3 20.3 1.0
CG A:MET147 4.3 29.7 1.0
CE1 A:TYR312 4.4 29.9 1.0
CD2 A:TYR312 4.4 28.4 1.0
C9 A:5JJ401 4.4 25.0 1.0
CG2 A:VAL144 4.5 22.9 1.0
CA A:LEU143 4.5 20.6 1.0
C14 A:5JJ401 4.5 21.5 1.0
C21 A:5JJ401 4.6 22.8 1.0
CZ A:PHE239 4.7 19.8 1.0
CZ A:TYR312 4.8 37.3 1.0
CE2 A:TYR312 4.9 29.8 1.0
CD1 A:LEU143 4.9 25.3 1.0

Chlorine binding site 2 out of 4 in 5mw3

Go back to Chlorine Binding Sites List in 5mw3
Chlorine binding site 2 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- 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 CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:26.5
occ:1.00
 CL2 A:5JJ401 0.0 26.5 1.0
C13 A:5JJ401 1.7 23.2 1.0
C12 A:5JJ401 2.7 22.7 1.0
C14 A:5JJ401 2.7 21.5 1.0
N11 A:5JJ401 3.0 23.2 1.0
C8 A:5JJ401 3.2 24.7 1.0
C9 A:5JJ401 3.5 25.0 1.0
C21 A:5JJ401 3.5 22.8 1.0
CB A:ASN241 3.6 21.6 1.0
CE1 A:PHE131 3.7 31.8 1.0
C22 A:5JJ401 3.7 26.6 1.0
CB A:SER269 3.8 21.3 1.0
C20 A:5JJ401 3.9 21.8 1.0
CG A:ASN241 3.9 33.3 1.0
CD1 A:PHE131 3.9 32.0 1.0
C25 A:5JJ401 3.9 32.9 1.0
C7 A:5JJ401 3.9 22.2 1.0
OD1 A:ASN241 3.9 23.7 1.0
CA A:ASN241 4.0 22.6 1.0
C17 A:5JJ401 4.0 23.7 1.0
C15 A:5JJ401 4.0 22.7 1.0
OG A:SER269 4.0 22.7 1.0
CZ A:PHE239 4.3 19.8 1.0
C10 A:5JJ401 4.4 24.4 1.0
C23 A:5JJ401 4.4 29.1 1.0
CE1 A:PHE239 4.4 21.5 1.0
C16 A:5JJ401 4.5 22.5 1.0
CA A:SER269 4.6 20.3 1.0
N A:SER269 4.7 20.2 1.0
N A:ASN241 4.7 22.8 1.0
ND2 A:ASN241 4.7 23.6 1.0
CZ A:PHE131 4.7 30.8 1.0
C4 A:5JJ401 4.8 24.0 1.0
O A:VAL240 4.9 22.7 1.0

Chlorine binding site 3 out of 4 in 5mw3

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Chlorine binding site 3 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- 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 CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:34.6
occ:1.00
 CL1 B:5JJ401 0.0 34.6 1.0
C17 B:5JJ401 1.7 34.6 1.0
C12 B:5JJ401 2.7 34.5 1.0
C16 B:5JJ401 2.7 32.6 1.0
N11 B:5JJ401 3.0 33.7 1.0
C20 B:5JJ401 3.3 31.0 1.0
CG B:LEU143 3.6 34.5 1.0
O B:LEU143 3.7 27.2 1.0
C B:LEU143 3.8 29.0 1.0
CD2 B:LEU143 3.9 37.5 1.0
C8 B:5JJ401 3.9 35.0 1.0
CD1 B:TYR312 3.9 39.8 1.0
CG B:TYR312 3.9 38.4 1.0
CB B:LEU143 4.0 27.6 1.0
C13 B:5JJ401 4.0 33.9 1.0
C15 B:5JJ401 4.0 32.5 1.0
CB B:MET147 4.1 33.2 1.0
N B:VAL144 4.1 25.1 1.0
CB B:TYR312 4.1 36.3 1.0
CE2 B:PHE239 4.2 30.1 1.0
C9 B:5JJ401 4.3 37.3 1.0
CA B:VAL144 4.3 25.8 1.0
CG B:MET147 4.3 37.8 1.0
CE1 B:TYR312 4.5 40.3 1.0
CD2 B:TYR312 4.5 40.5 1.0
CA B:LEU143 4.5 26.4 1.0
CG2 B:VAL144 4.5 27.7 1.0
C14 B:5JJ401 4.5 34.1 1.0
C21 B:5JJ401 4.6 30.6 1.0
CZ B:PHE239 4.6 28.6 1.0
CD1 B:LEU143 4.9 34.2 1.0
CZ B:TYR312 5.0 44.0 1.0
CE2 B:TYR312 5.0 41.3 1.0

Chlorine binding site 4 out of 4 in 5mw3

Go back to Chlorine Binding Sites List in 5mw3
Chlorine binding site 4 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- 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 CPD1 [N6-(2,6- Dichlorophenyl)-N6-(Pent-2-Yn-1-Yl)Quinoline-4,6-Diamine] and Inhibitor CPD2 [(R)-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3- Amine] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:37.4
occ:1.00
 CL2 B:5JJ401 0.0 37.4 1.0
C13 B:5JJ401 1.7 33.9 1.0
C12 B:5JJ401 2.7 34.5 1.0
C14 B:5JJ401 2.7 34.1 1.0
N11 B:5JJ401 3.0 33.7 1.0
C8 B:5JJ401 3.2 35.0 1.0
C9 B:5JJ401 3.5 37.3 1.0
C21 B:5JJ401 3.5 30.6 1.0
CB B:ASN241 3.5 34.3 1.0
C22 B:5JJ401 3.7 31.6 1.0
CE1 B:PHE131 3.7 41.3 1.0
CB B:SER269 3.7 38.1 1.0
C25 B:5JJ401 3.8 31.3 1.0
CG B:ASN241 3.8 50.2 1.0
C20 B:5JJ401 3.8 31.0 1.0
C7 B:5JJ401 3.8 34.2 1.0
OD1 B:ASN241 3.8 41.6 1.0
CA B:ASN241 3.9 36.0 1.0
CD1 B:PHE131 4.0 40.7 1.0
OG B:SER269 4.0 41.5 1.0
C17 B:5JJ401 4.0 34.6 1.0
C15 B:5JJ401 4.0 32.5 1.0
C23 B:5JJ401 4.3 31.1 1.0
CZ B:PHE239 4.3 28.6 1.0
C10 B:5JJ401 4.4 36.6 1.0
CE1 B:PHE239 4.4 30.3 1.0
C16 B:5JJ401 4.5 32.6 1.0
N B:ASN241 4.6 36.3 1.0
CA B:SER269 4.6 35.6 1.0
N B:SER269 4.7 36.0 1.0
ND2 B:ASN241 4.7 41.6 1.0
C4 B:5JJ401 4.7 35.7 1.0
CZ B:PHE131 4.7 39.9 1.0
O B:VAL240 4.9 37.3 1.0
C5 B:5JJ401 4.9 37.5 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: Sat Jul 12 05:41:32 2025

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