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Chlorine in PDB 5mw4: Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide], PDB code: 5mw4 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) 45.72 / 2.19
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.360, 158.360, 74.590, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 20.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide] (pdb code 5mw4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide], PDB code: 5mw4:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5mw4

Go back to Chlorine Binding Sites List in 5mw4
Chlorine binding site 1 out of 2 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide]


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 CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:62.7
occ:1.00
 CL A:5JU401 0.0 62.7 1.0
C13 A:5JU401 1.8 45.9 1.0
C12 A:5JU401 2.8 42.5 1.0
S14 A:5JU401 3.0 40.7 1.0
C6 A:5JU401 3.3 45.5 1.0
O A:SER311 3.4 46.3 1.0
CD2 A:LEU143 3.4 48.9 1.0
C5 A:5JU401 3.5 49.4 1.0
O A:HOH514 3.8 47.0 1.0
CB A:SER269 3.8 43.5 1.0
CB A:TYR312 3.9 36.4 1.0
CA A:SER269 3.9 40.2 1.0
C7 A:5JU401 4.1 39.6 1.0
C8 A:5JU401 4.2 39.4 1.0
C1 A:5JU401 4.3 45.8 1.0
CA A:TYR312 4.3 38.0 1.0
C A:SER311 4.4 46.7 1.0
CG2 A:VAL310 4.4 61.0 1.0
O A:SER268 4.6 34.7 1.0
N A:SER269 4.6 38.5 1.0
C4 A:5JU401 4.6 53.2 1.0
CG A:LEU143 4.6 45.0 1.0
N A:TYR312 4.7 40.7 1.0
C A:SER268 4.9 37.5 1.0
SD A:MET147 4.9 52.6 1.0
C45 A:5JU401 4.9 41.8 1.0

Chlorine binding site 2 out of 2 in 5mw4

Go back to Chlorine Binding Sites List in 5mw4
Chlorine binding site 2 out of 2 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide]


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 CPD7 [N-(3-(((R)- 1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidin-3-Yl)(Methyl)Amino) Propyl)-2-(3-(2-Chloro-3-(2-Methylpyridin-3-Yl)Benzo[B]Thiophen-5- Yl)Ureido)Acetamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:75.0
occ:1.00
 CL B:5JU401 0.0 75.0 1.0
C13 B:5JU401 1.7 57.8 1.0
C12 B:5JU401 2.7 52.4 1.0
S14 B:5JU401 3.0 51.4 1.0
C6 B:5JU401 3.3 53.2 1.0
CD2 B:LEU143 3.4 56.2 1.0
C5 B:5JU401 3.5 57.3 1.0
O B:SER311 3.5 59.9 1.0
CB B:SER269 3.8 55.8 1.0
O B:HOH517 3.8 57.0 1.0
CB B:TYR312 3.9 50.0 1.0
CA B:SER269 3.9 52.8 1.0
C7 B:5JU401 4.0 47.9 1.0
C8 B:5JU401 4.1 50.1 1.0
C1 B:5JU401 4.3 50.2 1.0
CA B:TYR312 4.4 52.8 1.0
C B:SER311 4.5 60.9 1.0
N B:SER269 4.6 52.9 1.0
CG B:LEU143 4.6 50.6 1.0
C4 B:5JU401 4.6 56.9 1.0
O B:SER268 4.6 50.9 1.0
SD B:MET147 4.8 58.4 1.0
N B:TYR312 4.8 55.6 1.0
C B:SER268 4.9 52.7 1.0
C45 B:5JU401 4.9 44.4 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 05:41:42 2025

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