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Chlorine in PDB 5drt: Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide], PDB code: 5drt was solved by C.Scheufler, C.Gaul, C.Be, H.Moebitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.82 / 2.69
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.712, 158.712, 73.645, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 19.7

Other elements in 5drt:

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide] also contains other interesting chemical elements:

Potassium (K) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide] (pdb code 5drt). 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 CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide], PDB code: 5drt:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5drt

Go back to Chlorine Binding Sites List in 5drt
Chlorine binding site 1 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide]


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 CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:75.3
occ:1.00
 CL1 A:5EG401 0.0 75.3 1.0
C16 A:5EG401 1.7 75.6 1.0
C11 A:5EG401 2.7 78.2 1.0
C15 A:5EG401 2.7 74.2 1.0
O10 A:5EG401 2.9 77.5 1.0
CB A:SER140 3.5 57.9 1.0
C29 A:5EG401 3.7 45.6 1.0
CG2 A:VAL169 3.7 37.5 1.0
OG A:SER140 3.9 67.8 1.0
CE2 A:TYR136 3.9 52.3 1.0
C12 A:5EG401 4.0 80.7 1.0
C14 A:5EG401 4.0 77.3 1.0
O21 A:5EG401 4.1 50.8 1.0
CG2 A:VAL144 4.1 41.5 1.0
C9 A:5EG401 4.3 75.6 1.0
CD2 A:TYR136 4.3 53.7 1.0
C3 A:5EG401 4.4 58.4 1.0
C28 A:5EG401 4.4 44.8 1.0
C20 A:5EG401 4.5 50.9 1.0
C13 A:5EG401 4.5 80.6 1.0
C23 A:5EG401 4.6 45.2 1.0
CA A:SER140 4.6 54.4 1.0
N22 A:5EG401 4.7 48.3 1.0
C8 A:5EG401 4.8 70.5 1.0
N4 A:5EG401 4.8 64.5 1.0
CZ A:TYR136 5.0 55.6 1.0

Chlorine binding site 2 out of 4 in 5drt

Go back to Chlorine Binding Sites List in 5drt
Chlorine binding site 2 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide]


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 CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:47.3
occ:1.00
 CL2 A:5EG401 0.0 47.3 1.0
C26 A:5EG401 1.7 43.4 1.0
C28 A:5EG401 2.7 44.8 1.0
C25 A:5EG401 2.7 42.1 1.0
O A:SER268 3.3 33.3 1.0
C A:SER268 3.3 33.2 1.0
N A:SER269 3.5 33.4 1.0
CB A:TYR312 3.9 36.5 1.0
O A:HOH580 3.9 57.5 1.0
CA A:SER269 3.9 34.3 1.0
CA A:SER268 3.9 28.1 1.0
C24 A:5EG401 4.0 44.2 1.0
C29 A:5EG401 4.0 45.6 1.0
SD A:MET147 4.1 53.4 1.0
CE A:MET147 4.1 50.6 1.0
CB A:SER269 4.2 37.0 1.0
N A:SER268 4.3 29.1 1.0
O A:VAL267 4.5 33.8 1.0
C23 A:5EG401 4.5 45.2 1.0
C A:VAL267 4.5 33.8 1.0
CG1 A:VAL267 4.6 33.5 1.0
O A:VAL240 4.8 39.7 1.0
CA A:TYR312 4.8 36.1 1.0
CG A:TYR312 4.9 37.2 1.0

Chlorine binding site 3 out of 4 in 5drt

Go back to Chlorine Binding Sites List in 5drt
Chlorine binding site 3 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide]


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 CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:82.1
occ:1.00
 CL1 B:5EG1002 0.0 82.1 1.0
C16 B:5EG1002 1.7 80.0 1.0
C11 B:5EG1002 2.7 80.6 1.0
C15 B:5EG1002 2.7 79.3 1.0
O10 B:5EG1002 2.9 79.7 1.0
CB B:SER140 3.4 54.4 1.0
CE2 B:TYR136 3.5 52.8 1.0
CG2 B:VAL169 3.6 39.5 1.0
C29 B:5EG1002 3.8 47.0 1.0
OG B:SER140 3.8 65.6 1.0
O21 B:5EG1002 4.0 53.2 1.0
C12 B:5EG1002 4.0 82.9 1.0
C14 B:5EG1002 4.0 80.4 1.0
CD2 B:TYR136 4.1 53.0 1.0
CG2 B:VAL144 4.1 40.9 1.0
C3 B:5EG1002 4.2 58.6 1.0
C9 B:5EG1002 4.2 75.0 1.0
C20 B:5EG1002 4.5 53.7 1.0
C13 B:5EG1002 4.5 82.6 1.0
CA B:SER140 4.6 52.9 1.0
C28 B:5EG1002 4.6 47.9 1.0
N4 B:5EG1002 4.6 61.4 1.0
CZ B:TYR136 4.6 55.7 1.0
C8 B:5EG1002 4.6 67.4 1.0
C23 B:5EG1002 4.7 49.1 1.0
N22 B:5EG1002 4.8 50.4 1.0
OH B:TYR136 4.8 52.0 1.0
O B:SER140 5.0 51.6 1.0

Chlorine binding site 4 out of 4 in 5drt

Go back to Chlorine Binding Sites List in 5drt
Chlorine binding site 4 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide]


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 CPD2 [2-(2-(5- ((2-Chlorophenoxy)Methyl)-1H-Tetrazol-1-Yl)Acetyl)-N-(4- Chlorophenyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:64.0
occ:1.00
 CL2 B:5EG1002 0.0 64.0 1.0
C26 B:5EG1002 1.7 53.2 1.0
C28 B:5EG1002 2.7 47.9 1.0
C25 B:5EG1002 2.7 51.9 1.0
C B:SER268 3.3 52.8 1.0
O B:SER268 3.3 53.0 1.0
N B:SER269 3.5 51.6 1.0
CA B:SER269 3.8 51.5 1.0
CB B:TYR312 3.8 48.3 1.0
CA B:SER268 3.9 45.0 1.0
O B:HOH1183 3.9 55.1 1.0
C24 B:5EG1002 4.0 51.5 1.0
C29 B:5EG1002 4.0 47.0 1.0
CE B:MET147 4.1 53.8 1.0
SD B:MET147 4.1 57.8 1.0
CB B:SER269 4.1 52.8 1.0
N B:SER268 4.3 44.7 1.0
C23 B:5EG1002 4.5 49.1 1.0
O B:VAL267 4.5 47.5 1.0
C B:VAL267 4.6 48.4 1.0
CG1 B:VAL267 4.7 44.6 1.0
CA B:TYR312 4.8 49.8 1.0
O B:VAL240 4.8 51.2 1.0
CG B:TYR312 4.9 48.0 1.0
OG B:SER269 4.9 61.3 1.0

Reference:

C.Chen, H.Zhu, F.Stauffer, G.Caravatti, S.Vollmer, R.Machauer, P.Holzer, H.Mobitz, C.Scheufler, M.Klumpp, R.Tiedt, K.S.Beyer, K.Calkins, D.Guthy, M.Kiffe, J.Zhang, C.Gaul. Discovery of Novel DOT1L Inhibitors Through A Structure-Based Fragmentation Approach. Acs Med.Chem.Lett. V. 7 735 2016.
ISSN: ISSN 1948-5875
PubMed: 27563395
DOI: 10.1021/ACSMEDCHEMLETT.6B00167
Page generated: Sat Jul 12 01:23:20 2025

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