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Chlorine in PDB 5dry: Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide], PDB code: 5dry 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) 45.83 / 2.41
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.760, 158.760, 74.460, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 19.9

Other elements in 5dry:

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] also contains other interesting chemical elements:

Potassium (K) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] (pdb code 5dry). 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 CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide], PDB code: 5dry:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5dry

Go back to Chlorine Binding Sites List in 5dry
Chlorine binding site 1 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)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 CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:65.2
occ:1.00
 CL3 A:5EK402 0.0 65.2 1.0
C29 A:5EK402 1.7 57.4 1.0
C28 A:5EK402 2.7 53.4 1.0
C24 A:5EK402 2.8 51.6 1.0
C8 A:5EK402 3.3 47.1 1.0
CE1 A:TYR136 3.5 28.7 1.0
OG A:SER140 3.6 46.5 1.0
C3 A:5EK402 3.7 39.7 1.0
N4 A:5EK402 3.7 43.1 1.0
O12 A:5EK402 3.8 33.0 1.0
CB A:SER140 3.8 39.8 1.0
CG2 A:VAL169 3.8 26.8 1.0
CD1 A:TYR136 3.8 32.2 1.0
CL6 A:5EK402 4.0 67.2 1.0
C27 A:5EK402 4.0 53.6 1.0
C25 A:5EK402 4.1 53.8 1.0
C32 A:5EK402 4.1 48.8 1.0
C31 A:5EK402 4.2 53.9 1.0
N7 A:5EK402 4.2 48.5 1.0
C11 A:5EK402 4.3 33.6 1.0
C15 A:5EK402 4.4 29.1 1.0
C2 A:5EK402 4.5 38.8 1.0
C26 A:5EK402 4.6 53.4 1.0
N5 A:5EK402 4.7 42.3 1.0
CZ A:TYR136 4.8 34.2 1.0
N10 A:5EK402 4.8 32.7 1.0
N13 A:5EK402 4.8 32.7 1.0
C33 A:5EK402 4.9 48.8 1.0
N9 A:5EK402 5.0 36.4 1.0
N6 A:5EK402 5.0 46.2 1.0

Chlorine binding site 2 out of 4 in 5dry

Go back to Chlorine Binding Sites List in 5dry
Chlorine binding site 2 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)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 CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:67.2
occ:1.00
 CL6 A:5EK402 0.0 67.2 1.0
C31 A:5EK402 1.7 53.9 1.0
C32 A:5EK402 2.6 48.8 1.0
C23 A:5EK402 2.7 44.6 1.0
N22 A:5EK402 3.2 37.1 1.0
CG2 A:VAL144 3.3 32.4 1.0
C16 A:5EK402 3.5 32.2 1.0
C15 A:5EK402 3.5 29.1 1.0
CE A:MET147 3.5 43.0 1.0
C33 A:5EK402 3.9 48.8 1.0
CD2 A:LEU143 3.9 38.7 1.0
CL3 A:5EK402 4.0 65.2 1.0
C35 A:5EK402 4.0 42.5 1.0
O A:SER140 4.1 37.9 1.0
C21 A:5EK402 4.1 31.5 1.0
CB A:SER140 4.3 39.8 1.0
CG A:LEU143 4.4 35.9 1.0
C34 A:5EK402 4.5 49.9 1.0
CB A:LEU143 4.5 31.5 1.0
N A:VAL144 4.5 29.7 1.0
C17 A:5EK402 4.6 27.4 1.0
CA A:SER140 4.6 38.2 1.0
C14 A:5EK402 4.6 27.4 1.0
CB A:VAL144 4.7 32.4 1.0
OG A:SER140 4.7 46.5 1.0
SD A:MET147 4.8 45.9 1.0
C A:SER140 4.8 38.5 1.0
CA A:VAL144 4.8 28.1 1.0
CG2 A:VAL169 4.9 26.8 1.0
C20 A:5EK402 4.9 30.0 1.0

Chlorine binding site 3 out of 4 in 5dry

Go back to Chlorine Binding Sites List in 5dry
Chlorine binding site 3 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)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 CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:74.9
occ:1.00
 CL3 B:5EK1002 0.0 74.9 1.0
C29 B:5EK1002 1.7 68.8 1.0
C28 B:5EK1002 2.7 67.8 1.0
C24 B:5EK1002 2.8 61.6 1.0
C8 B:5EK1002 3.2 54.4 1.0
OG B:SER140 3.6 48.7 1.0
N4 B:5EK1002 3.6 50.6 1.0
C3 B:5EK1002 3.6 49.0 1.0
CE1 B:TYR136 3.7 35.3 1.0
O12 B:5EK1002 3.8 40.9 1.0
CB B:SER140 3.8 41.1 1.0
CD1 B:TYR136 3.9 37.7 1.0
CG2 B:VAL169 4.0 32.9 1.0
C27 B:5EK1002 4.0 68.8 1.0
C25 B:5EK1002 4.1 64.6 1.0
C32 B:5EK1002 4.1 61.3 1.0
N7 B:5EK1002 4.1 54.6 1.0
CL6 B:5EK1002 4.2 68.6 1.0
C31 B:5EK1002 4.3 62.6 1.0
C11 B:5EK1002 4.3 43.2 1.0
C2 B:5EK1002 4.4 48.9 1.0
C26 B:5EK1002 4.6 68.0 1.0
N5 B:5EK1002 4.6 50.1 1.0
C15 B:5EK1002 4.6 42.0 1.0
N10 B:5EK1002 4.8 41.8 1.0
C33 B:5EK1002 4.8 62.2 1.0
N9 B:5EK1002 4.8 46.2 1.0
N6 B:5EK1002 4.9 52.0 1.0
CZ B:TYR136 4.9 39.7 1.0
N13 B:5EK1002 5.0 41.0 1.0

Chlorine binding site 4 out of 4 in 5dry

Go back to Chlorine Binding Sites List in 5dry
Chlorine binding site 4 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)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 CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:68.6
occ:1.00
 CL6 B:5EK1002 0.0 68.6 1.0
C31 B:5EK1002 1.7 62.6 1.0
C32 B:5EK1002 2.6 61.3 1.0
C23 B:5EK1002 2.7 58.0 1.0
N22 B:5EK1002 3.2 51.5 1.0
CG2 B:VAL144 3.5 34.5 1.0
C16 B:5EK1002 3.6 45.0 1.0
CE B:MET147 3.7 47.1 1.0
CD2 B:LEU143 3.7 47.9 1.0
C15 B:5EK1002 3.7 42.0 1.0
C33 B:5EK1002 3.9 62.2 1.0
C35 B:5EK1002 4.0 58.6 1.0
O B:SER140 4.1 43.6 1.0
C21 B:5EK1002 4.1 48.5 1.0
CG B:LEU143 4.2 42.2 1.0
CB B:SER140 4.2 41.1 1.0
CL3 B:5EK1002 4.2 74.9 1.0
CB B:LEU143 4.3 35.5 1.0
C34 B:5EK1002 4.5 62.3 1.0
N B:VAL144 4.5 32.8 1.0
CA B:SER140 4.5 42.5 1.0
OG B:SER140 4.6 48.7 1.0
C17 B:5EK1002 4.7 41.5 1.0
C B:SER140 4.8 42.2 1.0
CB B:VAL144 4.8 33.7 1.0
C14 B:5EK1002 4.8 40.5 1.0
SD B:MET147 4.9 51.3 1.0
C20 B:5EK1002 4.9 45.2 1.0
CA B:VAL144 4.9 31.8 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: Fri Jul 26 06:52:53 2024

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