Atomistry » Chlorine » PDB 5dj1-5dtj » 5dry
Atomistry »
  Chlorine »
    PDB 5dj1-5dtj »
      5dry »

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: Sat Jul 12 01:23:25 2025

Last articles

Mn in 6TEZ
Mn in 6TEX
Mn in 6TEU
Mn in 6T6L
Mn in 6TES
Mn in 6TEC
Mn in 6TE3
Mn in 6T2A
Mn in 6SX8
Mn in 6SRG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy