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Chlorine in PDB 5dtm: Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide], PDB code: 5dtm was solved by C.Scheufler, C.Be, H.Moebitz, F.Stauffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 2.20
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.559, 158.559, 73.396, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 19.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide] (pdb code 5dtm). 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 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide], PDB code: 5dtm:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5dtm

Go back to Chlorine Binding Sites List in 5dtm
Chlorine binding site 1 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide]


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 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:40.2
occ:1.00
 CL1 A:5F4401 0.0 40.2 1.0
C9 A:5F4401 1.7 35.7 1.0
C5 A:5F4401 2.7 34.7 1.0
C12 A:5F4401 2.8 30.9 1.0
C2 A:5F4401 3.0 37.2 1.0
C A:SER268 3.2 23.3 1.0
N A:SER269 3.3 21.8 1.0
O A:SER268 3.4 21.7 1.0
O6 A:5F4401 3.5 43.0 1.0
C1 A:5F4401 3.5 32.9 1.0
C4 A:5F4401 3.7 27.6 1.0
CA A:SER268 3.7 20.7 1.0
CA A:SER269 3.7 22.9 1.0
CB A:SER269 3.8 23.3 1.0
C10 A:5F4401 4.0 37.7 1.0
C18 A:5F4401 4.1 26.0 1.0
CB A:TYR312 4.1 21.8 1.0
CZ A:PHE239 4.2 26.4 1.0
N A:SER268 4.2 19.9 1.0
O A:VAL240 4.2 24.0 1.0
CG1 A:VAL267 4.4 30.2 1.0
CE2 A:PHE239 4.4 27.1 1.0
OG A:SER269 4.4 27.2 1.0
O A:VAL267 4.5 22.8 1.0
C A:VAL267 4.5 23.8 1.0
C14 A:5F4401 4.5 29.9 1.0
CA A:ASN241 4.5 26.2 1.0
C3 A:5F4401 4.6 32.0 1.0
C A:VAL240 4.7 26.7 1.0
N8 A:5F4401 4.7 30.4 1.0
CE1 A:PHE239 4.7 27.4 1.0
CB A:ASN241 4.8 24.4 1.0
N A:ASN241 4.9 26.0 1.0

Chlorine binding site 2 out of 4 in 5dtm

Go back to Chlorine Binding Sites List in 5dtm
Chlorine binding site 2 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide]


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 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:44.3
occ:1.00
 CL2 A:5F4401 0.0 44.3 1.0
C10 A:5F4401 1.7 37.7 1.0
C5 A:5F4401 2.7 34.7 1.0
C14 A:5F4401 2.7 29.9 1.0
C2 A:5F4401 3.0 37.2 1.0
OG A:SER140 3.4 36.3 1.0
CA A:SER140 3.5 23.7 1.0
O6 A:5F4401 3.5 43.0 1.0
CB A:SER140 3.6 27.6 1.0
C1 A:5F4401 3.7 32.9 1.0
O A:SER140 4.0 24.4 1.0
C9 A:5F4401 4.0 35.7 1.0
CD2 A:PHE131 4.0 44.8 1.0
CD2 A:LEU143 4.0 21.6 1.0
CB A:LEU143 4.0 21.6 1.0
C18 A:5F4401 4.0 26.0 1.0
O A:HOH641 4.1 49.0 1.0
C A:SER140 4.2 25.2 1.0
C4 A:5F4401 4.3 27.6 1.0
CG2 A:VAL144 4.3 21.5 1.0
CE2 A:PHE131 4.4 47.1 1.0
CG A:LEU143 4.4 24.5 1.0
N A:SER140 4.5 25.6 1.0
C12 A:5F4401 4.5 30.9 1.0
C3 A:5F4401 4.7 32.0 1.0
N A:VAL144 4.8 20.3 1.0
CZ A:PHE239 5.0 26.4 1.0
CG A:PHE131 5.0 42.4 1.0

Chlorine binding site 3 out of 4 in 5dtm

Go back to Chlorine Binding Sites List in 5dtm
Chlorine binding site 3 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide]


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 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:52.4
occ:1.00
 CL1 B:5F4401 0.0 52.4 1.0
C9 B:5F4401 1.7 47.0 1.0
C5 B:5F4401 2.7 46.0 1.0
C12 B:5F4401 2.7 41.6 1.0
C2 B:5F4401 3.0 47.4 1.0
C B:SER268 3.2 36.5 1.0
N B:SER269 3.2 34.3 1.0
O6 B:5F4401 3.5 48.8 1.0
O B:SER268 3.6 36.7 1.0
C1 B:5F4401 3.6 46.4 1.0
CA B:SER268 3.6 31.9 1.0
CA B:SER269 3.7 34.5 1.0
CB B:SER269 3.8 34.4 1.0
C4 B:5F4401 3.8 45.0 1.0
O B:VAL240 4.0 36.6 1.0
C10 B:5F4401 4.0 43.7 1.0
C18 B:5F4401 4.0 36.5 1.0
CZ B:PHE239 4.1 31.1 1.0
N B:SER268 4.1 32.4 1.0
CB B:TYR312 4.3 35.3 1.0
CE2 B:PHE239 4.3 32.3 1.0
CA B:ASN241 4.4 31.3 1.0
CG1 B:VAL267 4.4 38.1 1.0
OG B:SER269 4.4 39.4 1.0
O B:VAL267 4.5 35.9 1.0
C B:VAL240 4.5 35.7 1.0
C B:VAL267 4.5 36.4 1.0
C14 B:5F4401 4.5 37.2 1.0
CE1 B:PHE239 4.6 32.6 1.0
N B:ASN241 4.6 32.1 1.0
CB B:ASN241 4.7 30.2 1.0
C3 B:5F4401 4.7 44.6 1.0
N8 B:5F4401 4.9 44.1 1.0
CD2 B:PHE239 5.0 30.1 1.0
CB B:SER268 5.0 33.4 1.0

Chlorine binding site 4 out of 4 in 5dtm

Go back to Chlorine Binding Sites List in 5dtm
Chlorine binding site 4 out of 4 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD1 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide]


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 [4-(2,6- Dichlorobenzoyl)-N-Methyl-1H-Pyrrole-2-Carboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:50.5
occ:1.00
 CL2 B:5F4401 0.0 50.5 1.0
C10 B:5F4401 1.7 43.7 1.0
C5 B:5F4401 2.7 46.0 1.0
C14 B:5F4401 2.8 37.2 1.0
C2 B:5F4401 2.9 47.4 1.0
O6 B:5F4401 3.4 48.8 1.0
CA B:SER140 3.5 27.5 1.0
OG B:SER140 3.5 38.8 1.0
CB B:SER140 3.6 30.0 1.0
C1 B:5F4401 3.6 46.4 1.0
O B:SER140 4.0 28.4 1.0
C9 B:5F4401 4.0 47.0 1.0
CD2 B:LEU143 4.0 33.3 1.0
CD2 B:PHE131 4.0 48.0 1.0
C18 B:5F4401 4.1 36.5 1.0
C4 B:5F4401 4.1 45.0 1.0
CB B:LEU143 4.1 24.6 1.0
C B:SER140 4.2 28.3 1.0
CG2 B:VAL144 4.3 26.7 1.0
O B:HOH570 4.4 48.4 1.0
CE2 B:PHE131 4.4 49.6 1.0
CG B:LEU143 4.5 30.4 1.0
C12 B:5F4401 4.5 41.6 1.0
N B:SER140 4.5 29.6 1.0
C3 B:5F4401 4.6 44.6 1.0
O B:HOH677 4.8 42.7 1.0
N B:VAL144 4.8 22.5 1.0
CZ B:PHE239 5.0 31.1 1.0

Reference:

C.Scheufler, H.Mobitz, C.Gaul, C.Ragot, C.Be, C.Fernandez, K.S.Beyer, R.Tiedt, F.Stauffer. Optimization of A Fragment-Based Screening Hit Toward Potent DOT1L Inhibitors Interacting in An Induced Binding Pocket. Acs Med.Chem.Lett. V. 7 730 2016.
ISSN: ISSN 1948-5875
PubMed: 27563394
DOI: 10.1021/ACSMEDCHEMLETT.6B00168
Page generated: Fri Jul 26 06:56:47 2024

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