scPDB - 3sr4 entry

Protein Data Bank Entry:

PDB ID : 3sr4

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-07-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.960	6.420	6.540	0.230	6.540	5

List of CHEMBLId :

CHEMBL2171174

Binding Site :

Uniprot Annotation

Name:	Histone-lysine N-methyltransferase, H3 lysine-79 specific
ID:	DOT1L_HUMAN
AC:	Q8TEK3
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.43

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	54.161
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.257	870.750

% Hydrophobic	% Polar
54.26	45.74
According to VolSite

Ligand :

HET Code:	TT8
Formula:	C15H22N6O5S
Molecular weight:	398.437 g/mol
DrugBank ID:	-
Buried Surface Area:	77.8 %
Polar Surface area:	198.39 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
43.9967	49.0625	6.41726

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CB	CE1	TYR- 136	4.49	0	Hydrophobic	false
SD	CD1	TYR- 136	4.36	0	Hydrophobic	false
O	OG1	THR- 139	2.6	166.31	H-Bond (Protein Donor)	false
OXT	N	THR- 139	2.76	168.14	H-Bond (Protein Donor)	false
N	OD2	ASP- 161	2.91	156.37	H-Bond (Ligand Donor)	false
N	OD2	ASP- 161	2.91	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 161	3.2	0	Ionic (Ligand Cationic)	false
N	O	GLY- 163	2.82	177.92	H-Bond (Ligand Donor)	false
OXT	NE2	GLN- 168	2.75	139.91	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 186	3.38	131.82	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 186	2.61	159.24	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 186	2.7	173.8	H-Bond (Ligand Donor)	false
N3	N	LYS- 187	3.13	131.08	H-Bond (Protein Donor)	false
N6	OD1	ASP- 222	3.11	160.68	H-Bond (Ligand Donor)	false
C1	CE1	PHE- 223	3.81	0	Hydrophobic	false
N1	N	PHE- 223	3.02	159.09	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 223	3.8	0	Aromatic Face/Face	false
C1	CD1	LEU- 224	3.87	0	Hydrophobic	false
CG	CB	ASN- 241	3.87	0	Hydrophobic	false
C5'	CE1	PHE- 245	3.96	0	Hydrophobic	false