scPDB - 1nw3 entry

Protein Data Bank Entry:

PDB ID : 1nw3

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2003-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	43.847
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.619	634.500

% Hydrophobic	% Polar
46.81	53.19
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	76.47 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
87.9782	13.246	2.59648

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
O	OG1	THR- 139	2.6	160.78	H-Bond (Protein Donor)	false
OXT	N	THR- 139	2.55	166.4	H-Bond (Protein Donor)	false
OXT	OG1	THR- 139	3.37	137.72	H-Bond (Protein Donor)	false
N	OD2	ASP- 161	3.26	157.46	H-Bond (Ligand Donor)	false
N	OD2	ASP- 161	3.26	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 161	3.47	0	Ionic (Ligand Cationic)	false
N	O	GLY- 163	2.77	149.22	H-Bond (Ligand Donor)	false
OXT	NE2	GLN- 168	2.98	148.89	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 186	2.76	175.58	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 186	3.35	129.11	H-Bond (Ligand Donor)	false
N3	N	LYS- 187	3.18	130.09	H-Bond (Protein Donor)	false
N6	OD1	ASP- 222	3.11	167.81	H-Bond (Ligand Donor)	false
N1	N	PHE- 223	3.02	161.34	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 223	3.78	0	Aromatic Face/Face	false
CG	CB	ASN- 241	4.49	0	Hydrophobic	false
CE	CB	ASN- 241	4.05	0	Hydrophobic	false
C1'	CE1	PHE- 245	4.4	0	Hydrophobic	false
C5'	CE1	PHE- 245	3.99	0	Hydrophobic	false
N	O	HOH- 1025	3.12	122.48	H-Bond (Ligand Donor)	false